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1. Vehicle Detection With Automotive Radar Using Deep Learning on Range-Azimuth-Doppler Tensors.

Author: Bence Major, Daniel Fontijne, Amin Ansari, Ravi Teja Sukhavasi, Radhika Gowaiker, Michael Hamilton, Sean Lee, Slawomir K. Grzechnik, and Sundar Subramanian
Published: 2019
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2. An end-to-end system for crowdsourced 3D maps for autonomous vehicles: The mapping component.

Author: Onkar Dabeer, Wei Ding, Radhika Gowaiker, Slawomir K. Grzechnik, Mythreya J. Lakshman, Sean Lee, Gerhard Reitmayr, Arunandan Sharma, Kiran Somasundaram, Ravi Teja Sukhavasi, and Xinzhou Wu
Published: 2017
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3. Vehicle Detection With Automotive Radar Using Deep Learning on Range-Azimuth-Doppler Tensors

Author: Sean Lee, Hamilton Michael John, Amin Ansari, Sundar Subramanian, Radhika Gowaikar, Slawomir K. Grzechnik, Ravi Teja Sukhavasi, Fontijne Daniel Hendricus Franciscus, and Major Bence
Subjects: Computer science, business.industry, 010401 analytical chemistry, Real-time computing, Doppler radar, Point cloud, 020206 networking & telecommunications, Advanced driver assistance systems, 02 engineering and technology, 01 natural sciences, Signal, 0104 chemical sciences, law.invention, Azimuth, symbols.namesake, law, Radar imaging, 0202 electrical engineering, electronic engineering, information engineering, symbols, Clutter, Artificial intelligence, Radar, business, Doppler effect
Abstract: Radar has been a key enabler of advanced driver assistance systems in automotive for over two decades. Being an inexpensive, all-weather and long-range sensor that simultaneously provides velocity measurements, radar is expected to be indispensable to the future of autonomous driving. Traditional radar signal processing techniques often cannot distinguish reflections from objects of interest from clutter and are generally limited to detecting peaks in the received signal. These peak detection methods effectively collapse the image-like radar signal into a sparse point cloud. In this paper, we demonstrate a deep-learning-based vehicle detection solution which operates on the image-like tensor instead of the point cloud resulted by peak detection.To the best of our knowledge, we are the first to implement such a system.
Published: 2019
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4. An end-to-end system for crowdsourced 3D maps for autonomous vehicles: The mapping component

Author: Sean Lee, Kiran Kumar Somasundaram, Onkar Dabeer, Radhika Gowaiker, Wei Ding, Gerhard Reitmayr, Mythreya J. Lakshman, Arunandan Sharma, Ravi Teja Sukhavasi, Xinzhou Wu, and Slawomir K. Grzechnik
Subjects: 050210 logistics & transportation, Computer science, business.industry, 05 social sciences, Context (language use), Bundle adjustment, 02 engineering and technology, 0502 economics and business, 0202 electrical engineering, electronic engineering, information engineering, Global Positioning System, 020201 artificial intelligence & image processing, Computer vision, Artificial intelligence, Triangulation, Geographic coordinate system, business, Sign (mathematics)
Abstract: Autonomous vehicles rely on precise high definition (HD) 3D maps for navigation. This paper presents the mapping component of an end-to-end system for crowdsourcing precise 3D maps with semantically meaningful landmarks such as traffic signs (6 dof pose, shape and size) and traffic lanes (3D splines). The system uses consumer grade parts, and in particular, relies on a single front facing camera and a consumer grade GPS. Using real-time sign and lane triangulation on-device in the vehicle, with offline sign/lane clustering across multiple journeys and offline Bundle Adjustment across multiple journeys in the backend, we construct maps with mean absolute accuracy at sign corners of less than 20 cm from 25 journeys. To the best of our knowledge, this is the first end-to-end HD mapping pipeline in global coordinates in the automotive context using cost effective sensors.
Published: 2017
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5. Crystal structure of a phosphoribosylaminoimidazole mutase PurE (TM0446) from Thermotoga maritima at 1.77-A resolution

