70 results on '"Ron Reyes"'
Search Results
2. Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution
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Lukasz Jaroszewski, Eric Hampton, Carina Grittini, Keith O. Hodgson, Tanya Biorac, Said Eshaghi, Adam Godzik, Kin Moy, Kevin Quijano, Marc-André Elsliger, Daniel McMullan, Inna Levin, Fred Rezezadeh, John Wooley, Alyssa Robb, Raymond C. Stevens, Frank von Delft, Guenter Wolf, Heath E. Klock, Timothy M. McPhillips, Qingping Xu, Andrew T. Morse, Juli Vincent, Linda S. Brinen, Xiaoping Dai, Cathy Karlak, Eric Sims, Slawomir K. Grzechnik, Mike DiDonato, Jaume M. Canaves, Polat Abdubek, Henry van den Bedem, Peter Kuhn, Jie Ouyang, Bill West, Xianhong Wang, Scott A. Lesley, Ross Floyd, Jeff Velasquez, Eric Koesema, Ron Reyes, Robert Schwarzenbacher, Mitchell D. Miller, Andreas Kreusch, Rebecca Page, Ashley M. Deacon, Ian A. Wilson, Eileen Ambing, and Glen Spraggon
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chemistry.chemical_classification ,Models, Molecular ,Binding Sites ,Magnetic Resonance Spectroscopy ,biology ,Resolution (electron density) ,Molecular Sequence Data ,Crystal structure ,biology.organism_classification ,Biochemistry ,Protein Structure, Secondary ,Crystallography ,Enzyme ,chemistry ,Bacterial Proteins ,Structural Biology ,Structural Homology, Protein ,Thermotoga maritima ,Amino Acid Sequence ,Crystallization ,Molecular Biology ,Conserved Sequence - Published
- 2016
3. The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu
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Gye Won Han, Dana Weekes, Lian Duan, Keith O. Hodgson, Polat Abdubek, Winnie W Lam, Joanna C Grant, Hsiu-Ju Chiu, Herbert L. Axelrod, Mitchell D. Miller, Dennis Carlton, Ashley M. Deacon, Anna Grzechnik, Ian A. Wilson, Christina Puckett, Sanjay Krishna, Kyle Ellrott, Mark W. Knuth, John Wooley, Abhinav Kumar, Ron Reyes, Connie Chen, Thomas Clayton, Qingping Xu, Kevin K. Jin, Henry van den Bedem, Debanu Das, Andrew P. Yeh, Tiffany Wooten, Edward Nigoghossian, Tamara Astakhova, Christine B Trame, Jiadong Zhou, Robert D. Finn, Lukasz Jaroszewski, Julie Feuerhelm, Linda Okach, Scott A. Lesley, Marc C. Deller, Andrew T. Morse, Marc André Elsliger, Constantina Bakolitsa, Xiaohui Cai, Piotr Kozbial, David Marciano, Henry J Tien, Adam Godzik, Heath E. Klock, Carol L. Farr, Amanda Nopakun, and Michelle Chiu
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0303 health sciences ,Sequence analysis ,Repressor ,Sequence alignment ,Plasma protein binding ,Biology ,Biochemistry ,Hedgehog signaling pathway ,Structural genomics ,03 medical and health sciences ,0302 clinical medicine ,030220 oncology & carcinogenesis ,Molecular Biology ,Peptide sequence ,Function (biology) ,030304 developmental biology - Abstract
Sufu (Suppressor of Fused), a two-domain protein, plays a critical role in regulating Hedgehog signaling and is conserved from flies to humans. A few bacterial Sufu-like proteins have previously been identified based on sequence similarity to the N-terminal domain of eukaryotic Sufu proteins, but none have been structurally or biochemically characterized and their function in bacteria is unknown. We have determined the crystal structure of a more distantly related Sufu-like homolog, NGO1391 from Neisseria gonorrhoeae, at 1.4 A resolution, which provides the first biophysical characterization of a bacterial Sufu-like protein. The structure revealed a striking similarity to the N-terminal domain of human Sufu (r.m.s.d. of 2.6 A over 93% of the NGO1391 protein), despite an extremely low sequence identity of ∼15%. Subsequent sequence analysis revealed that NGO1391 defines a new subset of smaller, Sufu-like proteins that are present in ∼200 bacterial species and has resulted in expansion of the SUFU (PF05076) family in Pfam.
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- 2010
4. Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules
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Mark W. Knuth, Linda Okach, Keith O. Hodgson, Winnie W Lam, Tamara Astakhova, Debanu Das, Lukasz Jaroszewski, Kevin K. Jin, Abhinav Kumar, Scott A. Lesley, Joanna C Grant, Daniel McMullan, Gye Won Han, Herbert L. Axelrod, Amanda Nopakun, Kyle Ellrott, John Wooley, Piotr Kozbial, Henry J Tien, Polat Abdubek, Christine B Trame, Ashley M. Deacon, Sanjay Krishna, Christopher L. Rife, Henry van den Bedem, Ron Reyes, Lian Duan, Dana Weekes, Adam Godzik, Heath E. Klock, Marc André Elsliger, Carol L. Farr, David Marciano, Ian A. Wilson, Julie Feuerhelm, Christina Puckett, Edward Nigoghossian, Marc C. Deller, Qingping Xu, Constantina Bakolitsa, Connie Chen, Dennis Carlton, Hsiu-Ju Chiu, Mitchell D. Miller, Anna Grzechnik, Thomas Clayton, and Andrew T. Morse
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Models, Molecular ,Protein Structure ,Glycan ,Operon ,1.1 Normal biological development and functioning ,Molecular Sequence Data ,Biophysics ,gut microbiome ,Sequence (biology) ,Biology ,Crystallography, X-Ray ,Biochemistry ,Structural genomics ,Vaccine Related ,03 medical and health sciences ,Bacterial Proteins ,Models ,Underpinning research ,Structural Biology ,Genetics ,Bacteroides ,Amino Acid Sequence ,Peptide sequence ,Structural Homology ,030304 developmental biology ,metagenomics ,0303 health sciences ,Crystallography ,Human Gut Microbiome ,Protein ,030302 biochemistry & molecular biology ,Molecular ,structural genomics ,Biological Sciences ,Condensed Matter Physics ,biology.organism_classification ,Protein Structure, Tertiary ,Tetratricopeptide ,starch-utilization system ,Structural Homology, Protein ,Chemical Sciences ,X-Ray ,biology.protein ,Bacteroides thetaiotaomicron ,Tertiary - Abstract
The crystal structure of BT_3984, a SusD-family protein, reveals a TPR N-terminal region providing support for a loop-rich C-terminal subdomain and suggests possible interfaces involved in sus complex formation., The crystal structure of the Bacteroides thetaiotaomicron protein BT_3984 was determined to a resolution of 1.7 Å and was the first structure to be determined from the extensive SusD family of polysaccharide-binding proteins. SusD is an essential component of the sus operon that defines the paradigm for glycan utilization in dominant members of the human gut microbiota. Structural analysis of BT_3984 revealed an N-terminal region containing several tetratricopeptide repeats (TPRs), while the signature C-terminal region is less structured and contains extensive loop regions. Sequence and structure analysis of BT_3984 suggests the presence of binding interfaces for other proteins from the polysaccharide-utilization complex.
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- 2010
5. Structure ofBacteroides thetaiotaomicronBT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism
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Andrew P. Yeh, John Wooley, Edward Nigoghossian, Qingping Xu, Christine B Trame, Gye Won Han, Kevin K. Jin, Dana Weekes, Kyle Ellrott, David Marciano, Lian Duan, Scott A. Lesley, Lukasz Jaroszewski, Debanu Das, Ashley M. Deacon, Linda Okach, Herbert L. Axelrod, Hsiu-Ju Chiu, Abhinav Kumar, Thomas Clayton, Connie Chen, Heath E. Klock, Marc André Elsliger, Carol L. Farr, Henry van den Bedem, Andrew T. Morse, Mitchell D. Miller, Anna Grzechnik, Daniel McMullan, Dennis Carlton, Keith O. Hodgson, Joanna C Grant, Winnie W Lam, Amanda Nopakun, Polat Abdubek, Tiffany Wooten, Julie Feuerhelm, Sanjay Krishna, Michelle Chiu, Adam Godzik, Marc C. Deller, Tamara Astakhova, Constantina Bakolitsa, Xiaohui Cai, Piotr Kozbial, Henry J Tien, Ron Reyes, Ian A. Wilson, Christina Puckett, and Mark W. Knuth
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Models, Molecular ,gut microbiome ,Crystallography, X-Ray ,Biochemistry ,fluids and secretions ,Protein structure ,Models ,Structural Biology ,polycyclic compounds ,Bacteroides ,Peptide sequence ,0303 health sciences ,Crystallography ,Human Gut Microbiome ,030302 biochemistry & molecular biology ,Biological Sciences ,Condensed Matter Physics ,immunoglobulin-like fold ,GenBank ,Carbohydrate Metabolism ,Bacteroides thetaiotaomicron ,Protein Structure ,Protein family ,1.1 Normal biological development and functioning ,Molecular Sequence Data ,Carbohydrates ,Biophysics ,Sequence alignment ,Biology ,digestive system ,Structural genomics ,03 medical and health sciences ,jelly-roll fold ,Bacterial Proteins ,Underpinning research ,Genetics ,Amino Acid Sequence ,Binding site ,Structural Homology ,030304 developmental biology ,Binding Sites ,Protein ,Molecular ,structural genomics ,Protein Structure, Tertiary ,carbohydrates (lipids) ,sugars ,Structural Homology, Protein ,Chemical Sciences ,X-Ray ,bacteria ,Sequence Alignment ,Tertiary - Abstract
The crystal structure of BT2081 from B. thetaiotaomicron reveals a two-domain protein with a putative carbohydrate-binding site in the C-terminal domain., BT2081 from Bacteroides thetaiotaomicron (GenBank accession code NP_810994.1) is a member of a novel protein family consisting of over 160 members, most of which are found in the different classes of Bacteroidetes. Genome-context analysis lends support to the involvement of this family in carbohydrate metabolism, which plays a key role in B. thetaiotaomicron as a predominant bacterial symbiont in the human distal gut microbiome. The crystal structure of BT2081 at 2.05 Å resolution represents the first structure from this new protein family. BT2081 consists of an N-terminal domain, which adopts a β-sandwich immunoglobulin-like fold, and a larger C-terminal domain with a β-sandwich jelly-roll fold. Structural analyses reveal that both domains are similar to those found in various carbohydrate-active enzymes. The C-terminal β-jelly-roll domain contains a potential carbohydrate-binding site that is highly conserved among BT2081 homologs and is situated in the same location as the carbohydrate-binding sites that are found in structurally similar glycoside hydrolases (GHs). However, in BT2081 this site is partially occluded by surrounding loops, which results in a deep solvent-accessible pocket rather than a shallower solvent-exposed cleft.
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- 2010
6. Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger
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Lukasz Jaroszewski, Polat Abdubek, Sanjay Krishna, Adam Godzik, Henry van den Bedem, Dennis Carlton, Marc-André Elsliger, Natasha Sefcovic, Edward Nigoghossian, Piotr Kozbial, Henry J Tien, Thomas Clayton, Debanu Das, Qingping Xu, Joanna C Grant, Gye Won Han, Heath E. Klock, Carol L. Farr, Ron Reyes, Daniel McMullan, John Wooley, Hsiu-Ju Chiu, Marc C. Deller, Herbert L. Axelrod, Connie Chen, Amanda Nopakun, Tamara Astakhova, Ian A. Wilson, Kevin K. Jin, Christine B Trame, Christina Puckett, Constantina Bakolitsa, David Marciano, Keith O. Hodgson, Winnie W Lam, Ashley M. Deacon, Andrew T. Morse, Mitchell D. Miller, Anna Grzechnik, Julie Feuerhelm, Abhinav Kumar, Tiffany Wooten, Dana Weekes, Lian Duan, Linda Okach, Mark W. Knuth, Scott A. Lesley, and Kyle Ellrott
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Pfam family PF02663 ,Models, Molecular ,Secondary ,Ligands That Aid in Function Characterization ,metalloproteins ,Crystallography, X-Ray ,Biochemistry ,Protein Structure, Secondary ,Structural Biology ,Models ,domain swapping ,Zinc finger ,chemistry.chemical_classification ,0303 health sciences ,Crystallography ,biology ,030302 biochemistry & molecular biology ,Thermoplasma acidophilum ,Zinc Fingers ,methanogenesis ,Biological Sciences ,Condensed Matter Physics ,Aldehyde Oxidoreductases ,Methane ,Protein Structure ,Molecular Sequence Data ,Biophysics ,chemistry.chemical_element ,Context (language use) ,Zinc ,Desulfitobacterium ,Formylmethanofuran dehydrogenase ,Structural genomics ,03 medical and health sciences ,Rare Diseases ,Oxidoreductase ,Genetics ,Amino Acid Sequence ,030304 developmental biology ,Structural Homology ,Protein ,Active site ,Molecular ,structural genomics ,biology.organism_classification ,Protein Structure, Tertiary ,chemistry ,Structural Homology, Protein ,Chemical Sciences ,biology.protein ,X-Ray ,Tertiary - Abstract
The first structures from the FmdE Pfam family (PF02663) reveal that some members of this family form tightly intertwined dimers consisting of two domains (N-terminal α+β core and C-terminal zinc-finger domains), whereas others contain only the core domain. The presence of the zinc-finger domain suggests that some members of this family may perform functions associated with transcriptional regulation, protein–protein interaction, RNA binding or metal-ion sensing., Examination of the genomic context for members of the FmdE Pfam family (PF02663), such as the protein encoded by the fmdE gene from the methanogenic archaeon Methanobacterium thermoautotrophicum, indicates that 13 of them are co-transcribed with genes encoding subunits of molybdenum formylmethanofuran dehydrogenase (EC 1.2.99.5), an enzyme that is involved in microbial methane production. Here, the first crystal structures from PF02663 are described, representing two bacterial and one archaeal species: B8FYU2_DESHY from the anaerobic dehalogenating bacterium Desulfitobacterium hafniense DCB-2, Q2LQ23_SYNAS from the syntrophic bacterium Syntrophus aciditrophicus SB and Q9HJ63_THEAC from the thermoacidophilic archaeon Thermoplasma acidophilum. Two of these proteins, Q9HJ63_THEAC and Q2LQ23_SYNAS, contain two domains: an N-terminal thioredoxin-like α+β core domain (NTD) consisting of a five-stranded, mixed β-sheet flanked by several α-helices and a C-terminal zinc-finger domain (CTD). B8FYU2_DESHY, on the other hand, is composed solely of the NTD. The CTD of Q9HJ63_THEAC and Q2LQ23_SYNAS is best characterized as a treble-clef zinc finger. Two significant structural differences between Q9HJ63_THEAC and Q2LQ23_SYNAS involve their metal binding. First, zinc is bound to the putative active site on the NTD of Q9HJ63_THEAC, but is absent from the NTD of Q2LQ23_SYNAS. Second, whereas the structure of the CTD of Q2LQ23_SYNAS shows four Cys side chains within coordination distance of the Zn atom, the structure of Q9HJ63_THEAC is atypical for a treble-cleft zinc finger in that three Cys side chains and an Asp side chain are within coordination distance of the zinc.
