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1. The structure of the first representative of Pfam family PF06475 reveals a new fold with possible involvement in glycolipid metabolism

Author

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

2. Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 Å resolution

Author

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
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3. 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

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
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4. Crystal structures of MW1337R and lin2004: Representatives of a novel protein family that adopt a four-helical bundle fold

Author

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
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5. 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

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
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6. Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) fromThermotoga maritima at 1.88 Å resolution

Author

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
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7. 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

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
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8. Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA

Author

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
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9. Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 Å resolution

Author

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
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10. Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 Å resolution

Author

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
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11. Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 Å resolution

Author

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
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12. Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 Å resolution

Author

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
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13. Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 Å resolution

Author

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
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14. 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
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15. Crystal structure of S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 Å resolution reveals a new fold

Author

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
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16. 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

17. 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

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

18. Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster

Author

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

19. 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

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

20. Structural Basis of Murein Peptide Specificity of a γ-D-glutamyl-L-diamino Acid Endopeptidase

Author

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

21. Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution

Author

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

22. 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

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

23. Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif

Author

Ron Reyes, Slawomir K. Grzechnik, Andrew T. Morse, Gye Won Han, Silvya Oommachen, Abhinav Kumar, Mark W. Knuth, Marc-André Elsliger, Edward Nigoghossian, Dennis Carlton, Ian A. Wilson, Qingping Xu, Piotr Kozbial, Eric Hampton, Paul Schimmel, Mitchell D. Miller, Adam Godzik, Herbert L. Axelrod, Chloe Zubieta, John Wooley, Daniel McMullan, Thomas Clayton, Eileen Ambing, Christopher L. Rife, Aprilfawn White, Keith O. Hodgson, Dana Weekes, Scott A. Lesley, Hsiu-Ju Chiu, Kevin K. Jin, Joanna Hale, Henry van den Bedem, Tamara Astakhova, Ashley M. Deacon, Lukasz Jaroszewski, Polat Abdubek, Sanjay Krishna, Mili Kapoor, Heath E. Klock, Linda Okach, Julie Feuerhelm, Marc C. Deller, David Marciano, and Lian Duan

Subjects
Protein Folding, Shewanella, Heme binding, Amino Acid Motifs, Molecular Sequence Data, Heme, Random hexamer, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, chemistry.chemical_compound, Bacterial Proteins, Structural Biology, Multienzyme Complexes, Catalytic Domain, Bacteroides, Amino Acid Sequence, Shewanella oneidensis, Coloring Agents, Molecular Biology, Conserved Sequence, Dye decolorizing peroxidase, biology, Chemistry, Active site, Isothermal titration calorimetry, biology.organism_classification, A-site, Crystallography, Peroxidases, biology.protein, Protein Binding
Abstract

BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 Angstroms, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, {alpha}+{beta} ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein).

Published
2007

24. Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 angstroms resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases

Author

Ashley M. Deacon, Ian A. Wilson, Lutz Tautz, Eileen Ambing, Andrew T. Morse, Michael DiDonato, Justin Haugen, Dennis Carlton, Polat Abdubek, Slawomir K. Grzechnik, Thomas Clayton, Tomas Mustelin, Ron Reyes, Eric Koesema, Gye Won Han, Sanjay Krishna, Silvya Oommachen, Joanna Hale, Mark W. Knuth, John Wooley, Mitchell D. Miller, Aprilfawn White, Tamara Astakhova, Christopher L. Rife, Heath E. Klock, Kevin K. Jin, Lukasz Jaroszewski, Daniel McMullan, Scott A. Lesley, Qingping Xu, Dana Weekes, Eric Hampton, Lian Duan, Marc-André Elsliger, Edward Nigoghossian, Hsiu-Ju Chiu, Henry van den Bedem, Adam Godzik, Herbert L. Axelrod, and Keith O. Hodgson

Subjects
Scaffold, Binding Sites, Chemistry, Neisseria meningitidis, Phosphatase, Resolution (electron density), Amino Acid Motifs, Molecular Sequence Data, Crystal structure, medicine.disease_cause, Crystallography, X-Ray, Biochemistry, Phosphoric Monoester Hydrolases, Protein Structure, Secondary, Bacterial Proteins, Structural Biology, Hydrolase, medicine, Amino Acid Sequence, Molecular Biology
Published
2007