Author: Jeff Velasquez, Tanya Biorac, Adam Godzik, Peter Kuhn, Raymond C. Stevens, Guenter Wolf, Jie Ouyang, Heath E. Klock, Ross Floyd, Xiaoping Dai, Andreas Kreusch, Rebecca Page, Bill West, Keith O. Hodgson, Alyssa Robb, Hsiu-Ju Chiu, Jaume M. Canaves, Xianhong Wang, Scott A. Lesley, Linda S. Brinen, Andrew T. Morse, Juli Vincent, John S. Kovarik, Timothy M. McPhillips, Kin Moy, Marc-André Elsliger, Ashley M. Deacon, Mitchell D. Miller, Robert Schwarzenbacher, Ian A. Wilson, Frank von Delft, Eileen Ambing, Glen Spraggon, Mike DiDonato, Said Eshagi, Henry van den Bedem, Eric Hampton, Jamison Cambell, Eric Koesema, Carina Grittini, Kevin Quijano, Cathy Karlak, Polat Abdubek, Daniel McMullan, Inna Levin, John Wooley, Slawomir K. Grzechnik, Lukasz Jaroszewski, and Qingping Xu
Subjects: Models, Molecular, biology, Protein Conformation, Chemistry, Molecular Sequence Data, Resolution (electron density), Imidazoles, Reproducibility of Results, Crystal structure, Crystallography, X-Ray, biology.organism_classification, Lyase, Biochemistry, Crystallography, Mutase, Structural Biology, Thermotoga maritima, Amino Acid Sequence, Crystallization, Intramolecular Transferases, Molecular Biology
Published: 2016

6. Crystal structure of a methionine aminopeptidase (TM1478) from Thermotoga maritima at 1.9 A resolution

Author: Peter Kuhn, Ross Floyd, Linda S. Brinen, Jaume M. Canaves, Guenter Wolf, Fred Rezezadeh, John Wooley, Kevin Quijano, Mitchell D. Miller, Xiaoping Dai, Raymond C. Stevens, Xianhong Wang, Scott A. Lesley, Marc-André Elsliger, Andreas Kreusch, Rebecca Page, Cathy Karlak, Kin Moy, Slawomir K. Grzechnik, Carina Grittini, Jeff Velasquez, Bill West, Adam Godzik, Qingping Xu, Said Eshagi, Frank von Delft, Ian A. Wilson, Alyssa Robb, Andrew T. Morse, Glen Spraggon, Juli Vincent, John S. Kovarik, Jie Ouyang, Lukasz Jaroszewski, Daniel McMullan, Robert Schwarzenbacher, Heath E. Klock, Eric Koesema, Ashley M. Deacon, Keith O. Hodgson, Henry van den Bedem, Timothy M. McPhillips, and Eric Sims
Subjects: Models, Molecular, Binding Sites, biology, Protein Conformation, Chemistry, Stereochemistry, Methionine aminopeptidase, Molecular Sequence Data, Resolution (electron density), Crystal structure, Crystallography, X-Ray, biology.organism_classification, Aminopeptidases, Biochemistry, Protein Structure, Tertiary, Bacterial Proteins, Structural Biology, Thermotoga maritima, Hydrolase, Methionyl Aminopeptidases, Amino Acid Sequence, Molecular Biology
Published: 2016

7. Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution

Author: Jeff Velasquez, Mike DiDonato, Kevin Quijano, Xianhong Wang, Scott A. Lesley, Henry van den Bedem, Qingping Xu, Marc-André Elsliger, Polat Abdubek, Eric Hampton, Jie Ouyang, Timothy M. McPhillips, Xiaoping Dai, Jaume M. Canaves, Said Eshagi, Bill West, Guenter Wolf, Frank von Delft, Carina Grittini, Alyssa Robb, Lukasz Jaroszewski, Keith O. Hodgson, John Wooley, Andrew T. Morse, Mitchell D. Miller, Daniel McMullan, Inna Levin, Juli Vincent, H.-J. Chiu, Cathy Karlak, Robert Schwarzenbacher, Kin Moy, Slawomir K. Grzechnik, John S. Kovarik, Jamison Cambell, Eric Koesema, Peter Kuhn, Adam Godzik, Raymond C. Stevens, Tanja Biorac, Ross Floyd, Heath E. Klock, Linda S. Brinen, Andreas Kreusch, Rebecca Page, Glen Spraggon, Ashley M. Deacon, Ian A. Wilson, and Eileen Ambing
Subjects: Physics, Models, Molecular, biology, PII Nitrogen Regulatory Proteins, Resolution (electron density), Molecular Sequence Data, Synchrotron radiation, Reproducibility of Results, Particle accelerator, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, law.invention, Crystallography, Bacterial Proteins, Structural Biology, law, Signaling proteins, Thermotoga maritima, Amino Acid Sequence, Molecular Biology, Signal Transduction
Published: 2016
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8. Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution

