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1. Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima.

Author

Levisson M, Han GW, Deller MC, Xu Q, Biely P, Hendriks S, Ten Eyck LF, Flensburg C, Roversi P, Miller MD, McMullan D, von Delft F, Kreusch A, Deacon AM, van der Oost J, Lesley SA, Elsliger MA, Kengen SW, and Wilson IA

Subjects
Acetylesterase antagonists & inhibitors, Acetylesterase metabolism, Catalytic Domain, Computer Simulation, Crystallography, X-Ray, Enzyme Stability, Hot Temperature, Hydrogen-Ion Concentration, Models, Molecular, Protein Conformation, Reproducibility of Results, Serine chemistry, Serine metabolism, Acetylesterase chemistry, Thermotoga maritima enzymology
Abstract

TM0077 from Thermotoga maritima is a member of the carbohydrate esterase family 7 and is active on a variety of acetylated compounds, including cephalosporin C. TM0077 esterase activity is confined to short-chain acyl esters (C2-C3), and is optimal around 100°C and pH 7.5. The positional specificity of TM0077 was investigated using 4-nitrophenyl-β-D-xylopyranoside monoacetates as substrates in a β-xylosidase-coupled assay. TM0077 hydrolyzes acetate at positions 2, 3, and 4 with equal efficiency. No activity was detected on xylan or acetylated xylan, which implies that TM0077 is an acetyl esterase and not an acetyl xylan esterase as currently annotated. Selenomethionine-substituted and native structures of TM0077 were determined at 2.1 and 2.5 Å resolution, respectively, revealing a classic α/β-hydrolase fold. TM0077 assembles into a doughnut-shaped hexamer with small tunnels on either side leading to an inner cavity, which contains the six catalytic centers. Structures of TM0077 with covalently bound phenylmethylsulfonyl fluoride and paraoxon were determined to 2.4 and 2.1 Å, respectively, and confirmed that both inhibitors bind covalently to the catalytic serine (Ser188). Upon binding of inhibitor, the catalytic serine adopts an altered conformation, as observed in other esterase and lipases, and supports a previously proposed catalytic mechanism in which Ser hydroxyl rotation prevents reversal of the reaction and allows access of a water molecule for completion of the reaction., (Copyright © 2012 Wiley Periodicals, Inc.)

Published
2012
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2. Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity.

Author

Han GW, Ko J, Farr CL, Deller MC, Xu Q, Chiu HJ, Miller MD, Sefcikova J, Somarowthu S, Beuning PJ, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA, and Ondrechen MJ

Subjects
4-Nitrophenylphosphatase chemistry, 4-Nitrophenylphosphatase metabolism, Adenosine Diphosphate chemistry, Adenosine Diphosphate metabolism, Amino Acid Sequence, Binding Sites, Catalytic Domain, Computer Simulation, Crystallography, DNA Polymerase III chemistry, DNA Polymerase III metabolism, Histidinol-Phosphatase chemistry, Histidinol-Phosphatase metabolism, Models, Molecular, Molecular Sequence Data, Phylogeny, Reproducibility of Results, Structure-Activity Relationship, Bacterial Proteins chemistry, Bacterial Proteins metabolism, Bifidobacterium enzymology, Esterases chemistry, Esterases metabolism
Abstract

The crystal structures of an unliganded and adenosine 5'-monophosphate (AMP) bound, metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis are reported at 2.4 and 1.94 Å, respectively. Functional characterization of this enzyme was guided by computational analysis and then confirmed by experiment. The structure consists of a polymerase and histidinol phosphatase (PHP, Pfam: PF02811) domain with a second domain (residues 105-178) inserted in the middle of the PHP sequence. The insert domain functions in binding AMP, but the precise function and substrate specificity of this domain are unknown. Initial bioinformatics analyses yielded multiple potential functional leads, with most of them suggesting DNA polymerase or DNA replication activity. Phylogenetic analysis indicated a potential DNA polymerase function that was somewhat supported by global structural comparisons identifying the closest structural match to the alpha subunit of DNA polymerase III. However, several other functional predictions, including phosphoesterase, could not be excluded. Theoretical microscopic anomalous titration curve shapes, a computational method for the prediction of active sites from protein 3D structures, identified potential reactive residues in YP_910028.1. Further analysis of the predicted active site and local comparison with its closest structure matches strongly suggested phosphoesterase activity, which was confirmed experimentally. Primer extension assays on both normal and mismatched DNA show neither extension nor degradation and provide evidence that YP_910028.1 has neither DNA polymerase activity nor DNA-proofreading activity. These results suggest that many of the sequence neighbors previously annotated as having DNA polymerase activity may actually be misannotated., (Copyright © 2011 Wiley-Liss, Inc.)