25. Experimental and Computational Assessment of Conditionally Essential Genes in Escherichia coli▿

Author

Hirotada Mori, Aprilfawn White, Sanjay Agarwalla, Tomoya Baba, Andrei L. Osterman, Bernhard O. Palsson, Robert Edwards, Andrew R. Joyce, Jennifer L. Reed, and Scott A. Lesely

Subjects
Genetics, Glycerol, Genomics and Proteomics, Transcription, Genetic, Reverse Transcriptase Polymerase Chain Reaction, Mutant, Biology, medicine.disease_cause, Microbiology, Phenotype, Genome, Models, Biological, Culture Media, Metabolic pathway, Bacterial Proteins, Genes, Bacterial, Mutation, medicine, Escherichia coli, Minimal genome, Computer Simulation, Molecular Biology, Gene, Organism
Abstract

Genome-wide gene essentiality data sets are becoming available for Escherichia coli , but these data sets have yet to be analyzed in the context of a genome scale model. Here, we present an integrative model-driven analysis of the Keio E. coli mutant collection screened in this study on glycerol-supplemented minimal medium. Out of 3,888 single-deletion mutants tested, 119 mutants were unable to grow on glycerol minimal medium. These conditionally essential genes were then evaluated using a genome scale metabolic and transcriptional-regulatory model of E. coli , and it was found that the model made the correct prediction in ∼91% of the cases. The discrepancies between model predictions and experimental results were analyzed in detail to indicate where model improvements could be made or where the current literature lacks an explanation for the observed phenotypes. The identified set of essential genes and their model-based analysis indicates that our current understanding of the roles these essential genes play is relatively clear and complete. Furthermore, by analyzing the data set in terms of metabolic subsystems across multiple genomes, we can project which metabolic pathways are likely to play equally important roles in other organisms. Overall, this work establishes a paradigm that will drive model enhancement while simultaneously generating hypotheses that will ultimately lead to a better understanding of the organism.

Published
2006

26. Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution

Author

Daniel McMullan, Inna Levin, Hope A. Johnson, Ian A. Wilson, Scott A. Lesley, Herbert L. Axelrod, Eileen Ambing, Gye Won Han, Marc Fasnacht, Eric Sims, Silvya Oommachen, Tamara Astakhova, Glen Spraggon, Andreas Kreusch, Keith O. Hodgson, Ron Reyes, Rebecca Page, Justin Haugen, Mitchell D. Miller, Thomas Clayton, Sanjay Agarwalla, Mickey Kosloff, Vandana Sridhar, Jaume M. Canaves, Dennis Carlton, Polat Abdubek, Sanjay Krishna, Henry van den Bedem, Heath E. Klock, Raymond C. Stevens, Hsiu-Ju Chiu, Peter Kuhn, Eric Hampton, Slawomir K. Grzechnik, Robert Schwarzenbacher, Guenter Wolf, Christopher L. Rife, Joanna Hale, Carina Grittini, Ashley M. Deacon, Marc-André Elsliger, Edward Nigoghossian, Mark W. Knuth, Kevin Quijano, John Wooley, Eric Koesema, Aprilfawn White, Julie Feuerhelm, Adam Godzik, Qingping Xu, Andrew T. Morse, Lian Duan, Kin Moy, Kevin K. Jin, Michael DiDonato, Jeff Velasquez, Lukasz Jaroszewski, Linda Okach, and Jessica Paulsen

Subjects
Models, Molecular, Molecular Sequence Data, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Structural genomics, Bacterial Proteins, Structural Biology, Phylogenetics, Consensus sequence, Transferase, Amino Acid Sequence, Molecular Biology, Peptide sequence, Phylogeny, Glutathione Transferase, chemistry.chemical_classification, biology, Agrobacterium tumefaciens, Protein engineering, biology.organism_classification, Enzyme, chemistry, Dimerization
Abstract

Glutathione S-transferases (GSTs) comprise a diverse superfamily of enzymes found in organisms from all kingdoms of life. GSTs are involved in diverse processes, notably small-molecule biosynthesis or detoxification, and are frequently also used in protein engineering studies or as biotechnology tools. Here, we report the high-resolution X-ray structure of Atu5508 from the pathogenic soil bacterium Agrobacterium tumefaciens (atGST1). Through use of comparative sequence and structural analysis of the GST superfamily, we identified local sequence and structural signatures, which allowed us to distinguish between different GST classes. This approach enables GST classification based on structure, without requiring additional biochemical or immunological data. Consequently, analysis of the atGST1 crystal structure suggests a new GST class, distinct from previously characterized GSTs, which would make it an attractive target for further biochemical studies.