Author: 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
Subjects: 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
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9. Crystal structure of gamma-glutamyl phosphate reductase (TM0293) from Thermotoga maritima at 2.0 A resolution

Author: Slawomir K. Grzechnik, Marc-André Elsliger, Raymond C. Stevens, John Wooley, Frank von Delft, Peter Kuhn, Jaume M. Canaves, Ross Floyd, Timothy M. McPhillips, Jeff Velasquez, Kin Moy, Lukasz Jaroszewski, Jie Ouyang, Eric Koesema, Ian A. Wilson, Robert Schwarzenbacher, Daniel McMullan, Michael S. Nelson, Alyssa Robb, Guenter Wolf, Rebecca Page, Juli Vincent, Andrew C. Morse, Bill West, Xiaoping Dai, Kevin Rodrigues, Carina Grittini, Linda S. Brinen, H. Klock, Ashley M. Deacon, Glen Spraggon, John S. Kovarik, Adam Godzik, Henry van den Bedem, Xianhong Wang, Scott A. Lesley, Andreas Kreusch, Keith O. Hodgson, and Mitchell D. Miller
Subjects: chemistry.chemical_classification, Models, Molecular, biology, Stereochemistry, Glutamate-5-Semialdehyde Dehydrogenase, Resolution (electron density), Molecular Sequence Data, Crystal structure, Reductase, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Aldehyde Oxidoreductases, chemistry, Bacterial Proteins, Structural Biology, Oxidoreductase, Thermotoga maritima, Gamma-glutamyl phosphate, Amino Acid Sequence, Molecular Biology
Published: 2016
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10. Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution

Author: Guenter Wolf, Peter Kuhn, Daniel McMullan, Inna Levin, Ross Floyd, Hsiu-Ju Chiu, Carina Grittini, John S. Kovarik, Ian A. Wilson, Eric Hampton, Kin Moy, Eileen Ambing, Glen Spraggon, Alyssa Robb, Jaume M. Canaves, Heath E. Klock, Kevin Quijano, John Wooley, Marc-André Elsliger, Andrew T. Morse, Timothy M. McPhillips, Bill West, Juli Vincent, Christian C. Lee, Polat Abdubek, Jie Ouyang, Frank von Delft, Xiaoping Dai, Jeff Velasquez, Linda S. Brinen, Slawomir K. Grzechnik, Tanya Biorac, Adam Godzik, Raymond C. Stevens, Jamison Cambell, Eric Koesema, Ashley M. Deacon, Andreas Kreusch, Rebecca Page, Xianhong Wang, Scott A. Lesley, Robert Schwarzenbacher, Mike DiDonato, Cathy Karlak, Henry van den Bedem, Qingping Xu, Keith O. Hodgson, Lukasz Jaroszewski, Said Eshagi, and Mitchell D. Miller
Subjects: Models, Molecular, chemistry.chemical_classification, DNA ligase, biology, Chemistry, Molecular Sequence Data, Resolution (electron density), Crystal structure, Crystallography, X-Ray, biology.organism_classification, Biochemistry, Crystallography, Bacterial Proteins, UDP-N-acetylmuramate-alanine ligase, Structural Biology, Thermotoga maritima, Amino Acid Sequence, Peptide Synthases, Molecular Biology
Published: 2016

11. Crystal Structure of the First Eubacterial Mre11 Nuclease Reveals Novel Features that May Discriminate Substrates During DNA Repair

Author: 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
Subjects: 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.
Published: 2010
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12. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation

Author: 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
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13. Structure of LP2179, the first representative of Pfam family PF08866, suggests a new fold with a role in amino-acid metabolism

Author: 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
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14. 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

15. Crystal Structure of Histidine Phosphotransfer Protein ShpA, an Essential Regulator of Stalk Biogenesis in Caulobacter crescentus

