Search

Your search keyword '"Heath E Klock"' showing total 135 results
Start Over Author "Heath E Klock"
135 results on '"Heath E Klock"'

101. 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

102. 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

103. 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

104. 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

105. 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

106. 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

107. 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

108. 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

109. 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

110. 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

111. 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

112. 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

113. 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

114. 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

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

Author

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

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

116. Crystal structure of a tandem cystathionine-beta-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 A resolution

Author

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

Subjects
Models, Molecular, Crystallography, biology, Tandem, Resolution (electron density), Molecular Sequence Data, CBS domain, Cystathionine beta-Synthase, Crystal structure, biology.organism_classification, Biochemistry, Cystathionine beta synthase, Protein Structure, Secondary, Protein Structure, Tertiary, Bacterial Proteins, Structural Biology, Thermotoga maritima, biology.protein, Transferase, Amino Acid Sequence, Molecular Biology
Published
2004

117. Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution

Author

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

Subjects
Models, Molecular, biology, Chemistry, Molecular Sequence Data, Resolution (electron density), Saccharomyces cerevisiae, Crystal structure, Crystallography, X-Ray, biology.organism_classification, Biochemistry, Protein Structure, Secondary, Ureohydrolases, Protein Structure, Tertiary, Multienzyme Complexes, Structural Homology, Protein, Structural Biology, Hydrolase, Allantoicase, Amino Acid Sequence, Molecular Biology, Conserved Sequence
Published
2004

118. A scaleable and integrated crystallization pipeline applied to mining the Thermotoga maritima proteome

Author

Daniel McMullan, Scott A. Lesley, Michael DiDonato, Heath E. Klock, and Ashley M. Deacon

Subjects
Models, Molecular, Proteomics, Protein Folding, Proteome, Genomic data, Computational biology, Biology, Biochemistry, Structural genomics, Bacterial Proteins, Structural Biology, Genetics, Thermotoga maritima, Cloning, Molecular, General Medicine, Robotics, biology.organism_classification, Pipeline (software), Recombinant Proteins, Crystallography, Solubility, Fermentation, bacteria, Crystallization, Genome, Bacterial, Protein Structure Initiative
Abstract

The wealth of genomic data available for many organisms has set the stage for the next phase of structure—function analysis. High-throughput structural genomics is currently the method of choice for rapid analysis of protein structure—function relationships on a proteome-wide basis. The Joint Center for Structural Genomics (JCSG), established in 2000 under the NIH/NIGMS Protein Structure Initiative, has developed and implemented an integrated high-throughput structure pipeline and applied it in a 2-tiered approach to mining the proteome of the thermophilic bacterium Thermotoga maritima. In the first tier, the successful application of this integrated pipeline has resulted in the cloning and expression of 73% of the T. maritima proteome (1376 out of 1877 predicted genes), and has identified 465 proteins which produced crystal hits. These 465 proteins were compared with existing structural information and a subset of 269 targets were selected to process towards structure determination in a second tier effort. To date, the JCSG pipeline applied to the Thermotoga maritima proteome has resulted in 55 new structures and has identified 6 novel folds and continues to identify structures with novel features.

Published
2004

119. NMR for structural proteomics of Thermotoga maritima: screening and structure determination

Author

Kurt Wüthrich, T. Herrmann, Wolfgang Peti, Scott A. Lesley, Touraj Etezady-Esfarjani, and Heath E. Klock

Subjects
Proteomics, biology, General Medicine, biology.organism_classification, Biochemistry, Ribosome, Recombinant Proteins, Protein Structure, Tertiary, Folding (chemistry), Turn (biochemistry), Bacterial Proteins, Structural Biology, Ribosomal protein, Thermotoga maritima, Genetics, Proton NMR, Isoleucine, Nuclear Magnetic Resonance, Biomolecular
Abstract

This paper describes the NMR screening of 141 small (

Published
2004

120. Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution

Author

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

Subjects
chemistry.chemical_classification, Models, Molecular, Binding Sites, Chemistry, Stereochemistry, Resolution (electron density), Molecular Sequence Data, Crystal structure, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Protein Structure, Tertiary, Crystallography, Mice, Structural Biology, Oxidoreductase, Structural Homology, Protein, Animals, Amino Acid Sequence, Quinone Reductases, Oxidoreductases, Molecular Biology, NADP
Published
2004

121. Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 A resolution

Author

Xianhong Wang, Scott A. Lesley, Jie Ouyang, Timothy M. McPhillips, Marc-André Elsliger, Kevin Quijano, John S. Kovarik, Linda S. Brinen, Guenter Wolf, Ashley M. Deacon, Robert Schwarzenbacher, Kin Moy, Henry van den Bedem, Frank von Delft, John Wooley, Raymond C. Stevens, Glen Spraggon, Peter Kuhn, Alyssa Robb, Jeff Velasquez, Ross Floyd, Andrew T. Morse, Mitchell D. Miller, Juli Vincent, Jaume M. Canaves, Andreas Kreusch, Keith O. Hodgson, Rebecca Page, Xiaoping Dai, Slawomir K. Grzechnik, Bill West, Said Eshagi, Cathy Karlak, Ian A. Wilson, Carina Grittini, Eric Koesema, Adam Godzik, Daniel McMullan, Inna Levin, Lukasz Jaroszewski, Qingping Xu, and Heath E. Klock

Subjects
Models, Molecular, biology, Chemistry, Stereochemistry, Resolution (electron density), Reproducibility of Results, Isomerase, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Ribose-5-phosphate isomerase, Structural Biology, Thermotoga maritima, Crystallization, Molecular Biology, Aldose-Ketose Isomerases
Published
2004

122. Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution

Author

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

Subjects
Exonucleases, Models, Molecular, Protein Folding, Protein Conformation, Archaeal Proteins, Molecular Sequence Data, Crystal structure, Siphoviridae, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Viral Proteins, Protein structure, Structural Biology, Amino Acid Sequence, Molecular Biology, Peptide sequence, Binding Sites, Sequence Homology, Amino Acid, Resolution (electron density), Archaeoglobus fulgidus, Protein Structure, Tertiary, N-terminus, Crystallography, Protein folding, PIN domain
Published
2004

123. NMR structure determination of the hypothetical protein TM1290 from Thermotoga maritima using automated NOESY analysis

Author

Touraj, Etezady-Esfarjani, Torsten, Herrmann, Wolfgang, Peti, Heath E, Klock, Scott A, Lesley, and Kurt, Wüthrich

Subjects
Models, Molecular, Proteomics, Magnetic Resonance Spectroscopy, Bacterial Proteins, Protein Conformation, Amino Acid Motifs, Proteins, Thermotoga maritima, Algorithms, Protein Structure, Secondary, Software, Plasmids, Protein Structure, Tertiary
Published
2004

124. Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution

Author

Glen Spraggon, Slawomir K. Grzechnik, Andreas Kreusch, Rebecca Page, Kevin Quijano, Polat Abdubek, Jie Ouyang, Marc-André Elsliger, H.-J. Chiu, Cathy Karlak, Adam Godzik, Raymond C. Stevens, Alyssa Robb, Said Eshagi, Frank von Delft, Kin Moy, Tanja Biorac, Guenter Wolf, Andrew T. Morse, Juli Vincent, Linda S. Brinen, Heath E. Klock, Jaume M. Canaves, Carina Grittini, Robert Schwarzenbacher, John Wooley, Ashley M. Deacon, Daniel McMullan, Inna Levin, Peter Kuhn, Xiaoping Dai, Jamison Cambell, Ian A. Wilson, Ross Floyd, Eric Koesema, Mitchell D. Miller, Jeff Velasquez, Eileen Ambing, Xianhong Wang, Scott A. Lesley, Keith O. Hodgson, John S. Kovarik, Lukasz Jaroszewski, Mike DiDonato, Henry van den Bedem, Qingping Xu, Eric Hampton, Bill West, and Timothy M. McPhillips

Subjects
Models, Molecular, biology, Chemistry, Resolution (electron density), Molecular Sequence Data, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Crystallography, Bacterial Proteins, Structural Biology, Thermotoga maritima, Transferase, Amino Acid Sequence, Aspartate Aminotransferases, Molecular Biology, Peptide sequence
Published
2004