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- 2010
7. The structure ofHaemophilus influenzaeprephenate dehydrogenase suggests unique features of bifunctional TyrA enzymes
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Andrew T. Morse, Mark W. Knuth, Debanu Das, Marc C. Deller, John Wooley, Daniel McMullan, Dennis Carlton, Lian Duan, Dana Weekes, Ron Reyes, Heath E. Klock, Joanna C Grant, Tamara Astakhova, Adam Godzik, Gye Won Han, Kevin K. Jin, Piotr Kozbial, Henry J Tien, Julie Feuerhelm, Polat Abdubek, Hsiu-Ju Chiu, Sanjay Krishna, Edward Nigoghossian, Herbert L. Axelrod, Keith O. Hodgson, Henry van den Bedem, Ian A. Wilson, Ashley M. Deacon, Marc André Elsliger, Scott A. Lesley, Christine B Trame, David Marciano, Abhinav Kumar, Lukasz Jaroszewski, Qingping Xu, Thomas Clayton, Mitchell D. Miller, Anna Grzechnik, and Linda Okach
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Ligands That Aid in Function Characterization ,1.1 Normal biological development and functioning ,Biophysics ,Isomerase ,Crystallography, X-Ray ,chorismate ,Biochemistry ,03 medical and health sciences ,Bacterial Proteins ,Underpinning research ,Multienzyme Complexes ,Structural Biology ,Oxidoreductase ,Genetics ,Tyrosine ,030304 developmental biology ,Prephenate Dehydrogenase ,Tyrosine binding ,chemistry.chemical_classification ,0303 health sciences ,Crystallography ,biology ,030302 biochemistry & molecular biology ,Active site ,Prephenate dehydrogenase ,structural genomics ,Biological Sciences ,Condensed Matter Physics ,Haemophilus influenzae ,tyrosine biosynthesis ,3. Good health ,chemistry ,Arogenate dehydrogenase ,prephenate ,Chemical Sciences ,X-Ray ,biology.protein ,Chorismate mutase - Abstract
The crystal structure of the prephenate dehydrogenase component of the bifunctional H. influenzae TyrA reveals unique structural differences between bifunctional and monofunctional TyrA enzymes., Chorismate mutase/prephenate dehydrogenase from Haemophilus influenzae Rd KW20 is a bifunctional enzyme that catalyzes the rearrangement of chorismate to prephenate and the NAD(P)+-dependent oxidative decarboxylation of prephenate to 4-hydroxyphenylpyruvate in tyrosine biosynthesis. The crystal structure of the prephenate dehydrogenase component (HinfPDH) of the TyrA protein from H. influenzae Rd KW20 in complex with the inhibitor tyrosine and cofactor NAD+ has been determined to 2.0 Å resolution. HinfPDH is a dimeric enzyme, with each monomer consisting of an N-terminal α/β dinucleotide-binding domain and a C-terminal α-helical dimerization domain. The structure reveals key active-site residues at the domain interface, including His200, Arg297 and Ser179 that are involved in catalysis and/or ligand binding and are highly conserved in TyrA proteins from all three kingdoms of life. Tyrosine is bound directly at the catalytic site, suggesting that it is a competitive inhibitor of HinfPDH. Comparisons with its structural homologues reveal important differences around the active site, including the absence of an α–β motif in HinfPDH that is present in other TyrA proteins, such as Synechocystis sp. arogenate dehydrogenase. Residues from this motif are involved in discrimination between NADP+ and NAD+. The loop between β5 and β6 in the N-terminal domain is much shorter in HinfPDH and an extra helix is present at the C-terminus. Furthermore, HinfPDH adopts a more closed conformation compared with TyrA proteins that do not have tyrosine bound. This conformational change brings the substrate, cofactor and active-site residues into close proximity for catalysis. An ionic network consisting of Arg297 (a key residue for tyrosine binding), a water molecule, Asp206 (from the loop between β5 and β6) and Arg365′ (from the additional C-terminal helix of the adjacent monomer) is observed that might be involved in gating the active site.
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- 2010
8. Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiontBacteroides thetaiotaomicron
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Keith O. Hodgson, Kyle Ellrott, Debanu Das, Qingping Xu, Tamara Astakhova, Winnie W Lam, Polat Abdubek, Sanjay Krishna, Mark W. Knuth, Hsiu-Ju Chiu, Andrew Yeh, Jiadong Zhou, Henry van den Bedem, Lukasz Jaroszewski, Thomas Clayton, Linda Okach, Mitchell D. Miller, Anna Grzechnik, Dennis Carlton, Gye Won Han, Heath E. Klock, Abhinav Kumar, Kevin K. Jin, Edward Nigoghossian, Adam Godzik, Christine B Trame, Carol L. Farr, Andrew T. Morse, Dana Weekes, Ron Reyes, Marc C. Deller, Joanna C Grant, Scott A. Lesley, Herbert L. Axelrod, Xiaohui Cai, Piotr Kozbial, Henry J Tien, David Marciano, John Wooley, Tiffany Wooten, Lian Duan, Constantina Bakolitsa, Marc André Elsliger, Connie Chen, Julie Feuerhelm, Ashley M. Deacon, Ian A. Wilson, Christina Puckett, and Amanda Nopakun
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Models, Molecular ,Crystallography, X-Ray ,Biochemistry ,Protein structure ,Models ,Structural Biology ,2.2 Factors relating to the physical environment ,Bacteroides ,perforins ,Aetiology ,transmembrane pores ,Peptide sequence ,0303 health sciences ,MACPF ,Crystallography ,Human Gut Microbiome ,biology ,pathogenesis ,030302 biochemistry & molecular biology ,Biological Sciences ,Condensed Matter Physics ,Transmembrane protein ,Cell biology ,Infection ,Bacteroides thetaiotaomicron ,Protein Structure ,1.1 Normal biological development and functioning ,Molecular Sequence Data ,Biophysics ,Microbiology ,03 medical and health sciences ,Bacterial Proteins ,Underpinning research ,Genetics ,Amino Acid Sequence ,Structural Homology ,030304 developmental biology ,Perforin ,Protein ,Molecular ,membrane-attack complexes ,biology.organism_classification ,Protein Structure, Tertiary ,Structural Homology, Protein ,Chemical Sciences ,X-Ray ,biology.protein ,Complement membrane attack complex ,Sequence Alignment ,Tertiary - Abstract
The crystal structure of a novel MACPF protein, which may play a role in the adaptation of commensal bacteria to host environments in the human gut, was determined and analyzed., Membrane-attack complex/perforin (MACPF) proteins are transmembrane pore-forming proteins that are important in both human immunity and the virulence of pathogens. Bacterial MACPFs are found in diverse bacterial species, including most human gut-associated Bacteroides species. The crystal structure of a bacterial MACPF-domain-containing protein BT_3439 (Bth-MACPF) from B. thetaiotaomicron, a predominant member of the mammalian intestinal microbiota, has been determined. Bth-MACPF contains a membrane-attack complex/perforin (MACPF) domain and two novel C-terminal domains that resemble ribonuclease H and interleukin 8, respectively. The entire protein adopts a flat crescent shape, characteristic of other MACPF proteins, that may be important for oligomerization. This Bth-MACPF structure provides new features and insights not observed in two previous MACPF structures. Genomic context analysis infers that Bth-MACPF may be involved in a novel protein-transport or nutrient-uptake system, suggesting an important role for these MACPF proteins, which were likely to have been inherited from eukaryotes via horizontal gene transfer, in the adaptation of commensal bacteria to the host environment.
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- 2010
9. A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Å resolution
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Gye Won Han, Mark W. Knuth, Natasha Sefcovic, Marc André Elsliger, Tamara Astakhova, Marc C. Deller, Heath E. Klock, Carol L. Farr, Xiaohui Cai, Piotr Kozbial, Adam Godzik, Thomas Clayton, Edward Nigoghossian, Qingping Xu, Ian A. Wilson, Herbert L. Axelrod, Henry J Tien, Constantina Bakolitsa, Christine B Trame, Lian Duan, Dana Weekes, Debanu Das, Daniel McMullan, Amanda Nopakun, Christina Puckett, Keith O. Hodgson, Joanna C Grant, Ron Reyes, Kevin K. Jin, David Marciano, Connie Chen, Jiadong Zhou, Dennis Carlton, Abhinav Kumar, Kyle Ellrott, Lukasz Jaroszewski, Andrew Yeh, Tiffany Wooten, Andrew T. Morse, Polat Abdubek, Michelle Chiu, Henry van den Bedem, Linda Okach, Sanjay Krishna, John Wooley, Ashley M. Deacon, Hsiu-Ju Chiu, Mitchell D. Miller, Anna Grzechnik, Scott A. Lesley, and Julie Feuerhelm
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Models, Molecular ,Protein Folding ,Fimbria ,Crystallography, X-Ray ,Biochemistry ,fimbriae ,Pilus ,Fimbriae Proteins ,fluids and secretions ,Structural Biology ,Models ,Bacteroides ,Peptide sequence ,0303 health sciences ,Crystallography ,biology ,Human Gut Microbiome ,Bacterial ,food and beverages ,Biological Sciences ,Condensed Matter Physics ,pili ,PG0179 ,Bacteroides thetaiotaomicron ,Protein Structure ,DUF1812 ,Mfa2 ,Molecular Sequence Data ,Biophysics ,Sequence alignment ,digestive system ,Fimbriae ,03 medical and health sciences ,Genetics ,Amino Acid Sequence ,BT1062 ,Porphyromonas gingivalis ,PGN0288 ,030304 developmental biology ,Structural Homology ,030306 microbiology ,Protein ,Molecular ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,bacterial infections and mycoses ,Protein Structure, Tertiary ,carbohydrates (lipids) ,Structural Homology, Protein ,Fimbriae, Bacterial ,Chemical Sciences ,X-Ray ,bacteria ,PF08842 ,Digestive Diseases ,Sequence Alignment ,Tertiary - Abstract
The crystal structure of BT1062 from Bacteroides thetaiotaomicron revealed a conserved fold that is widely adopted by fimbrial components., BT1062 from Bacteroides thetaiotaomicron is a homolog of Mfa2 (PGN0288 or PG0179), which is a component of the minor fimbriae in Porphyromonas gingivalis. The crystal structure of BT1062 revealed a conserved fold that is widely adopted by fimbrial components.
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- 2010
10. Crystal Structure of the First Eubacterial Mre11 Nuclease Reveals Novel Features that May Discriminate Substrates During DNA Repair
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Mitchell D. Miller, Anna Grzechnik, Heath E. Klock, Keith O. Hodgson, Linda Okach, Prasad Burra, Polat Abdubek, John Wooley, Debanu Das, Qingping Xu, Sanjay Krishna, Thomas Clayton, Abhinav Kumar, Henry van den Bedem, Ian A. Wilson, Gye Won Han, Dana Weekes, Davide Moiani, Lian Duan, Christopher L. Rife, Jessica Paulsen, Julie Feuerhelm, Tamara Astakhova, Mark W. Knuth, Marc C. Deller, Ashley M. Deacon, Marc André Elsliger, Scott A. Lesley, Slawomir K. Grzechnik, John A. Tainer, Andrew T. Morse, Daniel McMullan, Lukasz Jaroszewski, Dennis Carlton, Edward Nigoghossian, Christine B Trame, David Marciano, Herbert L. Axelrod, Natasha Sefcovic, Hsiu-Ju Chiu, Joanna C Grant, Adam Godzik, Ron Reyes, Piotr Kozbial, Henry J Tien, Kevin K. Jin, and Dustin C. Ernst
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Exonuclease ,DNA Repair ,Protein Conformation ,DNA repair ,Molecular Sequence Data ,DNA, Single-Stranded ,Crystallography, X-Ray ,Article ,chemistry.chemical_compound ,Bacterial Proteins ,Structural Biology ,Hydrolase ,Thermotoga maritima ,Amino Acid Sequence ,Molecular Biology ,Nuclease ,Endodeoxyribonucleases ,Sequence Homology, Amino Acid ,biology ,DNA ,biology.organism_classification ,enzymes and coenzymes (carbohydrates) ,DNA/RNA non-specific endonuclease ,Exodeoxyribonucleases ,Models, Chemical ,chemistry ,Biochemistry ,biology.protein ,Micrococcal nuclease - Abstract
Mre11 nuclease plays a central role in the repair of cytotoxic and mutagenic DNA double-strand breaks. As X-ray structural information has been available only for the Pyrococcus furiosus enzyme (PfMre11), the conserved and variable features of this nuclease across the domains of life have not been experimentally defined. Our crystal structure and biochemical studies demonstrate that TM1635 from Thermotoga maritima, originally annotated as a putative nuclease, is an Mre11 endo/exonuclease (TmMre11) and the first such structure from eubacteria. TmMre11 and PfMre11 display similar overall structures, despite sequence identity in the twilight zone of only approximately 20%. However, they differ substantially in their DNA-specificity domains and in their dimeric organization. Residues in the nuclease domain are highly conserved, but those in the DNA-specificity domain are not. The structural differences likely affect how Mre11 from different organisms recognize and interact with single-stranded DNA, double-stranded DNA and DNA hairpin structures during DNA repair. The TmMre11 nuclease active site has no bound metal ions, but is conserved in sequence and structure with the exception of a histidine that is important in PfMre11 nuclease activity. Nevertheless, biochemical characterization confirms that TmMre11 possesses both endonuclease and exonuclease activities on single-stranded and double-stranded DNA substrates, respectively.
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- 2010
11. The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role
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Polat Abdubek, Sanjay Krishna, Mark W. Knuth, Adam Godzik, Jonathan M. Caruthers, Linda Okach, Christopher L. Rife, Marc-André Elsliger, Edward Nigoghossian, David Marciano, Tamara Astakhova, L Aravind, Marc C. Deller, Andrew T. Morse, Kevin K. Jin, Lukasz Jaroszewski, Henry van den Bedem, Joanna C Grant, Daniel McMullan, Mitchell D. Miller, Ashley M. Deacon, Abhinav Kumar, Ron Reyes, Keith O. Hodgson, Ian A. Wilson, Constantina Bakolitsa, Scott A. Lesley, Lian Duan, Gye Won Han, Qingping Xu, John Wooley, Hsiu-Ju Chiu, Herbert L. Axelrod, Thomas Clayton, Heath E. Klock, Julie Feuerhelm, Dana Weekes, and Dennis Carlton
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Models, Molecular ,Protein Folding ,Domains of Unknown Function ,acyl-coA ,Plasma protein binding ,Crystallography, X-Ray ,Biochemistry ,Protein structure ,Models ,Genome, Archaeal ,Structural Biology ,Acyl-CoA-binding protein ,2.1 Biological and endogenous factors ,Aetiology ,Peptide sequence ,0303 health sciences ,Crystallography ,Genome ,030302 biochemistry & molecular biology ,Biological Sciences ,Condensed Matter Physics ,Zinc ,Sulfolobus solfataricus ,polyketide biosynthesis ,Protein folding ,Biotechnology ,Protein Binding ,Protein Structure ,1.1 Normal biological development and functioning ,Archaeal Proteins ,Molecular Sequence Data ,Biophysics ,Biology ,acyl-carrier proteins ,Structural genomics ,03 medical and health sciences ,Polyketide ,Underpinning research ,Genetics ,Amino Acid Sequence ,030304 developmental biology ,Oligonucleotide ,Molecular ,structural genomics ,Protein Structure, Tertiary ,Archaeal ,Chemical Sciences ,X-Ray ,Acyl Coenzyme A ,Tertiary - Abstract
The crystal structure of SSO2064, the first structural representative of Pfam family PF01796 (DUF35), reveals a two-domain architecture comprising an N-terminal zinc-ribbon domain and a C-terminal OB-fold domain. Analysis of the domain architecture, operon organization and bacterial orthologs combined with the structural features of SSO2064 suggests a role involving acyl-CoA binding for this family of proteins., SSO2064 is the first structural representative of PF01796 (DUF35), a large prokaryotic family with a wide phylogenetic distribution. The structure reveals a novel two-domain architecture comprising an N-terminal, rubredoxin-like, zinc ribbon and a C-terminal, oligonucleotide/oligosaccharide-binding (OB) fold domain. Additional N-terminal helical segments may be involved in protein–protein interactions. Domain architectures, genomic context analysis and functional evidence from certain bacterial representatives of this family suggest that these proteins form a novel fatty-acid-binding component that is involved in the biosynthesis of lipids and polyketide antibiotics and that they possibly function as acyl-CoA-binding proteins. This structure has led to a re-evaluation of the DUF35 family, which has now been split into two entries in the latest Pfam release (v.24.0).