Author: 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
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16. 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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17. 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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18. Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus

Author: 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
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19. 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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20. 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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21. 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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22. Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) fromThermotoga maritimaat 2.05 Å resolution

Author: Timothy M. McPhillips, Kevin Quijano, Andreas Kreusch, Scott A. Lesley, Guenter Wolf, Henry van den Bedem, Irimpan I. Mathews, Andrew T. Morse, Lukasz Jaroszewski, Mitchell D. Miller, Dana Weekes, Christopher L. Rife, Marc-André Elsliger, Peter Kuhn, Ashley M. Deacon, Daniel McMullan, Adam Godzik, Ross Floyd, Robert Schwarzenbacher, Ian A. Wilson, Jaume M. Canaves, Keith O. Hodgson, Eric Koesema, John S. Kovarik, Heath E. Klock, Glen Spraggon, John Wooley, Raymond C. Stevens, and Slawomir K. Grzechnik
Subjects: biology, Structural Biology, Stereochemistry, Chemistry, Thermotoga maritima, Resolution (electron density), Transferase, 2-keto-3-deoxygluconate kinase, Crystal structure, biology.organism_classification, Molecular Biology, Biochemistry
Published: 2007
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23. 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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24. 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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25. 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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26. Crystal structure of a transcription regulator (TM1602) from Thermotoga maritima at 2.3 Å resolution

Author: Jaume M. Canaves, Ian A. Wilson, John Wooley, Claire Acosta, John S. Kovarik, Guenter Wolf, Timothy M. McPhillips, Glen Spraggon, Dana Weekes, Scott A. Lesley, Adam Godzik, Slawomir K. Grzechnik, Mitchell D. Miller, Henry van den Bedem, Daniel McMullan, Andreas Kreusch, Lukasz Jaroszewski, Sanjay Krishna, Kevin Quijano, Keith O. Hodgson, Ashley M. Deacon, Eric Koesema, Marc-André Elsliger, Andrew T. Morse, Ross Floyd, and Heath E. Klock
Subjects: Models, Molecular, biology, Computer science, Stereochemistry, Molecular Sequence Data, Crystal structure, Crystallography, X-Ray, biology.organism_classification, Biochemistry, DNA-Binding Proteins, Structural Biology, Transcription (biology), Thermotoga maritima, Amino Acid Sequence, Crystallization, Molecular Biology, Transcription regulator, Transcription Factors
Published: 2007
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27. Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 Å resolution reveals a new fold

Author: Ian A. Wilson, Guenter Wolf, Jaume M. Canaves, Keith O. Hodgson, John Wooley, Robert Schwarzenbacher, Andrew T. Morse, Peter Kuhn, Kevin Quijano, Andreas Kreusch, Sanjay Krishna, Marc-André Elsliger, Ross Floyd, Ashley M. Deacon, Glen Spraggon, Slawomir K. Grzechnik, Mitchell D. Miller, Timothy M. McPhillips, Eric Koesema, Daniel McMullan, Henry van den Bedem, Lukasz Jaroszewski, Scott A. Lesley, Adam Godzik, Qingping Xu, Raymond C. Stevens, John S. Kovarik, and Heath E. Klock
Subjects: Protein Folding, biology, Stereochemistry, Chemistry, Molecular Sequence Data, Fold (geology), Crystal structure, Crystallography, X-Ray, biology.organism_classification, Biochemistry, Phosphotransferases (Alcohol Group Acceptor), Bacterial Proteins, Structural Biology, Thermotoga maritima, Transferase, Amino Acid Sequence, Crystallization, Molecular Biology, Glycerate kinase
Published: 2006
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28. 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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29. 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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30. 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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31. 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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32. 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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33. 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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34. 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
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35. Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 Å resolution