125. Crystal structure of an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 A resolution

Author

Heidi, Erlandsen, Jaume M, Canaves, Marc-André, Elsliger, Frank, von Delft, Linda S, Brinen, Xiaoping, Dai, Ashley M, Deacon, Ross, Floyd, Adam, Godzik, Carina, Grittini, Slawomir K, Grzechnik, Lukasz, Jaroszewski, Heath E, Klock, Eric, Koesema, John S, Kovarik, Andreas, Kreusch, Peter, Kuhn, Scott A, Lesley, Daniel, McMullan, Timothy M, McPhillips, Mitchell D, Miller, Andrew, Morse, Kin, Moy, Jie, Ouyang, Rebecca, Page, Alyssa, Robb, Kevin, Quijano, Robert, Schwarzenbacher, Glen, Spraggon, Raymond C, Stevens, Henry, van den Bedem, Jeff, Velasquez, Juli, Vincent, Xianhong, Wang, Bill, West, Guenter, Wolf, Keith O, Hodgson, John, Wooley, and Ian A, Wilson

Subjects
Models, Molecular, Bacterial Proteins, Genes, Bacterial, Molecular Sequence Data, Reproducibility of Results, Thermotoga maritima, Amino Acid Sequence, Crystallography, X-Ray, Protein Structure, Tertiary
Published
2004

126. Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution

Author

John Wooley, Xiaoping Dai, Glen Spraggon, Said Eshaghi, Keith O. Hodgson, Slawomir K. Grzechnik, Jaume M. Canaves, Mitchell D. Miller, Lukasz Jaroszewski, John S. Kovarik, Jie Ouyang, Eric Koesema, Timothy M. McPhillips, Adam Godzik, Frank von Delft, Kin Moy, Alyssa Robb, Andrew T. Morse, Juli Vincent, Jeff Velasquez, Raymond C. Stevens, Guenter Wolf, Ian A. Wilson, Andreas Kreusch, Peter Kuhn, Rebecca Page, Ross Floyd, Robert Schwarzenbacher, Marc A. Elsliger, Xianhong Wang, Scott A. Lesley, Ashley M. Deacon, Linda S. Brinen, Henry van den Bedem, Kevin Rodrigues, Bill West, Thomas L. Selby, Daniel McMullan, Carina Grittini, Mark A. Miller, Cathy Karlak, Chittibabu Guda, and Heath E. Klock

Subjects
Models, Molecular, Stereochemistry, Molecular Sequence Data, Alcohol oxidoreductase, Dehydrogenase, Crystal structure, Crystallography, X-Ray, Biochemistry, chemistry.chemical_compound, Bacterial Proteins, Structural Biology, Oxidoreductase, Iron-Binding Proteins, Thermotoga maritima, 1,3-Propanediol, Amino Acid Sequence, Molecular Biology, Alcohol dehydrogenase, chemistry.chemical_classification, biology, Resolution (electron density), Alcohol Dehydrogenase, biology.organism_classification, Alcohol Oxidoreductases, chemistry, biology.protein
Published
2004

127. Crystal structure of uronate isomerase (TM0064) from Thermotoga maritima at 2.85 A resolution

Author

Robert, Schwarzenbacher, Jaume M, Canaves, Linda S, Brinen, Xiaoping, Dai, Ashley M, Deacon, Marc A, Elsliger, Said, Eshaghi, Ross, Floyd, Adam, Godzik, Carina, Grittini, Slawomir K, Grzechnik, Chittibabu, Guda, Lukasz, Jaroszewski, Cathy, Karlak, Heath E, Klock, Eric, Koesema, John S, Kovarik, Andreas, Kreusch, Peter, Kuhn, Scott A, Lesley, Daniel, McMullan, Timothy M, McPhillips, Mark A, Miller, Mitchell D, Miller, Andrew, Morse, Kin, Moy, Jie, Ouyang, Alyssa, Robb, Kevin, Rodrigues, Thomas L, Selby, Glen, Spraggon, Raymond C, Stevens, Henry, van den Bedem, Jeff, Velasquez, Juli, Vincent, Xianhong, Wang, Bill, West, Guenter, Wolf, Keith O, Hodgson, John, Wooley, and Ian A, Wilson