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- 2010
12. Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction
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Hope A. Johnson, Joanna C Grant, Marc C. Deller, Polat Abdubek, Keith O. Hodgson, Sanjay Krishna, Debanu Das, Qingping Xu, Mark W. Knuth, John Wooley, Abhinav Kumar, Constantina Bakolitsa, Linda Okach, Tamara Astakhova, Christopher L. Rife, Christine B Trame, Mitchell D. Miller, Anna Grzechnik, Ashley M. Deacon, Ron Reyes, David Marciano, Lian Duan, Daniel McMullan, Henry van den Bedem, Julie Feuerhelm, Hsiu-Ju Chiu, Connie Chen, Natasha Sefcovic, Piotr Kozbial, Dana Weekes, Henry J Tien, Marc-André Elsliger, Ian A. Wilson, Heath E. Klock, Herbert L. Axelrod, Edward Nigoghossian, Thomas Clayton, Kevin K. Jin, Dustin C. Ernst, Dennis Carlton, Adam Godzik, Gye Won Han, Andrew T. Morse, Scott A. Lesley, Rafael Najmanovich, and Lukasz Jaroszewski
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Models, Molecular ,Secondary ,Protein Folding ,Shewanella ,domain duplication ,Crystallography, X-Ray ,Biochemistry ,Protein Structure, Secondary ,domain of unknown function ,Protein structure ,Models ,Structural Biology ,2.1 Biological and endogenous factors ,oxidative stress ,Aetiology ,Rhodobacteraceae ,Structural motif ,Genetics ,0303 health sciences ,Crystallography ,Genome ,030302 biochemistry & molecular biology ,Bacterial ,Biological Sciences ,Condensed Matter Physics ,Pleckstrin homology domain ,Protein folding ,Domain of unknown function ,New Folds ,signaling ,Biotechnology ,Protein Structure Initiative ,Signal Transduction ,Protein Structure ,1.1 Normal biological development and functioning ,Molecular Sequence Data ,Biophysics ,Biology ,Structural genomics ,03 medical and health sciences ,Bacterial Proteins ,Underpinning research ,Amino Acid Sequence ,Binding site ,Structural Homology ,030304 developmental biology ,Protein ,Human Genome ,Molecular ,structural genomics ,Protein Structure, Tertiary ,Structural Homology, Protein ,Chemical Sciences ,X-Ray ,Generic health relevance ,Tertiary ,Genome, Bacterial - Abstract
The crystal structures of SPO0140 and Sbal_2486 revealed a two-domain structure that adopts a novel fold. Analysis of the interdomain cleft suggests a nucleotide-based ligand with a genome context indicating signaling as a possible role for this family., The crystal structures of SPO0140 and Sbal_2486 were determined using the semiautomated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). The structures revealed a conserved core with domain duplication and a superficial similarity of the C-terminal domain to pleckstrin homology-like folds. The conservation of the domain interface indicates a potential binding site that is likely to involve a nucleotide-based ligand, with genome-context and gene-fusion analyses additionally supporting a role for this family in signal transduction, possibly during oxidative stress.
- Published
- 2010
13. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation
- Author
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Christopher L. Rife, Kyle Ellrott, Linda Okach, Dustin C. Ernst, Prasad Burra, Dana Weekes, Edward Nigoghossian, Polat Abdubek, Gye Won Han, Silvya Oommachen, Piotr Kozbial, John Wooley, Jessica Paulsen, Henry J Tien, Slawomir K. Grzechnik, Sanjay Krishna, Amanda Nopakun, Julie Feuerhelm, Abhinav Kumar, Henry van den Bedem, Lian Duan, Mark W. Knuth, Marc C. Deller, Tamara Astakhova, Michelle Chiu, Heath E. Klock, Carol L. Farr, Hsiu-Ju Chiu, Connie Chen, Joanna C Grant, Ron Reyes, Daniel McMullan, Tiffany Wooten, Ashley M. Deacon, Nick V. Grishin, Constantina Bakolitsa, Mitchell D. Miller, Anna Grzechnik, Ian A. Wilson, Christina Puckett, Thomas Clayton, Marc André Elsliger, Andrew T. Morse, Dennis Carlton, Adam Godzik, Herbert L. Axelrod, Keith O. Hodgson, Kevin K. Jin, Scott A. Lesley, Christine B Trame, David Marciano, Hope A. Johnson, Natasha Sefcovic, Qingping Xu, Lukasz Jaroszewski, and Debanu Das
- Subjects
Models, Molecular ,Transcription, Genetic ,Domains of Unknown Function ,Crystallography, X-Ray ,medicine.disease_cause ,Biochemistry ,putative transcription regulators ,Models ,Structural Biology ,Transcription (biology) ,Transcriptional regulation ,Peptide sequence ,Genetics ,Regulation of gene expression ,0303 health sciences ,Crystallography ,Genome ,PF09836 ,030302 biochemistry & molecular biology ,Bacterial ,Biological Sciences ,Condensed Matter Physics ,Neisseria ,Transcription ,Protein Structure ,1.1 Normal biological development and functioning ,Molecular Sequence Data ,Biophysics ,Biology ,Structural genomics ,Quaternary ,DUF2063 ,03 medical and health sciences ,Genetic ,Bacterial Proteins ,Underpinning research ,medicine ,Amino Acid Sequence ,putative DNA-binding proteins ,Protein Structure, Quaternary ,Structural Homology ,030304 developmental biology ,Protein ,NGO1945 ,Molecular ,structural genomics ,biology.organism_classification ,Neisseria gonorrhoeae ,Sequence identity ,Protein Structure, Tertiary ,Gene Expression Regulation ,Structural Homology, Protein ,Chemical Sciences ,X-Ray ,Tertiary ,Genome, Bacterial - Abstract
The crystal structure of the NGO1945 gene product from N. gonorrhoeae (UniProt Q5F5IO) reveals that the N-terminal domain assigned as a domain of unknown function (DUF2063) is likely to bind DNA and that the protein may be involved in transcriptional regulation., Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from Neisseria gonorrhoeae, has been determined and reveals that the N-terminal DUF2063 domain is likely to be a DNA-binding domain. In conjunction with the rest of the protein, NGO1945 is likely to be involved in transcriptional regulation, which is consistent with genomic neighborhood analysis. Of the 216 currently known proteins that contain a DUF2063 domain, the most significant sequence homologs of NGO1945 (∼40–99% sequence identity) are from various Neisseria and Haemophilus species. As these are important human pathogens, NGO1945 represents an interesting candidate for further exploration via biochemical studies and possible therapeutic intervention.
- Published
- 2009
14. Structure of LP2179, the first representative of Pfam family PF08866, suggests a new fold with a role in amino-acid metabolism
- Author
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Polat Abdubek, Keith O. Hodgson, Sanjay Krishna, Henry van den Bedem, Mitchell D. Miller, Herbert L. Axelrod, Dana Weekes, Marc C. Deller, Constantina Bakolitsa, Joanna C Grant, Mark W. Knuth, Heath E. Klock, Tamara Astakhova, Julie Feuerhelm, Abhinav Kumar, Marc-André Elsliger, Edward Nigoghossian, Daniel McMullan, Gye Won Han, Lian Duan, Silvya Oommachen, Thomas Clayton, Christina V. Trout, Qingping Xu, Christopher L. Rife, Kevin K. Jin, Lukasz Jaroszewski, Andrew T. Morse, Hsiu-Ju Chiu, Dennis Carlton, Jessica Paulsen, David Marciano, Ashley M. Deacon, Ian A. Wilson, Piotr Kozbial, Henry J Tien, Ron Reyes, Adam Godzik, Scott A. Lesley, Slawomir K. Grzechnik, John Wooley, and Linda Okach
- Subjects
Models, Molecular ,S-adenosylmethionine decarboxylase ,Protein Folding ,Crystallography, X-Ray ,Biochemistry ,Protein structure ,Models ,Structural Biology ,Amino Acids ,Peptide sequence ,chemistry.chemical_classification ,0303 health sciences ,Crystallography ,030302 biochemistry & molecular biology ,Biological Sciences ,Condensed Matter Physics ,Amino acid ,DUFs ,Protein folding ,New Folds ,Biotechnology ,Protein Structure ,Protein family ,Structural similarity ,Molecular Sequence Data ,Biophysics ,Sequence alignment ,Computational biology ,Biology ,Structural genomics ,03 medical and health sciences ,Bacterial Proteins ,Genetics ,Amino Acid Sequence ,Structural Homology ,030304 developmental biology ,amino-acid metabolism ,Protein ,Human Genome ,Molecular ,structural genomics ,Protein Structure, Tertiary ,probiotics ,chemistry ,Structural Homology, Protein ,Chemical Sciences ,X-Ray ,Sequence Alignment ,Tertiary ,Lactobacillus plantarum - Abstract
The first structural representative of the PF08866 (DUF1831) protein family reveals a potential new α+β fold and indicates a possible involvement in amino-acid metabolism., The structure of LP2179, a member of the PF08866 (DUF1831) family, suggests a novel α+β fold comprising two β-sheets packed against a single helix. A remote structural similarity to two other uncharacterized protein families specific to the Bacillus genus (PF08868 and PF08968), as well as to prokaryotic S-adenosylmethionine decarboxylases, is consistent with a role in amino-acid metabolism. Genomic neighborhood analysis of LP2179 supports this functional assignment, which might also then be extended to PF08868 and PF08968.
- Published
- 2009
15. The structure of the first representative of Pfam family PF06475 reveals a new fold with possible involvement in glycolipid metabolism
- Author
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Edward Nigoghossian, Keith O. Hodgson, Mitchell D. Miller, Gye Won Han, Christopher L. Rife, Dennis Carlton, Aprilfawn White, Thomas Clayton, Abhinav Kumar, Silvya Oommachen, Scott A. Lesley, Daniel McMullan, Hsiu-Ju Chiu, Christina V. Trout, Henry van den Bedem, Jessica Paulsen, Linda Okach, Piotr Kozbial, Slawomir K. Grzechnik, Kevin K. Jin, Polat Abdubek, Dana Weekes, Adam Godzik, Ron Reyes, Marc André Elsliger, Ylva Elias, Sanjay Krishna, David Marciano, Andrew T. Morse, Joanna C Grant, Ashley M. Deacon, Ian A. Wilson, Mark W. Knuth, Tamara Astakhova, Rafael Najmanovich, Lian Duan, Julie Feuerhelm, Marc C. Deller, Constantina Bakolitsa, Qingping Xu, John Wooley, Heath E. Klock, and Lukasz Jaroszewski
- Subjects
Models, Molecular ,glycolipids ,Protein Folding ,Glycolipid metabolism ,Crystallography, X-Ray ,Biochemistry ,Models ,Structural Biology ,2.2 Factors relating to the physical environment ,2.1 Biological and endogenous factors ,Aetiology ,Peptide sequence ,0303 health sciences ,Crystallography ,Genome ,030302 biochemistry & molecular biology ,Bacterial ,food and beverages ,Biological Sciences ,Condensed Matter Physics ,DUFs ,Pseudomonas aeruginosa ,Protein folding ,lipids (amino acids, peptides, and proteins) ,New Folds ,host–pathogen interactions ,Protein Structure ,Structural similarity ,Molecular Sequence Data ,Biophysics ,Biology ,Structural genomics ,Quaternary ,03 medical and health sciences ,Glycolipid ,Bacterial Proteins ,Genetics ,Amino Acid Sequence ,Protein Structure, Quaternary ,030304 developmental biology ,A domain ,Molecular ,structural genomics ,Protein Structure, Tertiary ,Lipoprotein localization ,Chemical Sciences ,X-Ray ,osmotic stress ,Glycolipids ,Tertiary ,Genome, Bacterial - Abstract
PA1994, a Pfam PF06475 (DUF1089) family homolog from P. aeruginosa, reveals remote similarities to lipoprotein localization factors and a conserved putative glycolipid-binding site., The crystal structure of PA1994 from Pseudomonas aeruginosa, a member of the Pfam PF06475 family classified as a domain of unknown function (DUF1089), reveals a novel fold comprising a 15-stranded β-sheet wrapped around a single α-helix that assembles into a tight dimeric arrangement. The remote structural similarity to lipoprotein localization factors, in addition to the presence of an acidic pocket that is conserved in DUF1089 homologs, phospholipid-binding and sugar-binding proteins, indicate a role for PA1994 and the DUF1089 family in glycolipid metabolism. Genome-context analysis lends further support to the involvement of this family of proteins in glycolipid metabolism and indicates possible activation of DUF1089 homologs under conditions of bacterial cell-wall stress or host–pathogen interactions.
- Published
- 2009
16. The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold
- Author
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Thomas Clayton, Debanu Das, John Wooley, Marc-André Elsliger, Heath E. Klock, Polat Abdubek, Edward Nigoghossian, Marc C. Deller, Carol L. Farr, Christopher L. Rife, Sanjay Krishna, Linda Okach, Abhinav Kumar, Mark W. Knuth, Constantina Bakolitsa, Tamara Astakhova, Joanna C Grant, Adam Godzik, Kyle Ellrott, Scott A. Lesley, Qingping Xu, Hsiu-Ju Chiu, Lian Duan, Ron Reyes, Daniel McMullan, Mitchell D. Miller, Dustin C. Ernst, Dana Weekes, Anna Grzechnik, Andrew T. Morse, Gye Won Han, Julie Feuerhelm, Silvya Oommachen, Piotr Kozbial, Henry van den Bedem, Henry J Tien, Jessica Paulsen, Tiffany Wooten, Kevin K. Jin, Ashley M. Deacon, Ian A. Wilson, Christina Puckett, Keith O. Hodgson, Michelle Chiu, Amanda Nopakun, Herbert L. Axelrod, Lukasz Jaroszewski, Natasha Sefcovic, Christine B Trame, Connie Chen, David Marciano, Hope A. Johnson, and Dennis Carlton
- Subjects
Models, Molecular ,Protein Folding ,Klebsiella pneumoniae ,Gut flora ,Crystallography, X-Ray ,Biochemistry ,Protein structure ,Models ,Structural Biology ,BOF ,2.1 Biological and endogenous factors ,Aetiology ,Lung ,Peptide sequence ,0303 health sciences ,Crystallography ,biology ,030302 biochemistry & molecular biology ,toxins ,Hematology ,Biological Sciences ,Condensed Matter Physics ,3. Good health ,Infectious Diseases ,Pneumonia & Influenza ,Protein folding ,Infection ,Protein Structure ,1.1 Normal biological development and functioning ,Lipoproteins ,Molecular Sequence Data ,Biophysics ,single-stranded DNA-binding proteins ,DNA-binding protein ,Structural genomics ,Microbiology ,03 medical and health sciences ,Bacterial Proteins ,Underpinning research ,Genetics ,Amino Acid Sequence ,030304 developmental biology ,Molecular ,Pneumonia ,structural genomics ,biology.organism_classification ,Protein Structure, Tertiary ,NipE-like protein ,Chemical Sciences ,X-Ray ,human gut pathogens ,OB-fold ,Novel Variants of Known Folds and Function ,Tertiary ,Lipoprotein - Abstract
KPN03535 is a protein unique to K. pneumoniae. The crystal structure reveals that KPN03535 represents a novel variant of the OB-fold and is likely to be a DNA-binding lipoprotein., KPN03535 (gi|152972051) is a putative lipoprotein of unknown function that is secreted by Klebsiella pneumoniae MGH 78578. The crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the OB-fold and structurally similar to the bacterial Cpx-pathway protein NlpE, single-stranded DNA-binding (SSB) proteins and toxins. K. pneumoniae MGH 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pathogen that is linked to about 8% of all hospital-acquired infections in the USA. This structure provides the foundation for further investigations into this divergent member of the OB-fold family.
- Published
- 2009
17. Crystal Structure of Histidine Phosphotransfer Protein ShpA, an Essential Regulator of Stalk Biogenesis in Caulobacter crescentus
- Author
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Marc C. Deller, Adam Godzik, Mark W. Knuth, Kevin K. Jin, Joanna C Grant, Ron Reyes, Ylva Elias, Henry van den Bedem, Andrew T. Morse, Linda Okach, Mitchell D. Miller, Anna Grzechnik, Keith O. Hodgson, Christopher L. Rife, Hsiu-Ju Chiu, Piotr Kozbial, Prasad Burra, Lian Duan, Heath E. Klock, Tamara Astakhova, Julie Feuerhelm, Jessica Paulsen, Abhinav Kumar, Thomas Clayton, Marc André Elsliger, Dana Weekes, Christina V. Trout, Gye Won Han, Edward Nigoghossian, Silvya Oommachen, Daniel McMullan, John Wooley, Polat Abdubek, Sanjay Krishna, Dennis Carlton, Natasha Sefcovic, Lukasz Jaroszewski, Qingping Xu, Christine B Trame, David Marciano, Ian A. Wilson, Scott A. Lesley, Ashley M. Deacon, and Slawomir K. Grzechnik
- Subjects
Models, Molecular ,Helix bundle ,biology ,Protein Conformation ,Caulobacter crescentus ,Molecular Sequence Data ,Phosphotransferases ,Histidine kinase ,Crystallography, X-Ray ,biology.organism_classification ,Article ,Response regulator ,Protein structure ,Bacterial Proteins ,Biochemistry ,Structural Biology ,Phosphorylation ,Histidine ,Amino Acid Sequence ,Molecular Biology ,Biogenesis - Abstract
Cell cycle regulated stalk biogenesis in Caulobacter crescentus is controlled by a multi-step phosphorelay system consisting of the hybrid histidine kinase ShkA, the histidine-phosphotransfer protein ShpA and the response regulator TacA. ShpA shuttles phosphoryl groups between ShkA and TacA. When phosphorylated, TacA triggers a downstream transcription cascade for stalk synthesis in an RpoN-dependent manner. The crystal structure of ShpA was determined to 1.52 Å resolution. ShpA belongs to a family of monomeric histidine phosphotransfer (HPt) proteins, which feature a highly conserved four-helix bundle. The phosphorylatable histidine, His56, is located on the surface of the helix bundle and is fully solvent exposed. One end of the four-helix bundle in ShpA is shorter compared to other characterized histidine phosphotransfer proteins, whereas the face that potentially interacts with the response regulators is structurally conserved. Similarities of the interaction surface around the phosphorylation site suggest that ShpA is likely to share a common mechanism for molecular recognition and phosphotransfer with yeast phosphotransfer protein YPD1 despite low overall sequence similarity.