Published
2011
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3. Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution.

Author

Das D, Kozbial P, Axelrod HL, Miller MD, McMullan D, Krishna SS, Abdubek P, Acosta C, Astakhova T, Burra P, Carlton D, Chen C, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA, Ernst D, Farr C, Feuerhelm J, Grzechnik A, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Johnson HA, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Sudek S, Tien H, Trame C, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacteriophages genetics, Crystallography, X-Ray, Databases, Genetic, Escherichia coli genetics, Molecular Sequence Data, Protein Conformation, Protein Multimerization, RNA-Binding Proteins genetics, Sequence Homology, Amino Acid, Bacteriophages chemistry, RNA-Binding Proteins chemistry
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
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4. Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 A resolution.

Author

Das D, Krishna SS, McMullan D, Miller MD, Xu Q, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA, Ernst D, Feuerhelm J, Grzechnik A, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Sefcovic N, Tien H, Trame CB, Trout CV, van den Bedem H, Weekes D, White A, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Motifs, Amino Acid Sequence, Bacterial Proteins metabolism, Crystallography, X-Ray, DNA metabolism, Dimerization, Molecular Sequence Data, Protein Binding, Protein Conformation, Protein Structure, Tertiary, Shewanella metabolism, Bacterial Proteins chemistry, Shewanella chemistry
Published
2009
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5. Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus.

Author

Xu Q, Rife CL, Carlton D, Miller MD, Krishna SS, Elsliger MA, Abdubek P, Astakhova T, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, McMullan D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, van den Bedem H, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Crystallization, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Conformation, Adenosine Triphosphatases chemistry, Archaeal Proteins chemistry, Sulfolobus solfataricus enzymology
Published
2009
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6. Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle fold.

Author

Kozbial P, Xu Q, Chiu HJ, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Carlton D, Clayton T, Deller M, Duan L, Elias Y, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Spraggon G, Trout CV, van den Bedem H, Weekes D, White A, Wolf G, Zubieta C, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, Molecular Sequence Data, Protein Structure, Secondary, Protein Structure, Tertiary, Bacterial Proteins chemistry, Protein Folding
Published
2008
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7. 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

Xu Q, Kozbial P, McMullan D, Krishna SS, Brittain SM, Ficarro SB, DiDonato M, Miller MD, Abdubek P, Axelrod HL, Chiu HJ, Clayton T, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Klock HE, Morse AT, Nigoghossian E, Paulsen J, Reyes R, Rife CL, van den Bedem H, White A, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
ADP-Ribosylation Factors genetics, ADP-Ribosylation Factors physiology, Amino Acid Sequence, Bacterial Proteins genetics, Bacterial Proteins physiology, Crystallography, X-Ray, Cytidine Deaminase physiology, Molecular Sequence Data, Protein Structure, Tertiary, Ribosomal Proteins genetics, Ribosomal Proteins physiology, Thermotoga maritima physiology, ADP-Ribosylation Factors chemistry, Bacterial Proteins chemistry, Cytidine Deaminase chemistry, Protein Folding, Ribosomal Proteins chemistry, Thermotoga maritima chemistry
Published
2008
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8. Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 A resolution.

Author

Axelrod HL, McMullan D, Krishna SS, Miller MD, Elsliger MA, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Binding Sites, Crystallization, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Thermotoga maritima enzymology, Hydroxymethyl and Formyl Transferases chemistry, Multienzyme Complexes chemistry, Nucleotide Deaminases chemistry
Published
2008
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9. Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.