Author: Slawomir K. Grzechnik, Henry van den Bedem, Bill West, Kevin Quijano, Guenter Wolf, Jamison Cambell, Eric Koesema, Heath E. Klock, Timothy M. McPhillips, Daniel McMullan, Kin Moy, Jaume M. Canaves, Andreas Kreusch, Rebecca Page, Eric Sims, Glen Spraggon, John Wooley, Fred Rezezadeh, John S. Kovarik, Marc-André Elsliger, Keith O. Hodgson, Alyssa Robb, Cathy Karlak, Xiaoping Dai, Jie Ouyang, Raymond C. Stevens, Andrew T. Morse, Juli Vincent, Frank von Delft, Said Eshagi, Eugenio Santelli, Carina Grittini, Xianhong Wang, Scott A. Lesley, Jeff Velasquez, Lukasz Jaroszewski, Robert Schwarzenbacher, Mitchell D. Miller, Qingping Xu, Ian A. Wilson, Ashley M. Deacon, Tanya Biorac, Adam Godzik, Linda S. Brinen, Peter Kuhn, and Ross Floyd
Subjects: Models, Molecular, Glycerophosphodiester phosphodiesterase, biology, Phosphoric Diester Hydrolases, Stereochemistry, Chemistry, Resolution (electron density), Reproducibility of Results, Phosphodiesterase, Crystal structure, Crystallography, X-Ray, biology.organism_classification, Biochemistry, Protein Structure, Secondary, Protein Structure, Tertiary, Structural Biology, Thermotoga maritima, Hydrolase, Crystallization, Molecular Biology
Published: 2004
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36. Crystal structure of an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 Å resolution

Author: Adam Godzik, Jie Ouyang, Xiaoping Dai, Bill West, Timothy M. McPhillips, Daniel McMullan, John S. Kovarik, Mitchell D. Miller, Guenter Wolf, Andreas Kreusch, Keith O. Hodgson, Rebecca Page, Marc-André Elsliger, Kin Moy, Robert Schwarzenbacher, Frank von Delft, Henry van den Bedem, Linda S. Brinen, Heath E. Klock, Jeff Velasquez, Raymond C. Stevens, Lukasz Jaroszewski, Peter Kuhn, Jaume M. Canaves, Heidi Erlandsen, Ross Floyd, Eric Koesema, Alyssa Robb, Andrew T. Morse, Juli Vincent, Ashley M. Deacon, Glen Spraggon, Slawomir K. Grzechnik, Ian A. Wilson, Xianhong Wang, Scott A. Lesley, John Wooley, Carina Grittini, and Kevin Quijano
Subjects: Physics, biology, Protein domain, Resolution (electron density), Synchrotron radiation, Particle accelerator, Crystal structure, biology.organism_classification, Biochemistry, law.invention, Crystallography, Structural Biology, law, Chemical physics, Thermotoga maritima, Molecular Biology
Published: 2004
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37. Crystal structure of uronate isomerase (TM0064) fromThermotoga maritimaat 2.85 Å resolution

Author: Keith O. Hodgson, Andreas Kreusch, Ian A. Wilson, Jie Ouyang, Henry van den Bedem, Lukasz Jaroszewski, Glen Spraggon, Xianhong Wang, Scott A. Lesley, Jaume M. Canaves, Chittibabu Guda, Alyssa Robb, Marc A. Elsliger, Bill West, Thomas L. Selby, Said Eshaghi, Raymond C. Stevens, Andrew T. Morse, Juli Vincent, Linda S. Brinen, Peter Kuhn, John S. Kovarik, Robert Schwarzenbacher, Ross Floyd, Adam Godzik, Daniel McMullan, John Wooley, Eric Koesema, Mitchell D. Miller, Jeff Velasquez, Ashley M. Deacon, Carina Grittini, Mark A. Miller, Slawomir K. Grzechnik, Kevin Rodrigues, Heath E. Klock, Xiaoping Dai, Kin Moy, Timothy M. McPhillips, Cathy Karlak, and Guenter Wolf
Subjects: Physics, Crystallography, biology, Structural Biology, Thermotoga maritima, Resolution (electron density), Crystal structure, Isomerase, biology.organism_classification, Molecular Biology, Biochemistry
Published: 2003
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38. Shotgun crystallization strategy for structural genomics: an optimized two-tiered crystallization screen against theThermotoga maritimaproteome