- Published
- 2009
18. Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 Å resolution
- Author
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Lukasz Jaroszewski, Ashley M. Deacon, Julie Feuerhelm, Hsiu-Ju Chiu, Debanu Das, Dana Weekes, Jessica Paulsen, Qingping Xu, Marc C. Deller, Piotr Kozbial, Ian A. Wilson, Christina Puckett, Gye Won Han, Silvya Oommachen, Abhinav Kumar, Marc André Elsliger, Amanda Nopakun, Natasha Sefcovic, Linda Okach, Edward Nigoghossian, Herbert L. Axelrod, Keith O. Hodgson, Dennis Carlton, Scott A. Lesley, Mark W. Knuth, Heath E. Klock, Henry Tien, Carol L. Farr, Kevin D. Murphy, Hope A. Johnson, Slawomir K. Grzechnik, Kevin K. Jin, Henry van den Bedem, Ylva Elias, Adam Godzik, Dustin C. Ernst, Tamara Astakhova, Andrew T. Morse, Aprilfawn White, Thomas Clayton, John Wooley, Connie Chen, Christine B Trame, Daniel McMullan, Christina V. Trout, Joanna Hale, Ron Reyes, Claire Acosta, David Marciano, Polat Abdubek, Lian Duan, Sanjay Krishna, Christopher L. Rife, Prasad Burra, Sebastian Sudek, Mitchell D. Miller, and Anna Grzechnik
- Subjects
Genetics ,Viral protein ,RNA ,Cyanophage ,RNA-binding protein ,Biology ,medicine.disease_cause ,Biochemistry ,Structural genomics ,Protein structure ,Structural Biology ,Nucleic acid ,medicine ,Molecular Biology ,Peptide sequence - Abstract
ECX21941 represents a very large family (over 600 members) of novel, ocean metagenome-specific proteins identified by clustering of the dataset from the Global Ocean Sampling expedition. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity. The ECX21941 protein assembles as a homopentamer in solution and in the crystal structure when expressed in Escherichia coli and represents the first pentameric structure for this Sm/LSm family of proteins, although the actual oligomeric form in vivo is currently not known. The genomic neighborhood analysis of ECX21941 and its homologs combined with sequence similarity searches suggest a cyanophage origin for this protein. The specific functions of members of this family are unknown, but our structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing.
- Published
- 2008
19. Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 Å resolution
- Author
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Henry Tien, Keith O. Hodgson, Aprilfawn White, Linda Okach, Tamara Astakhova, Marc-André Elsliger, Qingping Xu, Edward Nigoghossian, Julie Feuerhelm, Kevin K. Jin, Dustin C. Ernst, Andrew T. Morse, Christine B Trame, Henry van den Bedem, Slawomir K. Grzechnik, Prasad Burra, Abhinav Kumar, Hsiu-Ju Chiu, Herbert L. Axelrod, Heath E. Klock, Thomas Clayton, David Marciano, Polat Abdubek, Gye Won Han, Marc C. Deller, Dennis Carlton, Christina V. Trout, Joanna Hale, Silvya Oommachen, Ashley M. Deacon, Natasha Sefcovic, Debanu Das, Scott A. Lesley, Sanjay Krishna, Lukasz Jaroszewski, Ylva Elias, Ian A. Wilson, Mitchell D. Miller, Anna Grzechnik, Christopher L. Rife, Daniel McMullan, John Wooley, Claire Acosta, Piotr Kozbial, Kevin D. Murphy, Mark W. Knuth, Adam Godzik, Dana Weekes, Lian Duan, Ron Reyes, and Jessica Paulsen
- Subjects
Shewanella ,Protein family ,Protein Conformation ,Protein subunit ,Amino Acid Motifs ,Molecular Sequence Data ,Protein Data Bank (RCSB PDB) ,Biology ,Crystallography, X-Ray ,Biochemistry ,DNA-binding protein ,Article ,Structural genomics ,Protein structure ,Bacterial Proteins ,Structural Biology ,Amino Acid Sequence ,Molecular Biology ,DNA ,DNA-binding domain ,computer.file_format ,Protein Data Bank ,Protein Structure, Tertiary ,Dimerization ,computer ,Protein Binding - Abstract
The protein SO4266 (gi|24375750) from the bacterium Shewanella oneidensis MR-1 is annotated as a member of Pfam PF02661. This family consists of Fic (filamentation induced by cAMP) proteins and their relatives, and is characterized by the presence of a well-conserved HPFXXGNG motif 1. The biochemistry of Fic proteins has not been characterized extensively and their exact molecular functions remain unknown. From early studies in Escherichia coli, it is believed that Fic proteins and cAMP may be involved in a regulatory mechanism of cell division, including folate metabolism by the synthesis of p-aminobenzoic acid (PABA) or folate 1. Proteins containing the Fic domain are present in all kingdoms of life and range in size from ~200 to 500 amino acids. The Fic protein family contains 647 members, including two human proteins, according to Pfam (May 2008). Sequence-based clustering 2 of this protein family, at 30% sequence identity, groups these proteins into 18 clusters. Three crystal structures of Fic proteins from bacteria (unpublished) are available in the Protein Data Bank [accession codes 2g03 (194 residues, 2.2 A), 2f6s (201 residues, 2.5 A) and 3cuc (262 residues, 2.7 A)]. The first two of these proteins belong to a single cluster of 16 members and share ~60% sequence identity. The anti-apoptotic bacterial effector protein BepA, which is a type IV secretion (T4S) system substrate, also contains an N-terminal Fic domain 3. In humans, the Fic domain is present in the Huntingtin Interacting Protein E (HYPE; Uniprot entry Q9BVA6_HUMAN), a protein of unknown function that is thought to interact with Huntingtin, one of the major proteins in the Huntington's disease protein interaction network (listed as NAD- or FAD-binding) 4. Bioinformatics analysis of prokaryotic toxin-antitoxin networks 5 suggests that Fic proteins are putative death-on-curing (Doc) toxins that are part of the Phd-Doc system. These proteins likely function as metal-dependent nucleases or RNA-processing enzymes, 5 while more recent studies suggest that Doc toxicity is caused by inhibition of translation elongation 6. SO4266 (Uniprot entry Q8E9K5_SHEON), at 372 amino acids, is one of the largest Fic domain-containing proteins to have its structure determined. Interestingly, both HYPE and SO4266 belong to the largest sequence cluster in this family (n.b. our B. thetaiotaomicron {"type":"entrez-protein","attrs":{"text":"NP_811426.1","term_id":"29347923","term_text":"NP_811426.1"}}NP_811426.1 structure with PDB id 3cuc also belongs to this cluster), which comprises 466 out of 647 proteins, and share ~32% sequence identity in the Fic domain. Here, we report the crystal structure of the SO4266 protein at 1.6 A resolution. The structure reveals a dimeric protein with additional electron density in the vicinity of the highly conserved HPFXXGNG motif in the Fic domain of one subunit that corresponds to the N-terminus of a symmetry-related molecule. In addition, the study also reveals a C-terminal winged-helix DNA-binding domain that sets it apart from the other Fic protein structures. The structure presented here is a representative of the largest sequence cluster and together with the structures of the other Fic proteins paves the way for further structure-based functional characterization.
- Published
- 2008
20. Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus
- Author
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John Wooley, Mark W. Knuth, Ashley M. Deacon, Lukasz Jaroszewski, Ian A. Wilson, Thomas Clayton, Hsiu-Ju Chiu, Lian Duan, Abhinav Kumar, Adam Godzik, Scott A. Lesley, Gye Won Han, Kevin K. Jin, Marc-André Elsliger, Joanna Hale, Silvya Oommachen, Edward Nigoghossian, Keith O. Hodgson, Heath E. Klock, Slawomir K. Grzechnik, Qingping Xu, Julie Feuerhelm, Mitchell D. Miller, Henry van den Bedem, Dennis Carlton, Christopher L. Rife, Ron Reyes, Andrew T. Morse, Jessica Paulsen, Linda Okach, Tamara Astakhova, Daniel McMullan, Polat Abdubek, and Sanjay Krishna
- Subjects
ved/biology ,Sulfolobus solfataricus ,ved/biology.organism_classification_rank.species ,Biology ,Biochemistry ,AAA proteins ,Structural genomics ,Protein structure ,Structural Biology ,NAIP ,Sequence motif ,Molecular Biology ,Peptide sequence ,Protein Structure Initiative - Abstract
Signal transduction ATPases with numerous domains (STAND), a large class of P-loop NTPases, belong to AAA+ ATPases. They include AP(apoptotic)-ATPases (e.g., animal apoptosis regulators CED4/Apaf-1, plant disease resistance proteins, and bacterial AfsR-like transcription regulators), NACHT NTPases (e.g. CARD4, NAIP, Het-E-1, TLP1), and several other less well-characterized families. STAND differ from other P-loop NTPases by their unique sequence motifs, which include an hhGRExE (h, hydrophobic; x, any residue) motif at the N-terminal region, a GxP/GxxP motif at the C-terminal region of the NTPase domain, in addition to a C-terminal helical domain and additional domains such as WD40, TPR, LRR or catalytic modules. Despite significant biological interests, structural coverage of STAND proteins is very limited and only two other structures are currently known: the cell death regulators Apaf-1 and CED-4. Here, we report the crystal structure of SSO1545 from Sulfolobus solfataricus, which was determined using the semi-automated, high-throughput pipeline of the Joint Center for Structural Genomics (JCSG; http://www.jcsg.org), as part of the National Institute of General Medical Sciences' Protein Structure Initiative (PSI). SSO1545 (NP-342973.1), a representative of the archaeal STANDs, is a member of Pfam PF01637 and encodes a protein of 356 residues with calculated molecular weight and isoelectric point of 41.7more » kD and 8.2, respectively.« less
- Published
- 2008
21. Crystal structures of MW1337R and lin2004: Representatives of a novel protein family that adopt a four-helical bundle fold
- Author
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Abhinav Kumar, Ron Reyes, Henry van den Bedem, Marc André Elsliger, Aprilfawn White, Scott A. Lesley, Ian A. Wilson, Keith O. Hodgson, Guenter Wolf, Linda Okach, David Marciano, Edward Nigoghossian, Piotr Kozbial, Christopher L. Rife, Chloe Zubieta, Ylva Elias, Eric Koesema, Ashley M. Deacon, Glen Spraggon, Kevin K. Jin, Kevin D. Murphy, Herbert L. Axelrod, Hsiu-Ju Chiu, Andrew T. Morse, Mitchell D. Miller, Dennis Carlton, Mark W. Knuth, Adam Godzik, Gye Won Han, Silvya Oommachen, John Wooley, Thomas Clayton, Christina V. Trout, Dana Weekes, Lian Duan, Daniel McMullan, Joanna Hale, Tamara Astakhova, Polat Abdubek, Sanjay Krishna, Claire Acosta, Slawomir K. Grzechnik, Lukasz Jaroszewski, Julie Feuerhelm, Marc C. Deller, Qingping Xu, and Heath E. Klock
- Subjects
Genetics ,Protein Folding ,Accession number (library science) ,Operon ,Molecular Sequence Data ,Bacillus subtilis ,Biology ,Crystallography, X-Ray ,biology.organism_classification ,Biochemistry ,Protein Structure, Secondary ,Protein Structure, Tertiary ,Structural genomics ,chemistry.chemical_compound ,Protein structure ,Bacterial Proteins ,chemistry ,Structural Biology ,Complementary DNA ,Amino Acid Sequence ,Molecular Biology ,Gene ,DNA - Abstract
To extend the structural coverage of proteins with unknown functions, we targeted a novel protein family (Pfam accession number PF08807, DUF1798) for which we proposed and determined the structures of two representative members. The MW1337R gene of Staphylococcus aureus subsp. aureus Rosenbach (Wood 46) encodes a protein with a molecular weight of 13.8 kDa (residues 1-116) and a calculated isoelectric point of 5.15. The lin2004 gene of the nonspore-forming bacterium Listeria innocua Clip11262 encodes a protein with a molecular weight of 14.6 kDa (residues 1-121) and a calculated isoelectric point of 5.45. MW1337R and lin2004, as well as their homologs, which, so far, have been found only in Bacillus, Staphylococcus, Listeria, and related genera (Geobacillus, Exiguobacterium, and Oceanobacillus), have unknown functions and are annotated as hypothetical proteins. The genomic contexts of MW1337R and lin2004 are similar and conserved in related species. In prokaryotic genomes, most often, functionally interacting proteins are coded by genes, which are colocated in conserved operons. Proteins from the same operon as MW1337R and lin2004 either have unknown functions (i.e., belong to DUF1273, Pfam accession number PF06908) or are similar to ypsB from Bacillus subtilis. The function of ypsB is unclear, although it has a strong similaritymore » to the N-terminal region of DivIVA, which was characterized as a bifunctional protein with distinct roles during vegetative growth and sporulation. In addition, members of the DUF1273 family display distant sequence similarity with the DprA/Smf protein, which acts downstream of the DNA uptake machinery, possibly in conjunction with RecA. The RecA activities in Bacillus subtilis are modulated by RecU Holliday-junction resolvase. In all analyzed cases, the gene coding for RecU is in the vicinity of MW1337R, lin2004, or their orthologs, but on a different operon located in the complementary DNA strand. Here, we report the crystal structures of MW1337R and lin2004, which were determined using the semiautomated, high-throughput pipeline of the Joint Center for Structural Genomics (JCSG), part of the National Institute of General Medical Sciences Protein Structure Initiative.« less
- Published
- 2008
22. Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 Å resolution
- Author
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Aprilfawn White, Jessica Paulsen, Polat Abdubek, Michael DiDonato, Sanjay Krishna, John Wooley, Daniel McMullan, Lian Duan, Andrew T. Morse, Henry van den Bedem, Christopher L. Rife, Slawomir K. Grzechnik, Mitchell D. Miller, Hsiu-Ju Chiu, Julie Feuerhelm, Keith O. Hodgson, Heath E. Klock, Marc-André Elsliger, Edward Nigoghossian, Thomas Clayton, Herbert L. Axelrod, Joanna Hale, Lukasz Jaroszewski, Qingping Xu, Scott A. Lesley, Piotr Kozbial, Ron Reyes, Scott M. Brittain, Ashley M. Deacon, Ian A. Wilson, Scott B. Ficarro, Adam Godzik, and Gye Won Han
- Subjects
Biochemistry ,Structural Biology ,Thermophile ,Thermotoga maritima ,Posttranslational modification ,Cytidine deaminase ,Crystal structure ,Biology ,biology.organism_classification ,Molecular Biology ,Structural genomics - Published
- 2008
23. Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) fromThermotoga maritima at 1.88 Å resolution
- Author
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Lukasz Jaroszewski, Keith O. Hodgson, Marc-André Elsliger, John Wooley, Edward Nigoghossian, Andrew T. Morse, Scott A. Lesley, Tamara Astakhova, Jessica Paulsen, Guenter Wolf, Ron Reyes, Henry van den Bedem, Polat Abdubek, Aprilfawn White, Gye Won Han, Sanjay Krishna, Adam Godzik, Hsiu-Ju Chiu, Mitchell D. Miller, Silvya Oommachen, Qingping Xu, Daniel McMullan, Christopher L. Rife, Slawomir K. Grzechnik, Herbert L. Axelrod, Thomas Clayton, Joanna Hale, Eric Koesema, Heath E. Klock, Lian Duan, Julie Feuerhelm, Ashley M. Deacon, Ian A. Wilson, Eileen Ambing, Dennis Carlton, Mark W. Knuth, Kevin Quijano, Dana Weekes, Kevin K. Jin, Justin Haugen, and Linda Okach
- Subjects
Hydroxymethyl and Formyl Transferases ,Models, Molecular ,Binding Sites ,Materials science ,AICAR TRANSFORMYLASE/IMP CYCLOHYDROLASE ,biology ,Stereochemistry ,Molecular Sequence Data ,Resolution (electron density) ,Crystal structure ,Crystallography, X-Ray ,Multienzyme complexes ,biology.organism_classification ,Biochemistry ,Multienzyme Complexes ,Nucleotide Deaminases ,Structural Biology ,Thermotoga maritima ,Phosphofructokinase 2 ,Amino Acid Sequence ,Crystallization ,Purine metabolism ,Molecular Biology - Published
- 2008
24. Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA
- Author
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Chloe Zubieta, Abhinav Kumar, Keith O. Hodgson, Aprilfawn White, Mark W. Knuth, Polat Abdubek, Rosanne Joseph, Marc C. Deller, David Marciano, Heath E. Klock, Sanjay Krishna, Lian Duan, Hsiu-Ju Chiu, Slawomir K. Grzechnik, Scott A. Lesley, Henry van den Bedem, Paul Schimmel, Linda Okach, Gye Won Han, Silvya Oommachen, John Wooley, Christopher L. Rife, Mitchell D. Miller, Claire Acosta, Marc-André Elsliger, Edward Nigoghossian, Daniel McMullan, Mili Kapoor, Dana Weekes, Herbert L. Axelrod, Ylva Elias, Dennis Carlton, Lukasz Jaroszewski, Thomas Clayton, Tamara Astakhova, Julie Feuerhelm, Christina V. Trout, Kevin K. Jin, Joanna Hale, Qingping Xu, Ashley M. Deacon, Ian A. Wilson, Andrew T. Morse, Kevin D. Murphy, Adam Godzik, Piotr Kozbial, and Ron Reyes
- Subjects
Shewanella ,Heme binding ,Stereochemistry ,Molecular Sequence Data ,Heme ,Crystallography, X-Ray ,Biochemistry ,Structural genomics ,chemistry.chemical_compound ,Bacterial Proteins ,Multienzyme Complexes ,Structural Biology ,Amino Acid Sequence ,Binding site ,Coloring Agents ,Molecular Biology ,Peptide sequence ,Dye decolorizing peroxidase ,Binding Sites ,biology ,Active site ,Peroxidases ,chemistry ,biology.protein ,Protein Binding ,Peroxidase - Abstract
TyrA is a member of the dye-decolorizing peroxidase (DyP) family, a new family of heme-dependent peroxidase recently identified in fungi and bacteria. Here, we report the crystal structure of TyrA in complex with iron protoporphyrin (IX) at 2.3 A. TyrA is a dimer, with each monomer exhibiting a two-domain, alpha/beta ferredoxin-like fold. Both domains contribute to the heme-binding site. Co-crystallization in the presence of an excess of iron protoporphyrin (IX) chloride allowed for the unambiguous location of the active site and the specific residues involved in heme binding. The structure reveals a Fe-His-Asp triad essential for heme positioning, as well as a novel conformation of one of the heme propionate moieties compared to plant peroxidases. Structural comparison to the canonical DyP family member, DyP from Thanatephorus cucumeris (Dec 1), demonstrates conservation of this novel heme conformation, as well as residues important for heme binding. Structural comparisons with representative members from all classes of the plant, bacterial, and fungal peroxidase superfamily demonstrate that TyrA, and by extension the DyP family, adopts a fold different from all other structurally characterized heme peroxidases. We propose that a new superfamily be added to the peroxidase classification scheme to encompass the DyP family of heme peroxidases.