Subjects
Models, Molecular, Molecular Structure, Thermotoga maritima, Crystallography, X-Ray, Aldose-Ketose Isomerases, Protein Structure, Tertiary
Published
2003

128. Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution

Author

Peter, Kuhn, Scott A, Lesley, Irimpan I, Mathews, Jaume M, Canaves, Linda S, Brinen, Xiaoping, Dai, Ashley M, Deacon, Marc A, Elsliger, Said, Eshaghi, Ross, Floyd, Adam, Godzik, Carina, Grittini, Slawomir K, Grzechnik, Chittibabu, Guda, Keith O, Hodgson, Lukasz, Jaroszewski, Cathy, Karlak, Heath E, Klock, Eric, Koesema, John M, Kovarik, Andreas T, Kreusch, Daniel, McMullan, Timothy M, McPhillips, Mark A, Miller, Mitchell, Miller, Andrew, Morse, Kin, Moy, Jie, Ouyang, Alyssa, Robb, Kevin, Rodrigues, Thomas L, Selby, Glen, Spraggon, Raymond C, Stevens, Susan S, Taylor, Henry, van den Bedem, Jeff, Velasquez, Juli, Vincent, Xianhong, Wang, Bill, West, Guenter, Wolf, John, Wooley, and Ian A, Wilson

Subjects
Models, Molecular, Thermotoga maritima, Thymidylate Synthase, Crystallography, X-Ray, Sensitivity and Specificity
Published
2002

129. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline

Author

Chittibabu Guda, Timothy M. McPhillips, I.I. Mathews, Tanya Shin, Adam Godzik, Jaume M. Canaves, Andreas Kreusch, Marc-André Elsliger, Peter G. Schultz, M. Miller, John Wooley, Alyssa Robb, Lukasz Jaroszewski, Mark A. Miller, Juli Vincent, Daniel McMullan, Raymond C. Stevens, Linda S. Brinen, Peter Kuhn, Heath E. Klock, Daniel Scheibe, Thomas L. Selby, Ian A. Wilson, Keith O. Hodgson, Ashley M. Deacon, Susan S. Taylor, Scott A. Lesley, and Glen Spraggon

Subjects
Models, Molecular, Multidisciplinary, biology, Proteome, Protein Conformation, Pipeline (computing), Computational biology, Biological Sciences, biology.organism_classification, Molecular biology, Aquatic organisms, Structural genomics, Open Reading Frames, Protein structure, Thermotoga maritima, bacteria, Cloning, Molecular, Throughput (business), Genome, Bacterial, Protein Structure Initiative
Abstract

Structural genomics is emerging as a principal approach to define protein structure–function relationships. To apply this approach on a genomic scale, novel methods and technologies must be developed to determine large numbers of structures. We describe the design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga maritima . By using this pipeline, we successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes (73%) and have identified crystallization conditions for 432 proteins, comprising 23% of the T. maritima proteome. Representative structures from TM0423 glycerol dehydrogenase and TM0449 thymidylate synthase-complementing protein are presented as examples of final outputs from the pipeline.

Published
2002

130. Structural Analysis of Papain-Like NlpC/P60 Superfamily Enzymes with a Circularly Permuted Topology Reveals Potential Lipid Binding Sites

Author

Lukasz Jaroszewski, Adam Godzik, Mitchell D. Miller, Mark W. Knuth, Marc-André Elsliger, Neil D. Rawlings, Qingping Xu, Scott A. Lesley, Hsiu-Ju Chiu, Heath E. Klock, Ian A. Wilson, Ashley M. Deacon, and Sussman, Joel L

