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1. 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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2. 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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3. 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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4. 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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5. 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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6. 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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7. Identification of coumarin derivatives as a novel class of allosteric MEK1 inhibitors

Author

Xiang-ju Gu, Vicki Zhou, Justin Haugen, Scott A. Lesley, Heath E. Klock, Yi Liu, Shifeng Pan, Nathanael S. Gray, Shulin Han, Michael Hornsby, Daniel McMullan, and Jeremy S. Caldwell

Subjects
Models, Molecular, Phosphopeptides, MAPK/ERK pathway, Protein Conformation, Stereochemistry, Clinical Biochemistry, Allosteric regulation, MAP Kinase Kinase 1, Pharmaceutical Science, Biochemistry, chemistry.chemical_compound, Allosteric Regulation, Coumarins, Drug Discovery, Humans, Enzyme Inhibitors, Phosphorylation, Extracellular Signal-Regulated MAP Kinases, Protein kinase A, Molecular Biology, chemistry.chemical_classification, Binding Sites, biology, Organic Chemistry, Coumarin, In vitro, Kinetics, Enzyme, chemistry, Enzyme inhibitor, biology.protein, Molecular Medicine, Signal transduction
Abstract

A homogenous TR-FRET-based in vitro coupling assay for the MAP3Ks-MEK1-ERK2 kinase cascade was established and was used to screen for inhibitors of the ERK/MAPK pathway. A series of coumarin derivatives were identified from the screen. These compounds potently inhibit the activation of the unactivated human MEK1 by upstream MAP3Ks (including BRAF and COT), but do not inhibit the activity of the activated MEK1. In addition, the potency of these compounds in inhibiting MEK1 activation is not affected by varying the ATP concentration, suggesting that these inhibitors are not competitive with ATP. As expected, the coumarin compounds potently inhibit LPS-induced TNFalpha production and ERK phosphorylation in THP-1 cells, with the most potent compound having an IC(50) of 90nM. Molecular modeling studies suggest that these coumarins bind to an allosteric site in the inactive conformation of MEK1. This site has been shown to be utilized by the biarylamine series of MEK inhibitors such as PD318088. Very interestingly, the identified coumarin derivatives are almost identical to a series of inhibitors recently reported that block LPS-induced TNFalpha production. Our findings have therefore raised the possibility that other naturally occurring or synthetic coumarins with anti-cancer and anti-inflammatory activities might exert their biological function through the inhibition of MEK1.

Published
2005
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8. 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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9. High-throughput Protein Production for X-ray Crystallography and Use of Size Exclusion Chromatography to Validate or Refute Computational Biological Unit Predictions

Author

Justin Haugen, Heath E. Klock, Joanna Hale, Juli Vincent, Edward Nigoghossian, Polat Abdubek, Daniel McMullan, Scott A. Lesley, Jaume M. Canaves, Kevin Quijano, and Jessica Paulsen

Subjects
Proteomics, Computational model, Protein Conformation, Size-exclusion chromatography, Computational Biology, General Medicine, Computational biology, Biology, Crystallography, X-Ray, biology.organism_classification, Biochemistry, Structural genomics, Crystallography, Protein structure, Bacterial Proteins, Structural Biology, Thermotoga maritima, Protein purification, Proteome, Chromatography, Gel, Genetics, Protein quaternary structure
Abstract

The production of large numbers of highly purified proteins for X-ray crystallography is a significant bottleneck in structural genomics. At the Joint Center for Structural Genomics (JCSG; http://www.jcsg.org), specific automated protein expression, purification, and analytical methods are being utilized to study the proteome of Thermotoga maritima. Anion exchange and size exclusion chromatography (SEC), intended for the production of highly purified proteins, have been automated and the procedures are described here in detail. Analytical SEC has been included as a standard quality control test. A biological unit (BU) is the macromolecule that has been proven or is presumed to be functional. Correct assignment of BUs from protein structures can be difficult. BU predictions obtained via the Protein Quaternary Structure file server (PQS; http://pqs.ebi.ac.uk/) were compared to SEC data for 16 representative T. maritima proteins whose structures were solved at the JCSG, revealing an inconsistency in five cases. Herein, we report that SEC can be used to validate or disprove PQS-derived oligomeric models. A substantial amount of associated SEC and structural data should enable us to use certain PQS parameters to gauge the accuracy of these computational models and to generally improve their predictions.

Published
2005
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10. 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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11. 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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12. 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

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

Author

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

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

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

Author

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

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

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

Published
2006

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

Author

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

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

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

Author

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

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

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

Published
2006

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

Author

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

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

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

Author

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

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

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

Author

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

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

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

Author

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

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

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

Author

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

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

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

Author

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

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

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

Author

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

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

24. Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold

Author

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

Subjects
Models, Molecular, Protein Folding, biology, ATP synthase, Chemistry, Stereochemistry, Protein Conformation, Fold (geology), Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Bacterial Proteins, Structural Biology, Thermotoga maritima, biology.protein, Molecular Biology, Indigoidine, Piperidones
Published
2005

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

Author

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

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

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

Author

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

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

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