- Published
- 2007
25. Crystal structure of MtnX phosphatase fromBacillus subtilisat 2.0 Å resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate
- Author
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Slawomir K. Grzechnik, Qingping Xu, Herbert L. Axelrod, Heath E. Klock, Aprilfawn White, Henry van den Bedem, John Wooley, Robert Schwarzenbacher, Guenter Wolf, Ian A. Wilson, Eric Koesema, Keith O. Hodgson, Justin Haugen, Polat Abdubek, Hsiu-Ju Chiu, Linda Okach, Sanjay Agarwalla, Christopher L. Rife, Ron Reyes, Andrew T. Morse, Eileen Ambing, Dennis Carlton, Sanjay Krishna, Mark W. Knuth, Mitchell D. Miller, Gye Won Han, Silvya Oommachen, Michael DiDonato, Marc-André Elsliger, Edward Nigoghossian, Eric Hampton, Lukasz Jaroszewski, Kumar Singh Saikatendu, Julie Feuerhelm, Jessica Paulsen, Thomas Clayton, Joanna Hale, Ashley M. Deacon, Adam Godzik, Daniel McMullan, Tamara Astakhova, Kevin K. Jin, Scott A. Lesley, and Lian Duan
- Subjects
biology ,Resolution (mass spectrometry) ,Chemistry ,Stereochemistry ,Hydrolysis ,Molecular Sequence Data ,Phosphatase ,Crystal structure ,Bacillus subtilis ,Crystallography, X-Ray ,biology.organism_classification ,Phosphate ,Biochemistry ,Organophosphates ,Phosphoric Monoester Hydrolases ,chemistry.chemical_compound ,Crystallography ,Bacterial Proteins ,Thioglycosides ,Structural Biology ,Hydrolase ,Amino Acid Sequence ,Molecular Biology - Published
- 2007
26. Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 Å resolution
- Author
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Lukasz Jaroszewski, Abhinav Kumar, John Wooley, Herbert L. Axelrod, Sanjay Agarwalla, Dennis Carlton, Adam Godzik, Marc-André Elsliger, Hsiu-Ju Chiu, Edward Nigoghossian, Dana Weekes, Daniel McMullan, Keith O. Hodgson, Justin Haugen, Ashley M. Deacon, Mitchell D. Miller, Henry van den Bedem, Mark W. Knuth, Polat Abdubek, Thomas Clayton, Christopher L. Rife, Heath E. Klock, Sanjay Krishna, Qingping Xu, Marc C. Deller, Joanna Hale, Slawomir K. Grzechnik, Scott A. Lesley, Ian A. Wilson, Tamara Astakhova, Lian Duan, Eileen Ambing, Ron Reyes, Kevin K. Jin, Aprilfawn White, Eric Koesema, Andrew T. Morse, Gye Won Han, Silvya Oommachen, Michael DiDonato, David Marciano, Eric Hampton, and Chloe Zubieta
- Subjects
Models, Molecular ,biology ,Protein Conformation ,Chemistry ,Stereochemistry ,Extramural ,Molecular Sequence Data ,Resolution (electron density) ,Bacillus cereus ,Homoserine O-Succinyltransferase ,Crystal structure ,Crystallography, X-Ray ,biology.organism_classification ,Haemophilus influenzae ,Biochemistry ,Microbiology ,Bacterial Proteins ,Structural Biology ,Homoserine Transsuccinylase ,Amino Acid Sequence ,Dimerization ,Molecular Biology - Published
- 2007
27. Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 Å resolution
- Author
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Peter Kuhn, Raymond C. Stevens, Keith O. Hodgson, Sanjay Agarwalla, Jaume M. Canaves, Marc-André Elsliger, Edward Nigoghossian, Henry van den Bedem, Jie Ouyang, Michael DiDonato, Heath E. Klock, Mitchell D. Miller, Mark W. Knuth, Kevin Quijano, Robert Schwarzenbacher, Guenter Wolf, Eric Koesema, Kin Moy, Aprilfawn White, Gye Won Han, Polat Abdubek, Kevin K. Jin, Eric Hampton, Scott M. Brittain, Slawomir K. Grzechnik, Sanjay Krishna, Xianhong Wang, Bill West, Scott A. Lesley, Hsiu-Ju Chiu, Herbert L. Axelrod, Justin Haugen, Jeff Velasquez, Andrew T. Morse, Daniel McMullan, Adam Godzik, Christopher L. Rife, Lukasz Jaroszewski, Joanna Hale, Tamara Astakhova, Ron Reyes, Sylvia Oommachen, John Wooley, Qingping Xu, Andreas Kreusch, Glen Spraggon, Jessica Paulsen, Ashley M. Deacon, Krzysztof Ginalski, Ian A. Wilson, and Eileen Ambing
- Subjects
Materials science ,biology ,Lipoproteins ,Molecular Sequence Data ,Resolution (electron density) ,Crystal structure ,Crystallography, X-Ray ,biology.organism_classification ,Biochemistry ,Crystallography ,Bacterial Proteins ,Structural Biology ,Thermotoga maritima ,Amino Acid Sequence ,Crystallization ,Sequence Alignment ,Molecular Biology - Published
- 2006
28. Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 Å resolution
- Author
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Glen Spraggon, John Wooley, Jeff Velasquez, Kevin Quijano, Daniel McMullan, Inna Levin, Marc-André Elsliger, Slawomir K. Grzechnik, Edward Nigoghossian, Robert Schwarzenbacher, Ian A. Wilson, Guenter Wolf, Gye Won Han, Adam Godzik, Eileen Ambing, Keith O. Hodgson, Jaume M. Canaves, Ron Reyes, Carina Grittini, Mitchell D. Miller, Peter Kuhn, Henry van den Bedem, Ashley M. Deacon, Eric Hampton, Polat Abdubek, Lukasz Jaroszewski, Aprilfawn White, Justin Haugen, Jessica Paulsen, Eric Koesema, Qingping Xu, Hsiu-Ju Chiu, Andreas Kreusch, Joanna Hale, S. Sri Krishna, Scott A. Lesley, Irimpan I. Mathews, Raymond C. Stevens, Heath E. Klock, Kin Moy, and Michael DiDonato
- Subjects
Models, Molecular ,chemistry.chemical_classification ,DNA ligase ,Binding Sites ,Molecular Sequence Data ,Resolution (electron density) ,Crystal structure ,Biology ,Crystallography, X-Ray ,biology.organism_classification ,Biochemistry ,Phosphoribosylformylglycinamidine synthase ,Protein Structure, Tertiary ,Crystallography ,chemistry ,Structural Homology, Protein ,Structural Biology ,Thermotoga maritima ,biology.protein ,Amino Acid Sequence ,Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor ,Protein Structure, Quaternary ,Molecular Biology ,Image resolution - Published
- 2006
29. Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 Å resolution
- Author
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Glen Spraggon, Ian A. Wilson, Eileen Ambing, Ashley M. Deacon, Guenter Wolf, Jessica Paulsen, Peter Kuhn, Michael Hornsby, Edward Nigoghossian, Henry van den Bedem, Linda Okach, John Wooley, Joanna Hale, Raymond C. Stevens, Daniel McMullan, Tanya Biorac, Adam Godzik, Mark W. Knuth, Kevin Quijano, Scott A. Lesley, Kin Moy, Julie Feuerhelm, Heath E. Klock, Ron Reyes, Polat Abdubek, Eric Hampton, Eric Koesema, Hsiu-Ju Chiu, Slawomir K. Grzechnik, Keith O. Hodgson, Aprilfawn White, Jeff Velasquez, Christopher L. Rife, S. Sri Krishna, M.A. Elsliger, Carina Grittini, Mitchell D. Miller, Herbert L. Axelrod, Justin Haugen, Michael DiDonato, Andreas Kreusch, Robert Schwarzenbacher, Sanjay Agarwalla, Qingping Xu, and Lukasz Jaroszewski
- Subjects
Models, Molecular ,HMG-box ,Molecular Sequence Data ,DNA, Single-Stranded ,Crystal structure ,Crystallography, X-Ray ,Biochemistry ,DNA-binding protein ,Protein Structure, Secondary ,chemistry.chemical_compound ,Plasmid ,Protein structure ,X-Ray Diffraction ,Structural Biology ,Escherichia coli ,Thermotoga maritima ,Amino Acid Sequence ,Molecular Biology ,Peptide sequence ,biology ,biology.organism_classification ,Mitochondria ,DNA-Binding Proteins ,Crystallography ,chemistry ,Anisotropy ,DNA ,Plasmids ,Transcription Factors - Published
- 2006
30. Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 Å resolution
- Author
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Slawomir K. Grzechnik, Gye Won Han, Michael DiDonato, Heath E. Klock, Sanjay Agarwalla, John Wooley, Robert Schwarzenbacher, Daniel McMullan, Hsiu-Ju Chiu, Guenter Wolf, Ron Reyes, Marc-André Elsliger, Lukasz Jaroszewski, Polat Abdubek, Edward Nigoghossian, Raymond C. Stevens, Eric Hampton, Ashley M. Deacon, Tanya Biorac, Adam Godzik, Jaume M. Canaves, Qingping Xu, Ian A. Wilson, Jeff Velasquez, Mitchell D. Miller, Justin Haugen, Aprilfawn White, Eric Koesema, Kin Moy, Jessica Paulsen, Peter Kuhn, Eileen Ambing, Glen Spraggon, Juli Vincent, Kevin Quijano, Joanna Hale, Carina Grittini, Christopher L. Rife, Andreas Kreusch, Scott A. Lesley, Michael Hornsby, Henry van den Bedem, Herbert L. Axelrod, and Keith O. Hodgson
- Subjects
biology ,Chemistry ,Molecular Sequence Data ,Zinc Fingers ,Crystal structure ,biology.organism_classification ,Biochemistry ,Crystallography ,Bacterial Proteins ,Structural Biology ,Thermotoga maritima ,Chaperone (protein) ,Hsp33 ,biology.protein ,Amino Acid Sequence ,Crystallization ,Molecular Biology ,Heat-Shock Proteins ,Molecular Chaperones - Published
- 2005
31. Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 Å resolution reveals a new fold
- Author
-
Keith O. Hodgson, Marc-André Elsliger, Edward Nigoghossian, Aprilfawn White, Lukasz Jaroszewski, Michael Hornsby, Henry van den Bedem, Guenter Wolf, Slawomir K. Grzechnik, Gye Won Han, Qingping Xu, Tanya Biorac, Adam Godzik, Kevin Quijano, Raymond C. Stevens, Joanna Hale, Hsiu-Ju Chiu, Herbert L. Axelrod, Heath E. Klock, Jessica Paulsen, Mitchell D. Miller, Scott A. Lesley, Carina Grittini, John Wooley, Christopher L. Rife, Robert Schwarzenbacher, Daniel McMullan, Michael DiDonato, Justin Haugen, Ron Reyes, Polat Abdubek, Jeff Velasquez, Eric Koesema, Juli Vincent, Eric Hampton, Peter Kuhn, Andreas Kreusch, Ian A. Wilson, Eileen Ambing, Kin Moy, Jaume M. Canaves, Ashley M. Deacon, Glen Spraggon, and Eric Sims
- Subjects
Models, Molecular ,Regulation of gene expression ,Protein Folding ,biology ,Pseudomonas putida ,Chemistry ,Molecular Sequence Data ,RNA-Binding Proteins ,RNA-binding protein ,Crystal structure ,Crystallography, X-Ray ,biology.organism_classification ,Biochemistry ,Microbiology ,Bacterial Proteins ,Structural Biology ,Amino Acid Sequence ,Dimerization ,Molecular Biology - Published
- 2005
32. Crystal structure of S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 Å resolution reveals a new fold
- Author
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Polat Abdubek, Slawomir K. Grzechnik, Scott A. Lesley, Raymond C. Stevens, Kevin Quijano, Michael Hornsby, Henry van den Bedem, Guenter Wolf, Marc-André Elsliger, Heath E. Klock, Edward Nigoghossian, Lukasz Jaroszewski, Keith O. Hodgson, Jie Ouyang, John Wooley, Justin Haugen, Jaume M. Canaves, Jessica Paulsen, Aprilfawn White, Daniel McMullan, Inna Levin, Eric Koesema, Peter Kuhn, Ashley M. Deacon, Mitchell D. Miller, Gye Won Han, Qingping Xu, Ian A. Wilson, Herbert L. Axelrod, Hsiu-Ju Chiu, Eileen Ambing, Glen Spraggon, Tanya Biorac, Adam Godzik, Ron Reyes, Joanna Hale, Juli Vincent, Carina Grittini, Irimpan I. Mathews, Kin Moy, Andreas Kreusch, Michael DiDonato, Robert Schwarzenbacher, Eric Hampton, and Jeff Velasquez
- Subjects
Models, Molecular ,Protein Folding ,biology ,Protein Conformation ,Chemistry ,Stereochemistry ,Crystal structure ,Isomerase ,Crystallography, X-Ray ,Ligands ,biology.organism_classification ,Biochemistry ,Protein structure ,Structural Biology ,Thermotoga maritima ,Transfer RNA ,Solvents ,Protein folding ,Isomerases ,Molecular Biology - Published
- 2005
33. Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 Å resolution
- Author
-
Keith O. Hodgson, Raymond C. Stevens, Guenter Wolf, Kevin Quijano, Alyssa Robb, Andrew T. Morse, Juli Vincent, Heath E. Klock, Adam Godzik, Eric Koesema, Marc-André Elsliger, Andreas Kreusch, Rebecca Page, Frank von Delft, Timothy M. McPhillips, Inna Levin, Lukasz Jaroszewski, Jaume M. Canaves, Carina Grittini, Eric Sims, Xianhong Wang, Qingping Xu, Scott A. Lesley, Ashley M. Deacon, Linda S. Brinen, Jeff Velasquez, Ron Reyes, Slawomir K. Grzechnik, Ian A. Wilson, Kin Moy, Mike DiDonato, Jie Ouyang, Said Eshagi, Fred Rezezadeh, Henry van den Bedem, Glen Spraggon, John S. Kovarik, John Wooley, Xiaoping Dai, Daniel McMullan, Peter Kuhn, Bill West, Eric Hampton, Ross Floyd, Cathy Karlak, Mitchell D. Miller, and Robert Schwarzenbacher
- Subjects
Models, Molecular ,Molecular Sequence Data ,chemistry.chemical_element ,Crystal structure ,Manganese ,Biochemistry ,Protein Structure, Secondary ,Bacterial protein ,Protein structure ,Bacterial Proteins ,Structural Biology ,Thermotoga maritima ,Amino Acid Sequence ,Molecular Biology ,Binding Sites ,biology ,Chemistry ,Resolution (electron density) ,biology.organism_classification ,Protein Structure, Tertiary ,Structural homology ,Crystallography ,Structural Homology, Protein ,Multiprotein Complexes ,Crystallization ,Oxidoreductases - Published
- 2004
34. Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 Å resolution
- Author
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Qingping Xu, Gye Won Han, Silvya Oommachen, Mark W. Knuth, John Wooley, Lian Duan, Ron Reyes, Daniel McMullan, Henry van den Bedem, Marc-André Elsliger, Andrew T. Morse, Scott A. Lesley, Christopher L. Rife, Joanna C Grant, Keith O. Hodgson, Ashley M. Deacon, Tamara Astakhova, Thomas Clayton, Edward Nigoghossian, Lukasz Jaroszewski, Kevin K. Jin, Polat Abdubek, Sanjay Krishna, Andrew P. Yeh, Dennis Carlton, Herbert L. Axelrod, Linda Okach, Julie Feuerhelm, Adam Godzik, Mitchell D. Miller, Hsiu-Ju Chiu, Heath E. Klock, Jessica Paulsen, and Ian A. Wilson
- Subjects
Models, Molecular ,ATPase ,Crystallography, X-Ray ,Biochemistry ,Structural Biology ,Models ,2.2 Factors relating to the physical environment ,Aetiology ,Peptide sequence ,0303 health sciences ,Crystallography ,biology ,TM0874 ,030302 biochemistry & molecular biology ,Resolution (electron density) ,Biological Sciences ,Condensed Matter Physics ,YgjD ,YeaZ ,Infection ,Protein Structure ,1.1 Normal biological development and functioning ,Molecular Sequence Data ,Biophysics ,Sequence alignment ,Bacterial protein ,Quaternary ,03 medical and health sciences ,Bacterial Proteins ,Underpinning research ,Hydrolase ,Genetics ,essential genes ,Thermotoga maritima ,Amino Acid Sequence ,Protein Structure, Quaternary ,030304 developmental biology ,protein complexes ,Molecular ,biology.organism_classification ,Protein Structure, Tertiary ,Chemical Sciences ,biology.protein ,X-Ray ,bacteria ,Generic health relevance ,Novel Variants of Known Folds and Function ,Sequence Alignment ,Bacteria ,Tertiary - Abstract
The crystal structure of an essential bacterial protein, YeaZ, from T. maritima identifies an interface that potentially mediates protein–protein interaction., YeaZ is involved in a protein network that is essential for bacteria. The crystal structure of YeaZ from Thermotoga maritima was determined to 2.5 Å resolution. Although this protein belongs to a family of ancient actin-like ATPases, it appears that it has lost the ability to bind ATP since it lacks some key structural features that are important for interaction with ATP. A conserved surface was identified, supporting its role in the formation of protein complexes.