Published
2006

27. Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 A resolution reveals a fold similar to the Ran-binding protein Mog1p

Author

Andreas Kreusch, Heath E. Klock, Marc-André Elsliger, Jaume M. Canaves, Edward Nigoghossian, Slawomir K. Grzechnik, Henry van den Bedem, Lukasz Jaroszewski, Justin Haugen, Guenter Wolf, Ron Reyes, Andrew T. Morse, Ashley M. Deacon, Hsiu-Ju Chiu, Thomas Clayton, Ian A. Wilson, Mark W. Knuth, Michael DiDonato, Kevin Quijano, John Wooley, Joanna Hale, Peter Kuhn, Kevin K. Jin, Eileen Ambing, Qingping Xu, Lian Duan, Glen Spraggon, Adam Godzik, Christopher L. Rife, Herbert L. Axelrod, Eric Koesema, Tamara Astakhova, Sanjay Agarwalla, Eric Hampton, Julie Feuerhelm, Gye Won Han, Silvya Oommachen, Dennis Carlton, Keith O. Hodgson, Scott A. Lesley, Robert Schwarzenbacher, Polat Abdubek, Sanjay Krishna, Linda Okach, Mitchell D. Miller, Daniel McMullan, Raymond C. Stevens, Aprilfawn White, and Jessica Paulsen

Subjects
Physics, Models, Molecular, Protein Folding, Saccharomyces cerevisiae Proteins, biology, Molecular Sequence Data, Fold (geology), Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Protein tertiary structure, Protein Structure, Secondary, ran GTP-Binding Protein, Ran-binding protein, Bacterial Proteins, Structural Biology, Signaling proteins, Thermotoga maritima, Amino Acid Sequence, Molecular Biology
Published
2006

28. Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site

Author

Lian Duan, Guenter Wolf, Polat Abdubek, Sanjay Krishna, Daniel McMullan, Inna Levin, Keith O. Hodgson, Jessica Paulsen, Jaume M. Canaves, Mark W. Knuth, Kevin Quijano, Joanna Hale, Linda Okach, Michael DiDonato, Andreas Kreusch, Hsiu-Ju Chiu, Sanjay Agarwalla, Marc-André Elsliger, Mitchell D. Miller, Edward Nigoghossian, Scott A. Lesley, Q. Xu, Heath E. Klock, Eric Hampton, Glen Spraggon, Herbert L. Axelrod, Henry van den Bedem, Adam Godzik, Lukasz Jaroszewski, Peter Kuhn, John Wooley, Justin Haugen, Ron Reyes, Robert Schwarzenbacher, Raymond C. Stevens, Eric Koesema, Aprilfawn White, Slawomir K. Grzechnik, Ian A. Wilson, Eileen Ambing, Silvya Oommachen, Scott M. Brittain, Christopher L. Rife, Andrew T. Morse, Ashley M. Deacon, and Kevin K. Jin

Subjects
Models, Molecular, Protein Folding, Binding Sites, Protein Conformation, media_common.quotation_subject, Acid Phosphatase, Molecular Sequence Data, Art, Crystallography, X-Ray, Biochemistry, Structural Biology, 2-phosphosulfolactate phosphatase, Clostridium acetobutylicum, Amino Acid Sequence, Molecular Biology, Humanities, media_common
Abstract