Author

Zubieta C, Krishna SS, Kapoor M, Kozbial P, McMullan D, Axelrod HL, Miller MD, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Motifs, Amino Acid Sequence, Bacterial Proteins physiology, Bacteroides enzymology, Catalytic Domain, Crystallography, X-Ray, Molecular Sequence Data, Multienzyme Complexes physiology, Peroxidases metabolism, Protein Binding, Protein Structure, Secondary, Shewanella enzymology, Bacterial Proteins chemistry, Coloring Agents metabolism, Conserved Sequence, Heme metabolism, Multienzyme Complexes chemistry, Peroxidases chemistry, Protein Folding
Abstract

BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 A, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, alpha+beta ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein)., ((c) 2007 Wiley-Liss, Inc.)

Published
2007
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10. Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA.

Author

Zubieta C, Joseph R, Krishna SS, McMullan D, Kapoor M, Axelrod HL, Miller MD, Abdubek P, Acosta C, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Binding Sites, Crystallography, X-Ray, Molecular Sequence Data, Protein Binding, Shewanella enzymology, Bacterial Proteins chemistry, Bacterial Proteins metabolism, Coloring Agents metabolism, Heme metabolism, Multienzyme Complexes chemistry, Multienzyme Complexes metabolism, Peroxidases chemistry, Peroxidases metabolism
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., ((c) 2007 Wiley-Liss, Inc.)

Published
2007
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11. Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 angstroms resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate.

Author

Xu Q, Saikatendu KS, Krishna SS, McMullan D, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Miller MD, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Schwarzenbacher R, van den Bedem H, White A, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins chemistry, Bacterial Proteins physiology, Crystallography, X-Ray, Hydrolysis, Molecular Sequence Data, Organophosphates chemistry, Thioglycosides chemistry, Bacillus subtilis enzymology, Organophosphates metabolism, Phosphoric Monoester Hydrolases chemistry, Phosphoric Monoester Hydrolases physiology, Thioglycosides metabolism
Published
2007
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12. Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 angstroms resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases.

Author

Krishna SS, Tautz L, Xu Q, McMullan D, Miller MD, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Morse AT, Mustelin T, Nigoghossian E, Oommachen S, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Motifs, Amino Acid Sequence, Bacterial Proteins metabolism, Bacterial Proteins physiology, Binding Sites, Crystallography, X-Ray, Molecular Sequence Data, Phosphoric Monoester Hydrolases metabolism, Phosphoric Monoester Hydrolases physiology, Protein Structure, Secondary, Bacterial Proteins chemistry, Neisseria meningitidis enzymology, Phosphoric Monoester Hydrolases chemistry
Published
2007
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13. Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution.

Author

Zubieta C, Krishna SS, McMullan D, Miller MD, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, Deller M, DiDonato M, Duan L, Elsliger MA, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kumar A, Marciano D, Morse AT, Nigoghossian E, Oommachen S, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins chemistry, Crystallography, X-Ray, Dimerization, Haemophilus influenzae enzymology, Models, Molecular, Molecular Sequence Data, Protein Conformation, Bacillus cereus enzymology, Homoserine O-Succinyltransferase chemistry
Published
2007
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14. Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function.

Author

Premkumar L, Rife CL, Sri Krishna S, McMullan D, Miller MD, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Floyd R, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kovarik JS, Kreusch A, Levin I, McPhillips TM, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rezezadeh F, Rodionov D, Schwarzenbacher R, Spraggon G, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins genetics, Crystallography, X-Ray, Molecular Sequence Data, Repressor Proteins genetics, Sequence Analysis, DNA, Thermotoga maritima genetics, Bacterial Proteins chemistry, Models, Molecular, Repressor Proteins chemistry, Thermotoga maritima chemistry
Published
2007
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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

Xu Q, Krishna SS, McMullan D, Schwarzenbacher R, Miller MD, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, Spraggon G, Stevens RC, van den Bedem H, White A, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins isolation & purification, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Folding, Protein Structure, Secondary, Saccharomyces cerevisiae Proteins chemistry, Thermotoga maritima chemistry, ran GTP-Binding Protein chemistry, Bacterial Proteins chemistry, Thermotoga maritima enzymology
Published
2006
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16. Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution.