- Published
- 2010
35. Conformational changes associated with the binding of zinc acetate at the putative active site of XcTcmJ, a cupin from Xanthomonas campestris pv. campestris
- Author
-
Kevin D. Murphy, Ian A. Wilson, Adam Godzik, Jonathan M. Caruthers, Kevin K. Jin, Marc-André Elsliger, Linda Okach, Edward Nigoghossian, Scott A. Lesley, John Wooley, Claire Acosta, Chloe Zubieta, Lukasz Jaroszewski, Aprilfawn White, Ron Reyes, Slawomir K. Grzechnik, Marc C. Deller, Mark W. Knuth, Ashley M. Deacon, David Marciano, Lian Duan, Qingping Xu, Christopher L. Rife, Hsiu-Ju Chiu, Piotr Kozbial, Abhinav Kumar, Henry J Tien, Julie Feuerhelm, Joanna C Grant, Jessica Paulsen, Dennis Carlton, Mitchell D. Miller, Dana Weekes, Daniel McMullan, Tamara Astakhova, Thomas Clayton, Christina V. Trout, Polat Abdubek, Ylva Elias, Sanjay Krishna, Andrew T. Morse, Heath E. Klock, Herbert L. Axelrod, Gye Won Han, Keith O. Hodgson, Silvya Oommachen, and Henry van den Bedem
- Subjects
Models, Molecular ,0106 biological sciences ,Ligands That Aid in Function Characterization ,metalloproteins ,Zinc Acetate ,Crystallography, X-Ray ,Xanthomonas campestris ,01 natural sciences ,Biochemistry ,Conserved sequence ,Structural Biology ,Models ,Catalytic Domain ,conformational changes ,Conserved Sequence ,0303 health sciences ,Crystallography ,biology ,Biological Sciences ,Condensed Matter Physics ,Ligand (biochemistry) ,ligand binding ,1.1 Normal biological development and functioning ,Molecular Sequence Data ,Biophysics ,chemistry.chemical_element ,Zinc ,Xanthomonas campestris pv. campestris ,zinc-binding sites ,03 medical and health sciences ,Bacterial Proteins ,Underpinning research ,Genetics ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,Binding site ,Histidine ,030304 developmental biology ,Structural Homology ,Protein ,Active site ,Molecular ,structural genomics ,biology.organism_classification ,chemistry ,Structural Homology, Protein ,Chemical Sciences ,biology.protein ,X-Ray ,Sequence Alignment ,010606 plant biology & botany - Abstract
The crystal structure of an RmlC-type cupin with zinc acetate bound at the putative active site reveals significant differences from a previous structure without any bound ligand. The functional implications of the ligand-induced conformational changes are discussed., In the plant pathogen Xanthomonas campestris pv. campestris, the product of the tcmJ gene, XcTcmJ, encodes a protein belonging to the RmlC family of cupins. XcTcmJ was crystallized in a monoclinic space group (C2) in the presence of zinc acetate and the structure was determined to 1.6 Å resolution. Previously, the apo structure has been reported in the absence of any bound metal ion [Chin et al. (2006 ▶), Proteins, 65, 1046–1050]. The most significant difference between the apo structure and the structure of XcTcmJ described here is a reorganization of the binding site for zinc acetate, which was most likely acquired from the crystallization solution. This site is located in the conserved metal ion-binding domain at the putative active site of XcTcmJ. In addition, an acetate was also bound within coordination distance of the zinc. In order to accommodate this binding, rearrangement of a conserved histidine ligand is required as well as several nearby residues within and around the putative active site. These observations indicate that binding of zinc serves a functional role in this cupin protein.
- Published
- 2010
36. Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases
- Author
-
Dennis Carlton, Andrew Yeh, Henry van den Bedem, Amanda Nopakun, Lukasz Jaroszewski, Dana Weekes, Polat Abdubek, Mark W. Knuth, Gye Won Han, Keith O. Hodgson, Qingping Xu, Sanjay Krishna, Michelle Chiu, Winnie W Lam, Joanna C Grant, Edward Nigoghossian, Tiffany Wooten, Marc André Elsliger, Connie Chen, Scott A. Lesley, John Wooley, Ron Reyes, Linda Okach, Julie Feuerhelm, Tamara Astakhova, Herbert L. Axelrod, Ashley M. Deacon, Abhinav Kumar, Kyle Ellrott, Lian Duan, Hsiu-Ju Chiu, Adam Godzik, Ian A. Wilson, Heath E. Klock, Christina Puckett, Carol L. Farr, Xiaohui Cai, Piotr Kozbial, Henry J Tien, Marc C. Deller, Christine B Trame, Constantina Bakolitsa, David Marciano, Kevin K. Jin, Debanu Das, Thomas Clayton, Mitchell D. Miller, Anna Grzechnik, and Andrew T. Morse
- Subjects
Models, Molecular ,Ligands That Aid in Function Characterization ,Bacillus subtilis ,Crystallography, X-Ray ,cysteine peptidases ,Biochemistry ,Conserved sequence ,Substrate Specificity ,chemistry.chemical_compound ,Protein structure ,Structural Biology ,Models ,Cysteine Proteases ,SH3b ,Alanine ,0303 health sciences ,Crystallography ,Genome ,biology ,030302 biochemistry & molecular biology ,Bacterial ,Biological Sciences ,Condensed Matter Physics ,Endopeptidase ,3. Good health ,Infectious Diseases ,Protein Binding ,Protein Structure ,Stereochemistry ,Molecular Sequence Data ,Biophysics ,Diamino acid ,03 medical and health sciences ,Bacillus cereus ,Endopeptidases ,Genetics ,Amino Acid Sequence ,enzyme specificity ,030304 developmental biology ,Structural Homology ,γ-d-glutamyl-l-diamino acid endopeptidase ,Protein ,fungi ,NlpC/P60 ,Active site ,Molecular ,biology.organism_classification ,Protein Structure, Tertiary ,chemistry ,Structural Homology, Protein ,cell-wall recycling ,Chemical Sciences ,biology.protein ,X-Ray ,bacteria ,Sequence Alignment ,Genome, Bacterial ,Tertiary ,Cysteine - Abstract
The crystal structure of the highly specific γ-d-glutamyl-l-diamino acid endopeptidase YkfC from Bacillus cereus in complex with l-Ala-γ-d-Glu reveals the structural basis for the substrate specificity of NlpC/P60-family cysteine peptidases., Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-d-glutamyl-l-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 Å resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (l-Ala-γ-d-Glu) enabled the identification of conserved sequence and structural signatures for recognition of l-Ala and γ-d-Glu and, therefore, provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both residues interact with the free amine group of the alanine. This structural feature allows the definition of a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial l-alanine-γ-d-glutamate endopeptidase that contains the two key components (an NlpC/P60 domain attached to an SH3b domain) for assembly of a YkfC-like active site.
- Published
- 2010
37. Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding
- Author
-
Gye Won Han, Henry van den Bedem, Kevin K. Jin, Polat Abdubek, Herbert L. Axelrod, Sanjay Krishna, Piotr Kozbial, Marc-André Elsliger, Henry J Tien, Edward Nigoghossian, Julie Feuerhelm, Natasha Sefcovic, Joanna C Grant, Keith O. Hodgson, Daniel McMullan, Ashley M. Deacon, Marc C. Deller, Andrew T. Morse, Christine B Trame, Ian A. Wilson, Abhinav Kumar, Ron Reyes, David Marciano, Adam Godzik, John Wooley, Tamara Astakhova, Debanu Das, Hsiu-Ju Chiu, Andrei L. Lomize, Scott A. Lesley, Dennis Carlton, Christopher L. Rife, Linda Okach, Heath E. Klock, Dana Weekes, Mark W. Knuth, Lian Duan, Mitchell D. Miller, Anna Grzechnik, Thomas Clayton, Lukasz Jaroszewski, and Qingping Xu
- Subjects
Models, Molecular ,Shewanella ,YP_749275.1 ,Sequence Homology ,Plasma protein binding ,Crystallography, X-Ray ,Ligands ,Biochemistry ,Cell membrane ,YP_001095227.1 ,Structural Biology ,Models ,Lipid bilayer ,Peptide sequence ,0303 health sciences ,Crystallography ,030302 biochemistry & molecular biology ,Biological Sciences ,Condensed Matter Physics ,Amino Acid ,medicine.anatomical_structure ,Protein Binding ,Protein Structure ,1.1 Normal biological development and functioning ,Molecular Sequence Data ,Biophysics ,Bioengineering ,Sequence alignment ,Biology ,Shewanella frigidimarina ,Structural genomics ,Quaternary ,03 medical and health sciences ,Bacterial Proteins ,Underpinning research ,Amphiphile ,Genetics ,medicine ,Amino Acid Sequence ,Protein Structure, Quaternary ,030304 developmental biology ,Structural Homology ,Sequence Homology, Amino Acid ,Protein ,Cell Membrane ,Molecular ,SpoIIAA-like proteins ,Protein Structure, Tertiary ,Structural Homology, Protein ,Chemical Sciences ,X-Ray ,Generic health relevance ,Novel Variants of Known Folds and Function ,Sequence Alignment ,Tertiary - Abstract
The crystal structures of two orthologous proteins from different Shewanella species have uncovered a resemblance to CRAL-TRIO carrier proteins, which suggest that they function as transporters of small nonpolar molecules. One protein adopts an open conformation, while the other adopts a closed structure that may act as a conformational switch in the transport of ligands at the membrane surface., The crystal structures of the proteins encoded by the YP_749275.1 and YP_001095227.1 genes from Shewanella frigidimarina and S. loihica, respectively, have been determined at 1.8 and 2.25 Å resolution, respectively. These proteins are members of a novel family of bacterial proteins that adopt the α/β SpoIIAA-like fold found in STAS and CRAL-TRIO domains. Despite sharing 54% sequence identity, these two proteins adopt distinct conformations arising from different dispositions of their α2 and α3 helices. In the ‘open’ conformation (YP_001095227.1), these helices are 15 Å apart, leading to the creation of a deep nonpolar cavity. In the ‘closed’ structure (YP_749275.1), the helices partially unfold and rearrange, occluding the cavity and decreasing the solvent-exposed hydrophobic surface. These two complementary structures are reminiscent of the conformational switch in CRAL-TRIO carriers of hydrophobic compounds. It is suggested that both proteins may associate with the lipid bilayer in their ‘open’ monomeric state by inserting their amphiphilic helices, α2 and α3, into the lipid bilayer. These bacterial proteins may function as carriers of nonpolar substances or as interfacially activated enzymes.
- Published
- 2010
38. The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 Å resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator
- Author
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Marc C. Deller, Henry Tien, Slawomir K. Grzechnik, Qingping Xu, Scott A. Lesley, Aprilfawn White, Constantina Bakolitsa, Kevin D. Murphy, Ylva Elias, Alex Bateman, Dana Weekes, Adam Godzik, John Wooley, Claire Acosta, Kevin K. Jin, Hsiu-Ju Chiu, Thomas Clayton, Polat Abdubek, Mark W. Knuth, Abhinav Kumar, Debanu Das, Julie Feuerhelm, Lian Duan, Christina V. Trout, Mitchell D. Miller, Sanjay Krishna, Anna Grzechnik, Ron Reyes, Joanna C Grant, Ian A. Wilson, Heath E. Klock, Marc-André Elsliger, Prasad Burra, Christopher L. Rife, Edward Nigoghossian, Andrew T. Morse, Daniel McMullan, Herbert L. Axelrod, Gye Won Han, Silvya Oommachen, Christine B Trame, Natasha Sefcovic, Piotr Kozbial, Keith O. Hodgson, Tamara Astakhova, David Marciano, Ashley M. Deacon, Dennis Carlton, Lukasz Jaroszewski, Jessica Paulsen, Linda Okach, and Henry van den Bedem
- Subjects
Models, Molecular ,Crystallography, X-Ray ,Biochemistry ,chemistry.chemical_compound ,Protein structure ,Structural Biology ,Models ,2.1 Biological and endogenous factors ,Rhodobacteraceae ,Aetiology ,Peptide sequence ,domains of unknown function ,Genetics ,Zinc finger ,0303 health sciences ,Crystallography ,Zinc Fingers ,Jannaschia ,Biological Sciences ,Condensed Matter Physics ,environmental stress ,New Folds ,Pfam ,Protein Structure ,1.1 Normal biological development and functioning ,bound metal identification ,030303 biophysics ,Molecular Sequence Data ,Biophysics ,Sequence alignment ,Biology ,Structural genomics ,Quaternary ,03 medical and health sciences ,Bacterial Proteins ,Underpinning research ,Amino Acid Sequence ,Protein Structure, Quaternary ,030304 developmental biology ,Molecular ,structural genomics ,biology.organism_classification ,Protein Structure, Tertiary ,chemistry ,Chemical Sciences ,X-Ray ,Generic health relevance ,Transcription regulator ,Sequence Alignment ,DNA ,Tertiary - Abstract
The crystal structure of the first representative of the Pfam PF07336 (DUF1470) family reveals a two-domain organization that contains a new fold, termed the ABATE domain, at the N-terminus and a treble-clef zinc finger that is likely to bind DNA at the C-terminus., The crystal structure of Jann_2411 from Jannaschia sp. strain CCS1, a member of the Pfam PF07336 family classified as a domain of unknown function (DUF1470), was solved to a resolution of 1.45 Å by multiple-wavelength anomalous dispersion (MAD). This protein is the first structural representative of the DUF1470 Pfam family. Structural analysis revealed a two-domain organization, with the N-terminal domain presenting a new fold called the ABATE domain that may bind an as yet unknown ligand. The C-terminal domain forms a treble-clef zinc finger that is likely to be involved in DNA binding. Analysis of the Jann_2411 protein and the broader ABATE-domain family suggests a role as stress-induced transcriptional regulators.