Michael DiDonato, S. Sri Krishna, Robert Schwarzenbacher, Daniel McMullan, Sanjay Agarwalla, Scott M. Brittain, Mitchell D. Miller, Polat Abdubek, Eileen Ambing, Herbert L. Axelrod, JaumeM. Canaves, Hsiu-Ju Chiu, Ashley M. Deacon, Lian Duan, Marc-Andre Elsliger, Adam Godzik, Slawomir K. Grzechnik, Joanna Hale, Eric Hampton, Justin Haugen, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Eric Koesema, Andreas Kreusch, Peter Kuhn, Scott A. Lesley, Inna Levin, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Silvya Oommachen, Jessica Paulsen, Kevin Quijano, Ron Reyes, Christopher L. Rife, Glen Spraggon, Raymond C. Stevens, Henry van den Bedem, AprilfawnWhite, Guenter Wolf, Qingping Xu, Keith O. Hodgson, John Wooley, and Ian A. Wilson* The Joint Center for Structural Genomics Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California The University of California, San Diego, La Jolla, California The Genomics Institute of the Novartis Research Foundation, San Diego, California The Scripps Research Institute, La Jolla, California

Published
2006

29. Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from Thermotoga maritima at 1.90 A resolution

Author

Glen Spraggon, Aprilfawn White, Lian Duan, Edward Nigoghossian, Sanjay Agarwalla, Andrew T. Morse, Dennis Carlton, Slawomir K. Grzechnik, Guenter Wolf, Adam Godzik, Marc-André Elsliger, Raymond C. Stevens, Sanjay Krishna, Keith O. Hodgson, Silvya Oommachen, John S. Kovarik, Polat Abdubek, Ian A. Wilson, Ron Reyes, Jaume M. Canaves, Christopher L. Rife, Eileen Ambing, Peter Kuhn, Hsiu-Ju Chiu, John Wooley, Jessica Paulsen, Kevin Quijano, Justin Haugen, Eric Hampton, Linda Okach, Inna Levin, Herbert L. Axelrod, Ashley M. Deacon, Michael Didonato, Henry van den Bedem, Eric Koesema, Scott A. Lesley, Kevin K. Jin, Daniel McMullan, Irimpan I. Mathews, Lukasz Jaroszewski, Robert Schwarzenbacher, Qingping Xu, Heath E. Klock, Andreas Kreusch, Mitchell D. Miller, Thomas Clayton, and Joanna Hale

Subjects
chemistry.chemical_classification, DNA ligase, biology, ATP synthase, Stereochemistry, Chemistry, Protein subunit, Resolution (electron density), Molecular Sequence Data, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Protein structure, Bacterial Proteins, Structural Biology, Thermotoga maritima, biology.protein, Amino Acid Sequence, Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor, Crystallization, Protein Structure, Quaternary, Molecular Biology, Peptide sequence
Published
2006

30. Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution

Author

Justin Haugen, Joanna Hale, John Wooley, Aprilfawn White, Daniel McMullan, Sanjay Agarwalla, Peter Kuhn, Robert Schwarzenbacher, Guenter Wolf, Jessica Paulsen, Ron Reyes, Andreas Kreusch, Mark W. Knuth, Kevin Quijano, Raymond C. Stevens, Kin Moy, Scott A. Lesley, Jaume M. Canaves, Qingping Xu, Slawomir K. Grzechnik, Mitchell D. Miller, Gye Won Han, Lukasz Jaroszewski, Polat Abdubek, Sanjay Krishna, Carina Grittini, Christopher L. Rife, Michael DiDonato, Heath E. Klock, Eric Koesema, Eric Hampton, Michael Hornsby, Henry van den Bedem, Hsiu-Ju Chiu, Keith O. Hodgson, Marc-André Elsliger, Ashley M. Deacon, Edward Nigoghossian, Jeff Velasquez, Glen Spraggon, Herbert L. Axelrod, Tanya Biorac, Adam Godzik, Ian A. Wilson, and Eileen Ambing

Subjects
chemistry.chemical_classification, Models, Molecular, Binding Sites, Molecular Structure, Stereochemistry, Resolution (electron density), Molecular Sequence Data, Crystal structure, Biochemistry, Protein Structure, Secondary, Dioxygenases, Protein Structure, Tertiary, Mice, Acireductone dioxygenase, chemistry, Structural Biology, Oxidoreductase, Metals, Animals, Amino Acid Sequence, Crystallization, Databases, Protein, Molecular Biology, Protein Binding
Published
2006

31. Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold

Author

Raymond C. Stevens, Lukasz Jaroszewski, John Wooley, Carina Grittini, Scott A. Lesley, Qingping Xu, Aprilfawn White, Ron Reyes, Adam Godzik, Ashley M. Deacon, Hsiu-Ju Chiu, Marc-André Elsliger, Edward Nigoghossian, Justin Haugen, Daniel McMullan, Joanna Hale, Eric Hampton, Michael Hornsby, Henry van den Bedem, Peter Kuhn, Polat Abdubek, Christopher L. Rife, Julie Feuerhelm, Sanjay Krishna, Slawomir K. Grzechnik, Heath E. Klock, Jaume M. Canaves, Keith O. Hodgson, Kevin K. Jin, Herbert L. Axelrod, Ian A. Wilson, Robert Schwarzenbacher, Gye Won Han, Silvya Oommachen, Guenter Wolf, Eileen Ambing, Glen Spraggon, Eric Koesema, Mitchell D. Miller, Kin Moy, Jeff Velasquez, Mark W. Knuth, Kevin Quijano, Andreas Kreusch, Michael DiDonato, Sanjay Agarwalla, Jessica Paulsen, and Linda Okach

Subjects
Models, Molecular, Protein Folding, Molecular Sequence Data, Crystal structure, Crystallography, X-Ray, Biochemistry, Polyethylene Glycols, Cyclophilins, Bacterial Proteins, Structural Biology, Humans, Thermotoga maritima, Amino Acid Sequence, Protein Structure, Quaternary, Molecular Biology, Cyclophilin, Peptidylprolyl isomerase, Binding Sites, biology, Chemistry, Fold (geology), Peptidylprolyl Isomerase, biology.organism_classification, Protein Structure, Tertiary, Crystallography
Published
2006

32. Crystal structure of virulence factor CJ0248 from Campylobacter jejuni at 2.25 A resolution reveals a new fold

Author

Glen Spraggon, Lukasz Jaroszewski, Robert Schwarzenbacher, Michael DiDonato, Guenter Wolf, Raymond C. Stevens, Christopher L. Rife, Hsiu-Ju Chiu, Carina Grittini, Kin Moy, Marc-André Elsliger, Ashley M. Deacon, Edward Nigoghossian, Andreas Kreusch, Jessica Paulsen, Kevin Quijano, Jaume M. Canaves, Aprilfawn White, Sanjay Agarwalla, Ian A. Wilson, Herbert L. Axelrod, Tanya Biorac, Adam Godzik, Gye Won Han, Scott A. Lesley, Eileen Ambing, Ron Reyes, Keith O. Hodgson, Eric Hampton, Slawomir K. Grzechnik, Jeff Velasquez, John Wooley, Michael Hornsby, Henry van den Bedem, Eric Koesema, Daniel McMullan, Polat Abdubek, Joanna Hale, Mitchell D. Miller, Heath E. Klock, Peter Kuhn, Justin Haugen, and Qingping Xu

Subjects
Physics, Models, Molecular, Protein Folding, biology, Virulence Factors, Fold (geology), Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Campylobacter jejuni, Virulence factor, Protein Structure, Secondary, Bacterial protein, Bacterial Proteins, Structural Biology, Protein folding, Molecular Biology
Published
2005

33. Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 A resolution reveals a new fold

Author

Ian A. Wilson, Eileen Ambing, Ashley M. Deacon, Andreas Kreusch, Jeff Velasquez, Jessica Paulsen, Juli Vincent, Hsiu-Ju Chiu, Herbert L. Axelrod, Polat Abdubek, Michael DiDonato, Gye Won Han, Carina Grittini, Jaume M. Canaves, Raymond C. Stevens, Guenter Wolf, Qingping Xu, Heath E. Klock, Slawomir K. Grzechnik, Michael Hornsby, Christopher L. Rife, Henry van den Bedem, Scott A. Lesley, Kevin Quijano, Marc-André Elsliger, Peter Kuhn, Edward Nigoghossian, Keith O. Hodgson, Aprilfawn White, Joanna Hale, Tanya Biorac, Adam Godzik, Eric Hampton, Mitchell D. Miller, Eric Koesema, Justin Haugen, Eric Sims, John Wooley, Ron Reyes, Daniel McMullan, Robert Schwarzenbacher, Kin Moy, Lukasz Jaroszewski, and Glen Spraggon