Author

Kosloff M, Han GW, Krishna SS, Schwarzenbacher R, Fasnacht M, Elsliger MA, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Feuerhelm J, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Jaroszewski L, Jin KK, Johnson H, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Levin I, McMullan D, Miller MD, Morse AT, Moy K, Nigoghossian E, Okach L, Oommachen S, Page R, Paulsen J, Quijano K, Reyes R, Rife CL, Sims E, Spraggon G, Sridhar V, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Agrobacterium tumefaciens chemistry, Agrobacterium tumefaciens cytology, Amino Acid Sequence, Bacterial Proteins classification, Crystallography, X-Ray, Dimerization, Glutathione Transferase classification, Models, Molecular, Molecular Sequence Data, Phylogeny, Protein Structure, Secondary, Agrobacterium tumefaciens enzymology, Bacterial Proteins chemistry, Glutathione Transferase chemistry
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., ((c) 2006 Wiley-Liss, Inc.)

Published
2006
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17. Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 A resolution.

Author

Han GW, Sri Krishna S, Schwarzenbacher R, McMullan D, Ginalski K, Elsliger MA, Brittain SM, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod H, Canaves JM, Chiu HJ, DiDonato M, Grzechnik SK, Hale J, Hampton E, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Miller MD, Morse AT, Moy K, Nigoghossian E, Oommachen S, Ouyang J, Paulsen J, Quijano K, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Wang X, West B, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Crystallization, Crystallography, X-Ray, Molecular Sequence Data, Sequence Alignment, Bacterial Proteins chemistry, Lipoproteins chemistry, Thermotoga maritima chemistry
Published
2006
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18. Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution.

Author

Xu Q, Schwarzenbacher R, Krishna SS, McMullan D, Agarwalla S, Quijano K, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Elsliger MA, Grittini C, Grzechnik SK, DiDonato M, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Miller MD, Moy K, Nigoghossian E, Paulsen J, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Animals, Binding Sites, Crystallization, Databases, Protein, Dioxygenases genetics, Dioxygenases metabolism, Metals chemistry, Mice, Models, Molecular, Molecular Sequence Data, Molecular Structure, Protein Binding, Protein Structure, Secondary, Protein Structure, Tertiary, Dioxygenases chemistry
Published
2006
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19. Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution.

Author

Mathews II, Krishna SS, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Binding Sites, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Structure, Quaternary, Protein Structure, Tertiary, Structural Homology, Protein, Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor chemistry, Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor metabolism, Thermotoga maritima enzymology
Published
2006
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20. Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold.

Author

Jin KK, Krishna SS, Schwarzenbacher R, McMullan D, Abdubek P, Agarwalla S, Ambing E, Axelrod H, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Feuerhelm J, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife C, Stevens RC, Spraggon G, van den Bedem H, Velasquez J, White A, Wolf G, Han GW, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins genetics, Binding Sites, Crystallography, X-Ray, Humans, Models, Molecular, Molecular Sequence Data, Peptidylprolyl Isomerase classification, Polyethylene Glycols, Protein Folding, Protein Structure, Quaternary, Protein Structure, Tertiary, Bacterial Proteins chemistry, Bacterial Proteins metabolism, Cyclophilins chemistry, Cyclophilins metabolism, Peptidylprolyl Isomerase chemistry, Peptidylprolyl Isomerase metabolism, Thermotoga maritima enzymology
Published
2006
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21. Crystal structure of virulence factor CJ0248 from Campylobacter jejuni at 2.25 A resolution reveals a new fold.