- Published
- 2010
39. Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster
- Author
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Qingping Xu, Lian Duan, Hsiu-Ju Chiu, Yeeting E. Chong, Christopher L. Rife, Jonathan M. Caruthers, Marc-André Elsliger, Edward Nigoghossian, Ian A. Wilson, Guenter Wolf, Eileen Ambing, Julie Feuerhelm, Joanna C Grant, Slawomir K. Grzechnik, Lukasz Jaroszewski, Tamara Astakhova, Paul Schimmel, Heath E. Klock, Mark W. Knuth, Thomas Clayton, Herbert L. Axelrod, Scott M. Brittain, Andrew T. Morse, Abhinav Kumar, Polat Abdubek, Keith O. Hodgson, Aprilfawn White, Sanjay Krishna, Linda Okach, Xiang-Lei Yang, Mitchell D. Miller, Dana Weekes, David Marciano, Daniel McMullan, John Wooley, Jessica Paulsen, Gye Won Han, Henry van den Bedem, Ashley M. Deacon, Scott A. Lesley, Kevin K. Jin, Dennis Carlton, Ron Reyes, and Adam Godzik
- Subjects
Models, Molecular ,Iron-Sulfur Proteins ,Ligands That Aid in Function Characterization ,Iron–sulfur cluster ,Tryptophan-tRNA Ligase ,Tryptophan—tRNA ligase ,iron–sulfur clusters ,Crystallography, X-Ray ,Ligands ,01 natural sciences ,Biochemistry ,chemistry.chemical_compound ,Structural Biology ,Models ,TM0492 ,Peptide sequence ,Conserved Sequence ,chemistry.chemical_classification ,0303 health sciences ,Crystallography ,biology ,Biological Sciences ,Condensed Matter Physics ,3. Good health ,Transfer RNA ,Protein Structure ,Molecular Sequence Data ,Biophysics ,tryptophanyl-tRNA ligase ,010402 general chemistry ,Quaternary ,03 medical and health sciences ,Genetics ,Animals ,Humans ,Thermotoga maritima ,Amino Acid Sequence ,Protein Structure, Quaternary ,030304 developmental biology ,DNA ligase ,tryptophanyl-tRNA synthetase class I ,Tryptophan ,Active site ,Molecular ,structural genomics ,biology.organism_classification ,Protein Structure, Tertiary ,0104 chemical sciences ,chemistry ,Chemical Sciences ,biology.protein ,X-Ray ,bacteria ,Sequence Alignment ,Tertiary - Abstract
The crystal structure of tryptophanyl-tRNA synthetase from T. maritima unexpectedly revealed an iron–sulfur cluster bound to the tRNA anticodon-binding region., A novel aminoacyl-tRNA synthetase that contains an iron–sulfur cluster in the tRNA anticodon-binding region and efficiently charges tRNA with tryptophan has been found in Thermotoga maritima. The crystal structure of TmTrpRS (tryptophanyl-tRNA synthetase; TrpRS; EC 6.1.1.2) reveals an iron–sulfur [4Fe–4S] cluster bound to the tRNA anticodon-binding (TAB) domain and an l-tryptophan ligand in the active site. None of the other T. maritima aminoacyl-tRNA synthetases (AARSs) contain this [4Fe–4S] cluster-binding motif (C-x 22-C-x 6-C-x 2-C). It is speculated that the iron–sulfur cluster contributes to the stability of TmTrpRS and could play a role in the recognition of the anticodon.
- Published
- 2010
40. The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function
- Author
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Debanu Das, Kevin K. Jin, Mark W. Knuth, Gye Won Han, Henry van den Bedem, Ian A. Wilson, Amanda Nopakun, Qingping Xu, Christina Puckett, Kyle Ellrott, Connie Chen, Adam Godzik, Christopher L. Rife, Thomas Clayton, Mitchell D. Miller, Anna Grzechnik, Herbert L. Axelrod, Marc André Elsliger, Lian Duan, Dana Weekes, Tamara Astakhova, Keith O. Hodgson, Heath E. Klock, Christine B Trame, Abhinav Kumar, Carol L. Farr, Andrew T. Morse, Joanna C Grant, Julie Feuerhelm, Natasha Sefcovic, David Marciano, Marc C. Deller, Michelle Chiu, Polat Abdubek, Constantina Bakolitsa, Lukasz Jaroszewski, Sanjay Krishna, John Wooley, Daniel McMullan, Ron Reyes, Robert D. Finn, Piotr Kozbial, Henry J Tien, Scott A. Lesley, Dennis Carlton, Linda Okach, Hsiu-Ju Chiu, Tiffany Wooten, Edward Nigoghossian, Ashley M. Deacon, and Dustin C. Ernst
- Subjects
Models, Molecular ,Plasma protein binding ,Crystallography, X-Ray ,Biochemistry ,Conserved sequence ,putative inhibitor proteins ,PF11396 ,Protein structure ,Structural Biology ,Models ,β-lactamase inhibitor protein-like fold ,Bacteroides ,Peptide sequence ,Conserved Sequence ,0303 health sciences ,Crystallography ,biology ,Human Gut Microbiome ,030302 biochemistry & molecular biology ,Biological Sciences ,Condensed Matter Physics ,BVU2987 ,3. Good health ,Infectious Diseases ,Periplasmic Proteins ,Protein Binding ,Protein Structure ,Sequence analysis ,1.1 Normal biological development and functioning ,Molecular Sequence Data ,Biophysics ,Sequence alignment ,Vaccine Related ,03 medical and health sciences ,Tandem repeat ,Underpinning research ,Biodefense ,Genetics ,Amino Acid Sequence ,030304 developmental biology ,Structural Homology ,Prevention ,Protein ,Molecular ,biology.organism_classification ,Protein Structure, Tertiary ,Emerging Infectious Diseases ,Structural Homology, Protein ,Chemical Sciences ,X-Ray ,DUF2874 ,Sequence Alignment ,Tertiary - Abstract
The crystal structure of the BVU2987 gene product from B. vulgatus (UniProt A6L4L1) reveals that members of the new Pfam family PF11396 (domain of unknown function; DUF2874) are similar to β-lactamase inhibitor protein and YpmB., Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a β-lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to β-lactamase inhibitor protein, PepSY and SmpA_OmlA proteins and hence are likely to function as inhibitory proteins.
- Published
- 2010
41. Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism
- Author
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Jessica Paulsen, Arne Skerra, Marc-André Elsliger, Marc C. Deller, Edward Nigoghossian, Thomas Clayton, Christopher L. Rife, Andrew T. Morse, Mark W. Knuth, Lian Duan, Polat Abdubek, Constantina Bakolitsa, Gye Won Han, Sanjay Krishna, Hsiu-Ju Chiu, Heath E. Klock, Julie Feuerhelm, Abhinav Kumar, Adam Godzik, John Wooley, Keith O. Hodgson, Andrei L. Lomize, Daniel McMullan, Q. Xu, Linda Okach, Tamara Astakhova, Henry van den Bedem, Piotr Kozbial, Kevin K. Jin, Mitchell D. Miller, Lukasz Jaroszewski, Slawomir K. Grzechnik, Ron Reyes, Dana Weekes, Dennis Carlton, Scott A. Lesley, Herbert L. Axelrod, David Marciano, Joanna C Grant, Ashley M. Deacon, and Ian A. Wilson
- Subjects
Models, Molecular ,Domains of Unknown Function ,Sequence Homology ,Crystallography, X-Ray ,Biochemistry ,Structural Biology ,Models ,Gene duplication ,Databases, Genetic ,2.1 Biological and endogenous factors ,Aetiology ,Peptide sequence ,Genetics ,0303 health sciences ,Crystallography ,030302 biochemistry & molecular biology ,Biological Sciences ,Condensed Matter Physics ,3. Good health ,Amino Acid ,Domain of unknown function ,lipocalin ,fatty-acid binding proteins ,Protein Structure ,Protein family ,1.1 Normal biological development and functioning ,Molecular Sequence Data ,Biophysics ,Nitrosomonas europaea ,Sequence alignment ,Biology ,Fatty acid-binding protein ,Structural genomics ,03 medical and health sciences ,Databases ,Bacterial Proteins ,Genetic ,Underpinning research ,Amino Acid Sequence ,030304 developmental biology ,calycin ,Sequence Homology, Amino Acid ,Molecular ,Lipid metabolism ,structural genomics ,Lipid Metabolism ,Protein Structure, Tertiary ,Oxidative Stress ,Chemical Sciences ,X-Ray ,Generic health relevance ,Sequence Alignment ,Tertiary - Abstract
NE1406, the first structural representative of PF09410, reveals a lipocalin-like fold with features that suggest involvement in lipid metabolism. In addition, NE1406 provides potential structural templates for two other protein families (PF07143 and PF08622)., The first structural representative of the domain of unknown function DUF2006 family, also known as Pfam family PF09410, comprises a lipocalin-like fold with domain duplication. The finding of the calycin signature in the N-terminal domain, combined with remote sequence similarity to two other protein families (PF07143 and PF08622) implicated in isoprenoid metabolism and the oxidative stress response, support an involvement in lipid metabolism. Clusters of conserved residues that interact with ligand mimetics suggest that the binding and regulation sites map to the N-terminal domain and to the interdomain interface, respectively.
- Published
- 2010
42. Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation
- Author
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Keith O. Hodgson, Linda Okach, Hsiu-Ju Chiu, Lian Duan, Joanna C Grant, Lukasz Jaroszewski, Tamara Astakhova, John Wooley, Dana Weekes, Scott A. Lesley, Christopher L. Rife, Marc-André Elsliger, Ashley M. Deacon, Kevin K. Jin, Piotr Kozbial, Edward Nigoghossian, Heath E. Klock, Thomas Clayton, Mark W. Knuth, Daniel McMullan, Abhinav Kumar, Henry van den Bedem, Polat Abdubek, L Aravind, Sanjay Krishna, Ian A. Wilson, Julie Feuerhelm, David Marciano, Marc C. Deller, Herbert L. Axelrod, Mitchell D. Miller, Ron Reyes, Qingping Xu, Constantina Bakolitsa, Dennis Carlton, Adam Godzik, Andrew T. Morse, and Gye Won Han
- Subjects
Models, Molecular ,Protein Folding ,Domains of Unknown Function ,Plasma protein binding ,Crystallography, X-Ray ,01 natural sciences ,Biochemistry ,Protein structure ,Structural Biology ,Models ,Catalytic Domain ,Peptide sequence ,0303 health sciences ,Crystallography ,010304 chemical physics ,biology ,Heavy ,Biological Sciences ,Condensed Matter Physics ,Metals ,Protein folding ,Biotechnology ,Protein Structure Initiative ,Protein Binding ,Protein Structure ,1.1 Normal biological development and functioning ,Molecular Sequence Data ,Biophysics ,Computational biology ,Desulfitobacterium ,Structural genomics ,03 medical and health sciences ,Bacterial Proteins ,Underpinning research ,Metals, Heavy ,0103 physical sciences ,Genetics ,Amino Acid Sequence ,030304 developmental biology ,rare metals ,siderophores ,Human Genome ,Active site ,Desulfitobacterium hafniense ,Molecular ,structural genomics ,biology.organism_classification ,Protein Structure, Tertiary ,Phosphopyruvate Hydratase ,pterins ,Chemical Sciences ,biology.protein ,X-Ray ,Tertiary - Abstract
The crystal structure of the first representative of DUF364 family reveals a combination of enolase N-terminal-like and C-terminal Rossmann-like folds. Analysis of the interdomain cleft combined with sequence and genome context conservation among homologs, suggests a unique catalytic site likely involved in the synthesis of a flavin or pterin derivative., The crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 Å using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation.
- Published
- 2010
43. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism
- Author
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Dennis Carlton, Jessica Paulsen, Kevin D. Murphy, Polat Abdubek, Mark W. Knuth, Sanjay Krishna, Prasad Burra, Joanna C Grant, Slawomir K. Grzechnik, Edward Nigoghossian, Adam Godzik, Abhinav Kumar, Debanu Das, Ylva Elias, Tamara Astakhova, Aprilfawn White, Andrew T. Morse, Ian A. Wilson, Connie Chen, Ron Reyes, Christopher L. Rife, Daniel McMullan, Christina Puckett, Hsiu-Ju Chiu, Thomas Clayton, Lian Duan, Christina V. Trout, Mitchell D. Miller, Kyle Ellrott, Anna Grzechnik, Claire Acosta, Linda Okach, Scott A. Lesley, Ashley M. Deacon, Christine B Trame, Marc André Elsliger, John Wooley, Dana Weekes, Piotr Kozbial, Hope A. Johnson, Henry J Tien, David Marciano, Julie Feuerhelm, Marc C. Deller, Heath E. Klock, Carol L. Farr, Constantina Bakolitsa, Kevin K. Jin, Dustin C. Ernst, Gye Won Han, Keith O. Hodgson, Herbert L. Axelrod, Henry van den Bedem, Amanda Nopakun, Natasha Sefcovic, Lukasz Jaroszewski, and Qingping Xu
- Subjects
Models, Molecular ,Protein Folding ,Domains of Unknown Function ,chorismate mutase ,Bacillus ,Random hexamer ,Crystallography, X-Ray ,Biochemistry ,domain of unknown function ,Structural Biology ,Models ,2.1 Biological and endogenous factors ,Rhodobacteraceae ,Amino Acids ,Aetiology ,Peptide sequence ,chemistry.chemical_classification ,0303 health sciences ,Crystallography ,030302 biochemistry & molecular biology ,Biological Sciences ,Condensed Matter Physics ,Amino acid ,Chorismate mutase ,Protein folding ,Domain of unknown function ,Protein Structure Initiative ,Protein Structure ,Molecular Sequence Data ,Biophysics ,Biology ,Bordetella bronchiseptica ,Structural genomics ,Quaternary ,03 medical and health sciences ,Genetics ,Amino Acid Sequence ,Protein Structure, Quaternary ,030304 developmental biology ,Structural Homology ,amino acids ,Protein ,fungi ,salt-dependent ,Molecular ,structural genomics ,Protein Structure, Tertiary ,chemistry ,Structural Homology, Protein ,Chemical Sciences ,X-Ray ,Generic health relevance ,pH-dependent ,Tertiary ,Chorismate Mutase - Abstract
Structures of the first representatives of PF06684 (DUF1185) reveal a Bacillus chorismate mutase-like fold with a potential role in amino-acid synthesis., The crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 Å by single-wavelength anomalous dispersion and multiple-wavelength anomalous dispersion, respectively, using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). These proteins are the first structural representatives of the PF06684 (DUF1185) Pfam family. Structural analysis revealed that both structures adopt a variant of the Bacillus chorismate mutase fold (BCM). The biological unit of both proteins is a hexamer and analysis of homologs indicates that the oligomer interface residues are highly conserved. The conformation of the critical regions for oligomerization appears to be dependent on pH or salt concentration, suggesting that this protein might be subject to environmental regulation. Structural similarities to BCM and genome-context analysis suggest a function in amino-acid synthesis.