Subjects
Models, Molecular, Protein Folding, Chemistry, Hypothetical protein, Proteins, Fold (geology), Crystal structure, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Molecular Weight, Crystallography, Mice, Open Reading Frames, Structural Biology, Transferase, Animals, Databases, Protein, Molecular Biology, Conserved Sequence
Published
2005

34. Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 A resolution reveals a new fold

Author

Peter Kuhn, Kevin Quijano, Slawomir K. Grzechnik, Marc-André Elsliger, Ian A. Wilson, Justin Haugen, Polat Abdubek, Edward Nigoghossian, Aprilfawn White, Eileen Ambing, John Wooley, Glen Spraggon, Kin Moy, Carina Grittini, Robert Schwarzenbacher, Daniel McMullan, Heath E. Klock, Hsiu-Ju Chiu, Raymond C. Stevens, Ashley M. Deacon, Guenter Wolf, Mitchell D. Miller, Ron Reyes, Joanna Hale, Jessica Paulsen, Eric Koesema, Gye Won Han, Scott A. Lesley, Andreas Kreusch, Lukasz Jaroszewski, Tanya Biorac, Adam Godzik, Juli Vincent, Qingping Xu, Keith O. Hodgson, Michael Hornsby, Henry van den Bedem, Eric Sims, Herbert L. Axelrod, Michael DiDonato, Jeff Velasquez, Christopher L. Rife, Eric Hampton, and Jaume M. Canaves

Subjects
Regulation of gene expression, Models, Molecular, Protein Folding, biology, Chemistry, Stereochemistry, Molecular Sequence Data, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, DNA gyrase, Bacterial Proteins, Structural Biology, DNA Gyrase, Thermotoga maritima, Amino Acid Sequence, Molecular Biology, Dimerization
Published
2005

35. Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution

Author

John Wooley, Justin Haugen, Peter Kuhn, Heath E. Klock, Scott A. Lesley, Joanna Hale, Hsiu-Ju Chiu, Guenter Wolf, Tanya Biorac, Adam Godzik, Qingping Xu, Xiaoping Dai, Polat Abdubek, Slawomir K. Grzechnik, Ron Reyes, Glen Spraggon, Michael DiDonato, Eric Koesema, Carina Grittini, Gye Won Han, Raymond C. Stevens, Marc-André Elsliger, Jeff Velasquez, Edward Nigoghossian, Daniel McMullan, Mitchell D. Miller, Kevin Quijano, Keith O. Hodgson, Aprilfawn White, Robert Schwarzenbacher, Eric Hampton, Juli Vincent, Kin Moy, Lukasz Jaroszewski, Ian A. Wilson, Herbert L. Axelrod, Michael Hornsby, Henry van den Bedem, Eileen Ambing, Ashley M. Deacon, Jessica Paulsen, Jaume M. Canaves, Andreas Kreusch, and Timothy M. McPhillips

Subjects
Models, Molecular, Messenger RNA, Chemistry, Resolution (electron density), DCPS, Molecular Sequence Data, RNA-binding protein, Crystal structure, Crystallography, X-Ray, Biochemistry, Sensitivity and Specificity, Protein Structure, Secondary, Mice, Apoenzymes, Structural Biology, Endoribonucleases, Animals, Amino Acid Sequence, RNA, Messenger, Molecular Biology, Decapping enzyme
Published
2005

36. Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor

Author

Guenter Wolf, Gye Won Han, Kin Moy, Kevin Quijano, Slawomir K. Grzechnik, Michael Hornsby, Henry van den Bedem, Andreas Kreusch, Jessica Paulsen, Heath E. Klock, Polat Abdubek, Hsiu-Ju Chiu, Rebecca Page, Qingping Xu, Ron Reyes, Marc-André Elsliger, Peter Kuhn, Edward Nigoghossian, Eric Hampton, Andrew T. Morse, Jeff Velasquez, Frank von Delft, Juli Vincent, Lukasz Jaroszewski, Tanya Biorac, Adam Godzik, Olga Zagnitko, Michael DiDonato, Daniel McMullan, Inna Levin, Carina Grittini, Bill West, Keith O. Hodgson, Joanna Hale, Xiaoping Dai, Eric Koesema, Mitchell D. Miller, Justin Haugen, John Wooley, Xianhong Wang, Scott A. Lesley, Timothy M. McPhillips, Ashley M. Deacon, Glen Spraggon, Eric Sims, Robert Schwarzenbacher, Ian A. Wilson, Eileen Ambing, Jie Ouyang, Raymond C. Stevens, Jaume M. Canaves, and Aprilfawn White