Subjects
Models, Molecular, Protein Data Bank (RCSB PDB), lcsh:Medicine, Ligands, Biochemistry, Conserved sequence, Protein structure, Models, Catalytic Domain, Papain, lcsh:Science, Peptide sequence, Conserved Sequence, chemistry.chemical_classification, 0303 health sciences, Multidisciplinary, Fatty Acids, 030302 biochemistry & molecular biology, Genomics, Circular permutation in proteins, Enzymes, Infectious Diseases, Hydrophobic and Hydrophilic Interactions, Research Article, Biotechnology, General Science & Technology, Lipoproteins, Molecular Sequence Data, Biophysics, Biology, Structural genomics, 03 medical and health sciences, Bacillus cereus, Bacterial Proteins, Chemical Biology, Humans, Amino Acid Sequence, Binding site, 030304 developmental biology, Binding Sites, Prevention, lcsh:R, Computational Biology, Molecular, Lipid Metabolism, Enzyme, chemistry, Enzyme Structure, Biocatalysis, Structural Genomics, lcsh:Q
Abstract

NlpC/P60 superfamily papain-like enzymes play important roles in all kingdoms of life. Two members of this superfamily, LRAT-like and YaeF/YiiX-like families, were predicted to contain a catalytic domain that is circularly permuted such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus. These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeF/YiiX-like family from Bacillus cereus in complex with lysine. The structure, which adopts a ligand-induced, "closed" conformation, confirms the circular permutation of catalytic residues. A comparative analysis of other related protein structures within the NlpC/P60 superfamily is presented. Permutated NlpC/P60 enzymes contain a similar conserved core and arrangement of catalytic residues, including a Cys/His-containing triad and an additional conserved tyrosine. More surprisingly, permuted enzymes have a hydrophobic S1 binding pocket that is distinct from previously characterized enzymes in the family, indicative of novel substrate specificity. Further analysis of a structural homolog, YiiX (PDB 2if6) identified a fatty acid in the conserved hydrophobic pocket, thus providing additional insights into possible function of these novel enzymes.

Published
2011
Full Text
View/download PDF

132. Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 Å resolution.

Author

Robert Schwarzenbacher, Frank von Delft, Jaume M. Canaves, Linda S. Brinen, Xiaoping Dai, Ashley M. Deacon, Marc A. Elsliger, Said Eshaghi, Ross Floyd, Adam Godzik, Carina Grittini, Slawomir K. Grzechnik, Chittibabu Guda, Lukasz Jaroszewski, Cathy Karlak, Heath E. Klock, Eric Koesema, John S. Kovarik, Andreas Kreusch, and Peter Kuhn

Published
2004
Full Text
View/download PDF

133. Structure of a Virulence Regulatory Factor CvfB Reveals a Novel Winged Helix RNA Binding Module

Author

Chikara Kaito, Adam Godzik, Hsiu-Ju Chiu, Scott A. Lesley, Ian A. Wilson, Herbert L. Axelrod, Mark W. Knuth, Shinya Miyazaki, Yasuhiko Matsumoto, Qingping Xu, Kazuhisa Sekimizu, Ashley M. Deacon, M.A. Elsliger, Mitchell D. Miller, Heath E. Klock, and Carol L. Farr

Subjects
Riboswitch, Staphylococcus aureus, MICROBIO, Protein Conformation, PROTEINS, 5.8S ribosomal RNA, Molecular Sequence Data, RNA-binding protein, Winged Helix, Biology, Article, 03 medical and health sciences, Hemolysin Proteins, Structural Biology, Nucleic Acids, Amino Acid Sequence, Molecular Biology, 030304 developmental biology, Helix-Turn-Helix Motifs, 0303 health sciences, Complement C3 Convertase, Alternative Pathway, Sequence Homology, Amino Acid, Virulence, 030306 microbiology, RNA, RNA-Binding Proteins, Non-coding RNA, Cell biology, Protein Structure, Tertiary, S1 domain, Kinetics, Biochemistry, Sequence motif, Protein Binding
Abstract

SummaryCvfB is a conserved regulatory protein important for the virulence of Staphylococcus aureus. We show here that CvfB binds RNA. The crystal structure of the CvfB ortholog from Streptococcus pneumoniae at 1.4 Å resolution reveals a unique RNA binding protein that is formed from a concatenation of well-known structural modules that bind nucleic acids: three consecutive S1 RNA binding domains and a winged helix (WH) domain. The third S1 and the WH domains are required for cooperative RNA binding and form a continuous surface that likely contributes to the RNA interaction. The WH domain is critical to CvfB function and contains a unique sequence motif. Thus CvfB represents a novel assembly of modules for binding RNA.