Author: Raymond C. Stevens, Glen Spraggon, Slawomir K. Grzechnik, Jaume M. Canaves, Andreas Kreusch, Rebecca Page, Peter Kuhn, and Scott A. Lesley
Subjects: Glycerol, Proteome, Shotgun, Genomics, Computational biology, Crystallography, X-Ray, Structural genomics, law.invention, Diffusion, Bacterial protein, Bacterial Proteins, X-Ray Diffraction, Structural Biology, law, Cloning, Molecular, Crystallization, Selenomethionine, Bacteria, biology, Chemistry, Temperature, General Medicine, Hydrogen-Ion Concentration, biology.organism_classification, Crystallography, Thermotoga maritima, Protein crystallization
Abstract: As the field of structural genomics continues to grow and new technologies are developed, novel strategies are needed to efficiently crystallize large numbers of protein targets, thus increasing output, not just throughput [Chayen & Saridakis (2002). Acta Cryst. D58, 921-927]. One strategy, developed for the high-throughput structure determination of the Thermotoga maritima proteome, is to quickly determine which proteins have a propensity for crystal formation followed by focused SeMet-incorporated protein crystallization attempts. This experimental effort has resulted in over 320 000 individual crystallization experiments. As such, it has provided one of the most extensive systematic data sets of commonly used crystallization conditions against a wide range of proteins to date. Analysis of this data shows that many of the original screening conditions are redundant, as all of the T. maritima proteins that crystallize readily could be identified using just 23% of the original conditions. It also shows that proteins that contain selenomethionine and are more extensively purified often crystallize in distinctly different conditions from those of their native less pure counterparts. Most importantly, it shows that the two-tiered strategy employed here is extremely successful for predicting which proteins will readily crystallize, as greater than 99% of the proteins identified as having a propensity to crystallize under non-optimal native conditions did so again as selenomethionine derivatives during the focused crystallization trials. This crystallization strategy can be adopted for both large-scale genomics programs and individual protein studies with multiple constructs and has the potential to significantly accelerate future crystallographic efforts.
Published: 2003
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39. Challenges of structural genomics: bioinformatics

Author: Slawomir K. Grzechnik, Lukasz Jaroszewski, Jie Ouyang, John Wooley, Jaume M. Canaves, Andrew T. Morse, Xianhong Wang, Adam Godzik, and Bill West
Subjects: Computer science, General Engineering, General Earth and Planetary Sciences, Center (algebra and category theory), Joint (building), Investment (macroeconomics), Bioinformatics, Data science, General Environmental Science, Structural genomics
Abstract: Structural genomics projects bring us many challenges, many of which were not anticipated when such initiatives were first planned and introduced. For instance, the huge amount of data generated within the project must be collected, displayed and analyzed to reap the benefits of this huge investment. Projects at the San Diego based Joint Center for Structural Genomics provide an example of how data can be managed within a structural genomics project, and how results can be presented on the web, as well as highlight some of the issues concerning data analysis.
Published: 2003
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40. Crystal structure of thy1, a thymidylate synthase complementing protein fromThermotoga maritimaat 2.25 Å resolution

Author: Susan S. Taylor, Xiaoping Dai, Peter Kuhn, H. Klock, Eric Koesema, Ross Floyd, Ian A. Wilson, Irimpan I. Mathews, Jie Ouyang, Mark A. Miller, Kin Moy, Guenter Wolf, Lukasz Jaroszewski, Slawomir K. Grzechnik, Andreas Kreusch, Cathy Karlak, John M. Kovarik, Jeff Velasquez, Raymond C. Stevens, Alyssa Robb, Xianhong Wang, Scott A. Lesley, Timothy M. McPhillips, Linda S. Brinen, Carina Grittini, Ashley M. Deacon, Glen Spraggon, Andrew T. Morse, Juli Vincent, Mitchell D. Miller, Said Eshaghi, John Wooley, Jaume M. Canaves, Chittibabu Guda, Bill West, Thomas L. Selby, Kevin Rodrigues, Daniel McMullan, Adam Godzik, Henry van den Bedem, Keith O. Hodgson, and Marc A. Elsliger
Subjects: biology, Biochemistry, Structural Biology, Thermotoga maritima, Resolution (electron density), biology.protein, Crystal structure, biology.organism_classification, Molecular Biology, Thymidylate synthase
Published: 2002
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41. 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

42. 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

43. 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

44. 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: 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

45. 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

46. 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

47. 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

48. Structural and Functional Characterizations of SsgB, a Conserved Activator of Developmental Cell Division in Morphologically Complex Actinomycetes

Author: 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

49. Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus

Author: 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

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: 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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