- Published
- 2010
44. Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15
- Author
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Dana Weekes, Debanu Das, Daniel McMullan, Scott A. Lesley, Todd O. Yeates, Herbert L. Axelrod, Connie Chen, Hsiu-Ju Chiu, Qingping Xu, Piotr Kozbial, Christopher L. Rife, Andrew T. Morse, Mark W. Knuth, Keith O. Hodgson, Dennis Carlton, Henry J Tien, Gye Won Han, Tamara Astakhova, Marc-André Elsliger, Winnie W Lam, Edward Nigoghossian, Kevin K. Jin, Dustin C. Ernst, Lian Duan, Adam Godzik, Alexey G. Murzin, Polat Abdubek, Thomas Clayton, Henry van den Bedem, Marc C. Deller, Abhinav Kumar, Sanjay Krishna, Ron Reyes, Joanna C Grant, Christine B Trame, Hope A. Johnson, Julie Feuerhelm, Linda Okach, Natasha Sefcovic, David Marciano, Lukasz Jaroszewski, Heath E. Klock, Ashley M. Deacon, Ian A. Wilson, John Wooley, Mitchell D. Miller, and Anna Grzechnik
- Subjects
Models, Molecular ,viruses ,Dimer ,Crystallography, X-Ray ,Biochemistry ,putative NTP pyrophosphohydrolase ,chemistry.chemical_compound ,Structural Biology ,Models ,Pyrophosphatases ,Peptide sequence ,chemistry.chemical_classification ,Helix bundle ,0303 health sciences ,Crystallography ,biology ,030302 biochemistry & molecular biology ,MazG nucleotide pyrophosphohydrolase ,Biological Sciences ,Condensed Matter Physics ,3. Good health ,Protein Structure ,1.1 Normal biological development and functioning ,Molecular Sequence Data ,Biophysics ,Divalent ,Structural genomics ,Quaternary ,03 medical and health sciences ,dUTPases ,Underpinning research ,Hydrolase ,Genetics ,Amino Acid Sequence ,Protein Structure, Quaternary ,030304 developmental biology ,Structural Homology ,Bacillales ,Protein ,Prevention ,Active site ,Molecular ,structural genomics ,Protein Structure, Tertiary ,chemistry ,Structural Homology, Protein ,Chemical Sciences ,biology.protein ,X-Ray ,Protein Multimerization ,Novel Variants of Known Folds and Function ,Tertiary - Abstract
The crystal structure of a putative NTP pyrophosphohydrolase, YP_001813558.1 from E. sibiricum, reveals a novel segment-swapped linked-dimer assembly., The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a ‘linked dimer’ that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity.
- Published
- 2010
45. Structural Basis of Murein Peptide Specificity of a γ-D-glutamyl-L-diamino Acid Endopeptidase
- Author
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Keith O. Hodgson, Jessica Paulsen, Sanjay Krishna, Chloe Zubieta, Marc C. Deller, Polat Abdubek, Ian A. Wilson, Jonathan M. Caruthers, Scott A. Lesley, Lian Duan, Tamara Astakhova, M.A. Elsliger, John Wooley, Claire Acosta, Aprilfawn White, Gye Won Han, Silvya Oommachen, Badry Bursalay, Eileen Ambing, Piotr Kozbial, Christopher L. Rife, Guenter Wolf, Slawomir K. Grzechnik, Kevin K. Jin, Justin Haugen, David H. Jones, Mark W. Knuth, Thomas Clayton, Julie Feuerhelm, Hsiu-Ju Chiu, Heath E. Klock, Adam Godzik, Bernhard H. Geierstanger, David Marciano, Abhinav Kumar, Edward Nigoghossian, Daniel McMullan, Ashley M. Deacon, Dana Weekes, Glen Spraggon, Andrew T. Morse, Ron Reyes, Lukasz Jaroszewski, Linda Okach, Herbert L. Axelrod, Henry van den Bedem, Qingping Xu, Dennis Carlton, Ylva Elias, Christina V. Trout, Joanna Hale, Sebastian Sudek, and Mitchell D. Miller
- Subjects
Models, Molecular ,PROTEINS ,Molecular Sequence Data ,Diamino acid ,Peptidoglycan ,Models, Biological ,Article ,Substrate Specificity ,src Homology Domains ,03 medical and health sciences ,chemistry.chemical_compound ,Structural Biology ,Catalytic Domain ,Catalytic triad ,Hydrolase ,Endopeptidases ,Anabaena variabilis ,Amino Acid Sequence ,Nostoc ,Peptide sequence ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,biology ,Sequence Homology, Amino Acid ,030306 microbiology ,Nostoc punctiforme ,Active site ,biology.organism_classification ,Endopeptidase ,Peptide Fragments ,Protein Structure, Tertiary ,Cysteine Endopeptidases ,Biochemistry ,chemistry ,biology.protein ,Cysteine - Abstract
Crystal structures of two homologous peptidases from cyanobacteria Anabaena variabilis and Nostoc punctiforme at 1.05 A and 1.60 A resolution represent the first structures of a large class of cell-wall, cysteine peptidases that contain an N-terminal bacterial SH3-like domain (SH3b) and a C-terminal NlpC/P60 cysteine peptidase domain. The NlpC/P60 domain is a primitive, papain-like peptidase in the CA clan of cysteine peptidases with a Cys126/His176/His188 catalytic triad and a conserved catalytic core. We deduced from structure and sequence analysis, and then experimentally, that that these two proteins act as γ-D-glutamyl-L-diamino acid endopeptidases (EC 3.4.22.-). The active site is located near the interface between the SH3b and NlpC/P60 domains, where the SH3b domain may help define substrate specificity, instead of functioning as a targeting domain, so that only muropeptides with an N-terminal L-alanine can bind to the active site.
- Published
- 2009
46. Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution
- Author
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Debanu, Das, Piotr, Kozbial, Herbert L, Axelrod, Mitchell D, Miller, Daniel, McMullan, S Sri, Krishna, Polat, Abdubek, Claire, Acosta, Tamara, Astakhova, Prasad, Burra, Dennis, Carlton, Connie, Chen, Hsiu-Ju, Chiu, Thomas, Clayton, Marc C, Deller, Lian, Duan, Ylva, Elias, Marc-André, Elsliger, Dustin, Ernst, Carol, Farr, Julie, Feuerhelm, Anna, Grzechnik, Slawomir K, Grzechnik, Joanna, Hale, Gye Won, Han, Lukasz, Jaroszewski, Kevin K, Jin, Hope A, Johnson, Heath E, Klock, Mark W, Knuth, Abhinav, Kumar, David, Marciano, Andrew T, Morse, Kevin D, Murphy, Edward, Nigoghossian, Amanda, Nopakun, Linda, Okach, Silvya, Oommachen, Jessica, Paulsen, Christina, Puckett, Ron, Reyes, Christopher L, Rife, Natasha, Sefcovic, Sebastian, Sudek, Henry, Tien, Christine, Trame, Christina V, Trout, Henry, van den Bedem, Dana, Weekes, Aprilfawn, White, Qingping, Xu, Keith O, Hodgson, John, Wooley, Ashley M, Deacon, Adam, Godzik, Scott A, Lesley, and Ian A, Wilson
- Subjects
Sequence Homology, Amino Acid ,Protein Conformation ,Databases, Genetic ,Molecular Sequence Data ,Escherichia coli ,RNA-Binding Proteins ,Bacteriophages ,Amino Acid Sequence ,Protein Multimerization ,Crystallography, X-Ray ,Article - Abstract
ECX21941 represents a very large family (over 600 members) of novel, ocean metagenome–specific proteins identified by clustering of the dataset from the Global Ocean Sampling expedition. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity. The ECX21941 protein assembles as a homopentamer in solution and in the crystal structure when expressed in Escherichia coli and represents the first pentameric structure for this Sm/LSm family of proteins, although the actual oligomeric form in vivo is currently not known. The genomic neighborhood analysis of ECX21941 and its homologs combined with sequence similarity searches suggest a cyanophage origin for this protein. The specific functions of members of this family are unknown, but our structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing.
- Published
- 2009
47. Structural and Functional Characterizations of SsgB, a Conserved Activator of Developmental Cell Division in Morphologically Complex Actinomycetes
- Author
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Julie Feuerhelm, Marc C. Deller, Constantina Bakolitsa, Lukasz Jaroszewski, Bjørn A. Traag, Edward Nigoghossian, Mark W. Knuth, Jessica Paulsen, Mitchell D. Miller, Slawomir K. Grzechnik, Anna Grzechnik, John Wooley, Ian A. Wilson, Andrew T. Morse, Kevin K. Jin, Polat Abdubek, Scott A. Lesley, Connie Chen, Gye Won Han, Sanjay Krishna, Marc André Elsliger, Adam Godzik, Ron Reyes, Dustin C. Ernst, Silvya Oommachen, Christina Puckett, Abhinav Kumar, Linda Okach, Hsiu-Ju Chiu, Lian Duan, Herbert L. Axelrod, Dana Weekes, Amanda Nopakun, Thomas Clayton, Maksymilian Chruszcz, Natasha Sefcovic, Daniel McMullan, Keith O. Hodgson, Piotr Kozbial, Dennis Carlton, Wladek Minor, Qingping Xu, Shuren Wang, A. Mieke Mommaas, Henry J Tien, Henry van den Bedem, Tamara Astakhova, Heath E. Klock, Gilles P. van Wezel, Carol L. Farr, Ashley M. Deacon, Debanu Das, Joost Willemse, Christopher L. Rife, Christine B Trame, David Marciano, Kyle Ellrott, and Joanna C Grant
- Subjects
Subfamily ,Cell division ,Mutant ,Molecular Sequence Data ,Crystallography, X-Ray ,Biochemistry ,Streptomyces ,DNA-binding protein ,chemistry.chemical_compound ,Molecular Basis of Cell and Developmental Biology ,Bacterial Proteins ,Escherichia coli ,Microscopy, Phase-Contrast ,Amino Acid Sequence ,Molecular Biology ,Peptide sequence ,Genetics ,Spores, Bacterial ,Binding Sites ,biology ,Sequence Homology, Amino Acid ,Streptomyces coelicolor ,Cryoelectron Microscopy ,Genetic Complementation Test ,Cell Biology ,biology.organism_classification ,Actinobacteria ,chemistry ,Microscopy, Fluorescence ,Mutation ,DNA ,Cell Division - Abstract
SsgA-like proteins (SALPs) are a family of homologous cell division-related proteins that occur exclusively in morphologically complex actinomycetes. We show that SsgB, a subfamily of SALPs, is the archetypal SALP that is functionally conserved in all sporulating actinomycetes. Sporulation-specific cell division of Streptomyces coelicolor ssgB mutants is restored by introduction of distant ssgB orthologues from other actinomycetes. Interestingly, the number of septa (and spores) of the complemented null mutants is dictated by the specific ssgB orthologue that is expressed. The crystal structure of the SsgB from Thermobifida fusca was determined at 2.6 Å resolution and represents the first structure for this family. The structure revealed similarities to a class of eukaryotic “whirly” single-stranded DNA/RNA-binding proteins. However, the electro-negative surface of the SALPs suggests that neither SsgB nor any of the other SALPs are likely to interact with nucleotide substrates. Instead, we show that a conserved hydrophobic surface is likely to be important for SALP function and suggest that proteins are the likely binding partners.
- Published
- 2009
48. Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus
- Author
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Qingping, Xu, Christopher L, Rife, Dennis, Carlton, Mitchell D, Miller, S Sri, Krishna, Marc-André, Elsliger, Polat, Abdubek, Tamara, Astakhova, Hsiu-Ju, Chiu, Thomas, Clayton, Lian, Duan, Julie, Feuerhelm, Slawomir K, Grzechnik, Joanna, Hale, Gye Won, Han, Lukasz, Jaroszewski, Kevin K, Jin, Heath E, Klock, Mark W, Knuth, Abhinav, Kumar, Daniel, McMullan, Andrew T, Morse, Edward, Nigoghossian, Linda, Okach, Silvya, Oommachen, Jessica, Paulsen, Ron, Reyes, Henry, van den Bedem, Keith O, Hodgson, John, Wooley, Ashley M, Deacon, Adam, Godzik, Scott A, Lesley, and Ian A, Wilson
- Subjects
Adenosine Triphosphatases ,Models, Molecular ,Protein Conformation ,Archaeal Proteins ,Molecular Sequence Data ,Sulfolobus solfataricus ,Amino Acid Sequence ,Crystallization ,Crystallography, X-Ray ,Article - Published
- 2008
49. A structural basis for the regulatory inactivation of DnaA
- Author
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Polat Abdubek, Sanjay Krishna, Daniel McMullan, Tamara Astakhova, Ron Reyes, Amanda Nopakun, Lian Duan, Scott A. Lesley, Debanu Das, Dana Weekes, Henry van den Bedem, Adam Godzik, Piotr Kozbial, Edward Nigoghossian, Marc André Elsliger, Keith O. Hodgson, Linda Okach, Christine B Trame, Mark W. Knuth, John Wooley, David Marciano, Mitchell D. Miller, Dennis Carlton, Hope A. Johnson, Christopher L. Rife, Jessica Paulsen, Thomas Clayton, Hsiu-Ju Chiu, Gye Won Han, Silvya Oommachen, Abhinav Kumar, Ashley M. Deacon, Joanna Hale, Ian A. Wilson, Christina Puckett, Andrew T. Morse, Marc C. Deller, Heath E. Klock, Natasha Sefcovic, Qingping Xu, Lukasz Jaroszewski, Julie Feuerhelm, Kevin K. Jin, and Connie Chen
- Subjects
Models, Molecular ,Shewanella ,ATPase ,Dimer ,Molecular Sequence Data ,Antiparallel (biochemistry) ,Crystallography, X-Ray ,DNA-binding protein ,Article ,chemistry.chemical_compound ,Adenosine Triphosphate ,Bacterial Proteins ,Structural Biology ,ATP hydrolysis ,Amino Acid Sequence ,Protein Structure, Quaternary ,Molecular Biology ,Adenosine Triphosphatases ,DNA clamp ,biology ,DnaA ,AAA proteins ,DNA-Binding Proteins ,chemistry ,Biochemistry ,biology.protein ,Biophysics ,bacteria ,Dimerization ,Sequence Alignment - Abstract
Regulatory inactivation of DnaA is dependent on Hda (homologous to DnaA), a protein homologous to the AAA+ (ATPases associated with diverse cellular activities) ATPase region of the replication initiator DnaA. When bound to the sliding clamp loaded onto duplex DNA, Hda can stimulate the transformation of active DnaA-ATP into inactive DnaA-ADP. The crystal structure of Hda from Shewanella amazonensis SB2B at 1.75 A resolution reveals that Hda resembles typical AAA+ ATPases. The arrangement of the two subdomains in Hda (residues 1-174 and 175-241) differs dramatically from that of DnaA. A CDP molecule anchors the Hda domains in a conformation that promotes dimer formation. The Hda dimer adopts a novel oligomeric assembly for AAA+ proteins in which the arginine finger, crucial for ATP hydrolysis, is fully exposed and available to hydrolyze DnaA-ATP through a typical AAA+ type of mechanism. The sliding clamp binding motifs at the N-terminus of each Hda monomer are partially buried and combine to form an antiparallel beta-sheet at the dimer interface. The inaccessibility of the clamp binding motifs in the CDP-bound structure of Hda suggests that conformational changes are required for Hda to form a functional complex with the clamp. Thus, the CDP-bound Hda dimer likely represents an inactive form of Hda.
- Published
- 2008
50. Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution
- Author
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Qingping, Xu, Piotr, Kozbial, Daniel, McMullan, S Sri, Krishna, Scott M, Brittain, Scott B, Ficarro, Michael, DiDonato, Mitchell D, Miller, Polat, Abdubek, Herbert L, Axelrod, Hsiu-Ju, Chiu, Thomas, Clayton, Lian, Duan, Marc-André, Elsliger, Julie, Feuerhelm, Slawomir K, Grzechnik, Joanna, Hale, Gye Won, Han, Lukasz, Jaroszewski, Heath E, Klock, Andrew T, Morse, Edward, Nigoghossian, Jessica, Paulsen, Ron, Reyes, Christopher L, Rife, Henry, van den Bedem, Aprilfawn, White, Keith O, Hodgson, John, Wooley, Ashley M, Deacon, Adam, Godzik, Scott A, Lesley, and Ian A, Wilson
- Subjects
Ribosomal Proteins ,Protein Folding ,Bacterial Proteins ,ADP-Ribosylation Factors ,Cytidine Deaminase ,Molecular Sequence Data ,Thermotoga maritima ,Amino Acid Sequence ,Crystallography, X-Ray ,Protein Structure, Tertiary - Published
- 2008
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