Subjects
Models, Molecular, Protein Conformation, Stereochemistry, Molecular Sequence Data, Anabaena sp, Alanine glyoxylate aminotransferase, Electrons, Crystal structure, Crystallography, X-Ray, Biochemistry, Cofactor, Structural Biology, Humans, Transferase, Amino Acid Sequence, Molecular Biology, Transaminases, Sequence Homology, Amino Acid, biology, Chemistry, Resolution (electron density), Proteins, Stereoisomerism, Anabaena, Protein Structure, Tertiary, biology.protein
Published
2005

37. Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution

Author

Timothy M. McPhillips, Eric Sims, Eric Hampton, Xiaoping Dai, Jaume M. Canaves, John Wooley, Aprilfawn White, Carina Grittini, Slawomir K. Grzechnik, Daniel McMullan, Inna Levin, Joanna Hale, Heath E. Klock, Lukasz Jaroszewski, Peter Kuhn, Keith O. Hodgson, Justin Haugen, Olga Zagnitko, Guenter Wolf, Kevin Quijano, Kin Moy, Hsiu-Ju Chiu, W. Peti, Joseph W. Arndt, Qingping Xu, Polat Abdubek, Mitchell D. Miller, Andrew T. Morse, Jeff Velasquez, Juli Vincent, Bill West, Jie Ouyang, Marc-André Elsliger, Gye Won Han, Edward Nigoghossian, Andreas Kreusch, Michael Hornsby, Henry van den Bedem, Rebecca Page, Robert Schwarzenbacher, Michael Didonato, Eric Koesema, Frank von Delft, Xianhong Wang, Scott A. Lesley, Ashley M. Deacon, Glen Spraggon, Raymond C. Stevens, Ian A. Wilson, Eileen Ambing, Ron Reyes, Tanya Biorac, and Adam Godzik

Subjects
Models, Molecular, Saccharomyces cerevisiae Proteins, Hydrolases, Protein Conformation, Molecular Sequence Data, Saccharomyces cerevisiae, Molecular Conformation, Alpha (ethology), Crystal structure, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Structural Biology, Hydrolase, Serine, Amino Acid Sequence, Beta (finance), Molecular Biology, Binding Sites, biology, Chemistry, Resolution (electron density), Computational Biology, Serine hydrolase, biology.organism_classification, Protein Structure, Tertiary, Software
Published
2005

38. Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold

Author

Keith O. Hodgson, Kin Moy, Jie Ouyang, Polat Abdubek, Guenter Wolf, Heath E. Klock, Hsiu-Ju Chiu, Xiaoping Dai, Mitchell D. Miller, Marc-André Elsliger, Frank von Delft, Robert Schwarzenbacher, Michael Hornsby, Henry van den Bedem, Carina Grittini, Jeff Velasquez, Tanya Biorac, Adam Godzik, Lukasz Jaroszewski, Olga Zagnitko, Eric Sims, Raymond C. Stevens, Qingping Xu, Eric Koesema, Andreas Kreusch, Michael DiDonato, Rebecca Page, Bill West, Jaume M. Canaves, Peter Kuhn, Aprilfawn White, Daniel McMullan, Inna Levin, Alyssa Robb, Andrew T. Morse, Juli Vincent, Eric Hampton, Ian A. Wilson, Slawomir K. Grzechnik, Xianhong Wang, Scott A. Lesley, Eileen Ambing, Ashley M. Deacon, Glen Spraggon, John Wooley, Kevin Quijano, and Ron Reyes

Subjects
Models, Molecular, Ammonia-Lyases, Stereochemistry, Protein Conformation, Molecular Sequence Data, Molecular Conformation, Crystal structure, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Formiminotetrahydrofolate cyclodeaminase, Structural Biology, Enzyme Stability, Thermotoga maritima, Amino Acid Sequence, Molecular Biology, Binding Sites, biology, Chemistry, Fold (geology), Lyase, biology.organism_classification, Protein Structure, Tertiary, Models, Chemical, Crystallization
Published
2005

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