Author

Xu Q, Schwarzenbacher R, McMullan D, Abdubek P, Agarwalla S, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Hodgson KO, Wooley J, and Wilson IA

Subjects
Bacterial Proteins metabolism, Crystallography, X-Ray, Models, Molecular, Protein Folding, Protein Structure, Secondary, Virulence Factors metabolism, Bacterial Proteins chemistry, Campylobacter jejuni pathogenicity, Virulence Factors chemistry
Published
2006
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22. Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 A resolution reveals a new fold.

Author

Klock HE, Schwarzenbacher R, Xu Q, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Koesema E, Kreusch A, Kuhn P, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Rife C, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Hodgson KO, Wooley J, Lesley SA, and Wilson IA

Subjects
Animals, Conserved Sequence, Crystallography, X-Ray, Mice, Models, Molecular, Molecular Weight, Open Reading Frames, Protein Folding, Protein Structure, Secondary, Databases, Protein, Proteins chemistry
Published
2005
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23. Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 A resolution.

Author

Jaroszewski L, Schwarzenbacher R, McMullan D, Abdubek P, Agarwalla S, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Crystallization, Molecular Sequence Data, Zinc Fingers, Bacterial Proteins chemistry, Heat-Shock Proteins chemistry, Molecular Chaperones chemistry, Thermotoga maritima chemistry
Published
2005
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24. Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 A resolution reveals a new fold.

Author

Rife C, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, Dimerization, Molecular Sequence Data, Protein Folding, Bacterial Proteins chemistry, Models, Molecular, Pseudomonas putida, RNA-Binding Proteins chemistry
Published
2005
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25. Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 A resolution reveals a new fold.

Author

Rife C, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, DNA Gyrase metabolism, Dimerization, Molecular Sequence Data, Protein Folding, Bacterial Proteins chemistry, Models, Molecular, Thermotoga maritima enzymology
Published
2005
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26. Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution.

Author

Han GW, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Animals, Crystallography, X-Ray, Mice, Models, Molecular, Molecular Sequence Data, Protein Structure, Secondary, Sensitivity and Specificity, Apoenzymes chemistry, Endoribonucleases chemistry, RNA, Messenger metabolism
Published
2005
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27. Crystal structure of S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 A resolution reveals a new fold.

Author

Mathews I, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Miller MD, Moy K, Nigoghossian E, Ouyang J, Paulsen J, Quijano K, Reyes R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Crystallography, X-Ray methods, Isomerases metabolism, Ligands, Models, Molecular, Protein Conformation, Solvents, Isomerases chemistry, Protein Folding, Thermotoga maritima enzymology
Published
2005
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28. Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold.

Author

Levin I, Miller MD, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Biorac T, Cambell J, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Morse A, Moy K, Nigoghossian E, Ouyang J, Page R, Quijano K, Reyes R, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Zagnitko O, Hodgson KO, Wooley J, and Wilson IA

Subjects
Bacterial Proteins metabolism, Crystallography, X-Ray, Models, Molecular, Piperidones metabolism, Protein Conformation, Protein Folding, Bacterial Proteins chemistry, Thermotoga maritima enzymology
Published
2005
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29. Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor.

Author

Han GW, Schwarzenbacher R, Page R, Jaroszewski L, Abdubek P, Ambing E, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Nigoghossian E, Ouyang J, Paulsen J, Quijano K, Reyes R, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, White A, Wolf G, Xu Q, Zagnitko O, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, Electrons, Humans, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Stereoisomerism, Anabaena enzymology, Proteins chemistry, Transaminases chemistry
Published
2005
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30. Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution.

Author

Arndt JW, Schwarzenbacher R, Page R, Abdubek P, Ambing E, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Klock HE, Koesema E, Kreusch A, Kuhn P, Jaroszewski L, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Nigoghossian E, Ouyang J, Peti WS, Quijano K, Reyes R, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, White A, Wolf G, Xu Q, Zagnitko O, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Binding Sites, Computational Biology, Models, Molecular, Molecular Conformation, Molecular Sequence Data, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Software, Crystallography, X-Ray methods, Hydrolases chemistry, Saccharomyces cerevisiae metabolism, Saccharomyces cerevisiae Proteins chemistry, Serine chemistry
Published
2005
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