Full Text
View/download PDF

134. Bacterial Pleckstrin Homology Domains: A Prokaryotic Origin for the PH Domain

Author

Lukasz Jaroszewski, Dustin C. Ernst, Keith O. Hodgson, Lian Duan, Tamara Astakhova, Abhinav Kumar, Tiffany Wooten, Michelle Chiu, Julie Feuerhelm, Edward Nigoghossian, Daniel McMullan, Gye Won Han, Qingping Xu, Christine B Trame, Linda Okach, Debanu Das, Herbert L. Axelrod, Polat Abdubek, Heath E. Klock, Carol L. Farr, Mitchell D. Miller, Sanjay Krishna, Alex Bateman, Henry van den Bedem, Anna Grzechnik, David Marciano, Thomas Clayton, Marc C. Deller, Connie Chen, Christopher L. Rife, Natasha Sefcovic, John Wooley, Constantina Bakolitsa, Kevin K. Jin, Hsiu-Ju Chiu, Amanda Nopakun, Marc André Elsliger, Andrew T. Morse, Dennis Carlton, Ian A. Wilson, Christina Puckett, Adam Godzik, Ashley M. Deacon, Kyle Ellrott, Joanna C Grant, Robert D. Finn, Dana Weekes, Piotr Kozbial, Henry J Tien, Mark W. Knuth, Ron Reyes, and Scott A. Lesley

Subjects
Models, Molecular, asu, asymmetric unit, Protein Data Bank (RCSB PDB), SSRL, Stanford Synchrotron Radiation Lightsource, Crystallography, X-Ray, Protein Structure, Secondary, chemistry.chemical_compound, PH, Pleckstrin homology, Structural Biology, Pleckstrin homology (PH) domain, Conserved Sequence, 0303 health sciences, 030302 biochemistry & molecular biology, bacterial PH domain (PHb), Pleckstrin homology domain, Eukaryotic Cells, Biochemistry, Domain (ring theory), TCEP, higher-order symmetry, DUF1696, domain of unknown function family 1696, lipids (amino acids, peptides, and proteins), VPS36, vacuolar protein sorting protein 36, Protein Binding, Protein family, Surface Properties, Stereochemistry, Molecular Sequence Data, PTB, phosphotyrosine binding, protein assembly, Biology, Ring (chemistry), Article, TEV, tobacco etch virus, Structural genomics, Evolution, Molecular, 03 medical and health sciences, TCEP, tris(2-carboxyethyl)phosphine–HCl, Bacterial Proteins, PDB, Protein Data Bank, MAD, multiwavelength anomalous diffraction, ALS, Advanced Light Source, Amino Acid Sequence, Protein Structure, Quaternary, PIPE, Polymerase Incomplete Primer Extension, protein evolution, Molecular Biology, PEG, polyethylene glycol, 030304 developmental biology, Binding Sites, Bacteria, Sequence Homology, Amino Acid, biology.organism_classification, Protein Structure, Tertiary, JCSG, Joint Center for Structural Genomics, Prokaryotic Cells, chemistry, PHb, bacterial PH domain, Sequence Alignment
Abstract

Pleckstrin homology (PH) domains have been identified only in eukaryotic proteins to date. We have determined crystal structures for three members of an uncharacterized protein family (Pfam PF08000), which provide compelling evidence for the existence of PH-like domains in bacteria (PHb). The first two structures contain a single PHb domain that forms a dome-shaped, oligomeric ring with C5 symmetry. The third structure has an additional helical hairpin attached at the C-terminus and forms a similar but much larger ring with C12 symmetry. Thus, both molecular assemblies exhibit rare, higher-order, cyclic symmetry but preserve a similar arrangement of their PHb domains, which gives rise to a conserved hydrophilic surface at the intersection of the β-strands of adjacent protomers that likely mediates protein–protein interactions. As a result of these structures, additional families of PHb domains were identified, suggesting that PH domains are much more widespread than originally anticipated. Thus, rather than being a eukaryotic innovation, the PH domain superfamily appears to have existed before prokaryotes and eukaryotes diverged.

Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results