Author: "Canaves, JM" - Searchworks@Jio Institute Digital Library Search Results

2. Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution.

Author: Mathews II, McMullan D, Miller MD, Canaves JM, Elsliger MA, Floyd R, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, McPhillips TM, Morse AT, Quijano K, Rife CL, Schwarzenbacher R, Spraggon G, Stevens RC, van den Bedem H, Weekes D, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA
Subjects: Amino Acid Sequence, Crystallography, Molecular Sequence Data, Protein Conformation, Sequence Homology, Amino Acid, Phosphotransferases (Alcohol Group Acceptor) chemistry, Thermotoga maritima enzymology
Published: 2008
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3. 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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4. Crystal structure of a transcription regulator (TM1602) from Thermotoga maritima at 2.3 A resolution.

Author: Weekes D, Miller MD, Krishna SS, McMullan D, McPhillips TM, Acosta C, Canaves JM, Elsliger MA, Floyd R, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Morse AT, Quijano K, Spraggon G, van den Bedem H, Wolf G, 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, DNA-Binding Proteins chemistry, Thermotoga maritima chemistry, Transcription Factors chemistry
Published: 2007
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5. 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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6. 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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7. 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: DiDonato M, Krishna SS, Schwarzenbacher R, McMullan D, Agarwalla S, Brittain SM, Miller MD, Abdubek P, Ambing E, Axelrod HL, Canaves JM, Chiu HJ, Deacon AM, Duan L, Elsliger MA, Godzik A, Grzechnik SK, Hale J, Hampton E, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, 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, Xu Q, Hodgson KO, Wooley J, and Wilson IA
Subjects: Acid Phosphatase isolation & purification, Amino Acid Sequence, Binding Sites, Clostridium acetobutylicum chemistry, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Folding, Acid Phosphatase chemistry, Clostridium acetobutylicum enzymology
Published: 2006
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8. Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 A resolution reveals a new fold.

Author: Schwarzenbacher R, McMullan D, Krishna SS, Xu Q, Miller MD, Canaves JM, Elsliger MA, Floyd R, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, McPhillips TM, Morse AT, Quijano K, Spraggon G, Stevens RC, van den Bedem H, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA
Subjects: Amino Acid Sequence, Bacterial Proteins chemistry, Crystallization, Crystallography, X-Ray, Molecular Sequence Data, Protein Folding, Phosphotransferases (Alcohol Group Acceptor) chemistry, Thermotoga maritima enzymology
Published: 2006
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9. Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from Thermotoga maritima at 1.90 A resolution.

Author: Mathews II, Krishna SS, Schwarzenbacher R, McMullan D, Jaroszewski L, Miller MD, Abdubek P, Agarwalla S, Ambing E, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Grzechnik SK, Hale J, Hampton E, Haugen J, Jin KK, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Levin I, 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, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA
Subjects: Amino Acid Sequence, Bacterial Proteins chemistry, Crystallization, Crystallography, X-Ray, Molecular Sequence Data, Protein Structure, Quaternary, Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor chemistry, Thermotoga maritima enzymology
Published: 2006
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10. 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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11. 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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12. 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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13. 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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14. 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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15. 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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16. 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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17. 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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18. 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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19. 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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20. 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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21. 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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22. Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold.

Author: Xu Q, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hampton E, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Reyes R, Robb A, 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, Zagnitko O, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Binding Sites, Crystallization, Crystallography, X-Ray, Enzyme Stability, Models, Chemical, Models, Molecular, Molecular Conformation, Molecular Sequence Data, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Ammonia-Lyases chemistry, Thermotoga maritima enzymology
Published: 2005
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23. 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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24. 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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25. High-throughput protein production for X-ray crystallography and use of size exclusion chromatography to validate or refute computational biological unit predictions.

Author: McMullan D, Canaves JM, Quijano K, Abdubek P, Nigoghossian E, Haugen J, Klock HE, Vincent J, Hale J, Paulsen J, and Lesley SA
Subjects: Chromatography, Gel methods, Computational Biology instrumentation, Protein Conformation, Bacterial Proteins chemistry, Bacterial Proteins isolation & purification, Computational Biology methods, Crystallography, X-Ray methods, Proteomics methods, Thermotoga maritima genetics
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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26. Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics.

Author: Canaves JM, Page R, Wilson IA, and Stevens RC
Subjects: Amino Acid Sequence, Amino Acids chemistry, Bacterial Proteins isolation & purification, Crystallography, X-Ray, Isoelectric Point, Open Reading Frames, Protein Conformation, Protein Sorting Signals, Thermotoga maritima genetics, Bacterial Proteins analysis, Proteome analysis, Thermotoga maritima chemistry
Abstract: Cost and time reduction are two of the driving forces in the development of new strategies for protein crystallization and subsequent structure determination. Here, we report the analysis of the Thermotoga maritima proteome, in which we compare the proteins that were successfully expressed, purified and crystallized versus the rest of the proteome. This set of almost 500 proteins represents one of the largest, internally consistent, protein expression and crystallization datasets available. The analysis shows that individual parameters, such as isoelectric point, sequence length, average hydropathy, low complexity regions (SEG), and combinations of these biophysical properties for crystallized proteins define a distinct subset of the T. maritima proteome. The distribution profiles of the various biophysical properties in the expression/crystallization set are then used to extract rules to improve target selection and improve the efficiency and output of structural genomics, as well as general structural biology efforts.
Published: 2004
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27. Crystal structure of a tandem cystathionine-beta-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 A resolution.

Author: Miller MD, Schwarzenbacher R, von Delft F, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Crystallography, Models, Molecular, Molecular Sequence Data, Protein Structure, Secondary, Protein Structure, Tertiary, Bacterial Proteins chemistry, Cystathionine beta-Synthase chemistry, Thermotoga maritima enzymology
Published: 2004
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28. Circular dichroism spectra of human hemoglobin reveal a reversible structural transition at body temperature.

Author: Artmann GM, Burns L, Canaves JM, Temiz-Artmann A, Schmid-Schönbein GW, Chien S, and Maggakis-Kelemen C
Subjects: Body Temperature, Hemoglobin A analysis, Hemoglobin A radiation effects, Hemoglobin, Sickle analysis, Hemoglobin, Sickle radiation effects, Humans, Phase Transition radiation effects, Protein Conformation radiation effects, Protein Denaturation radiation effects, Protons, Circular Dichroism, Hemoglobin A chemistry, Hemoglobin, Sickle chemistry, Hot Temperature
Abstract: Previously we have shown that human red blood cells (RBCs) undergo a sudden change from blocking to passing through a 1.3+/-0.2-microm micropipette when applying an aspiration pressure of 2.3 kPa at a critical transition temperature (Tc = 36.4+/-0.3 degrees C). Low-shear viscosity measurements suggested that changes in the molecular properties of hemoglobin might be responsible for this effect. To evaluate structural changes in hemoglobin at the critical temperature, we have used circular dichroism (CD) spectroscopy. The thermal denaturation curves of human hemoglobin A (HbA) and hemoglobin S (HbS) upon heating between 25 and 60 degrees C were non-linear and showed accelerated denaturation between 35 and 39 degrees C with a midpoint at 37.2+/-0.6 degrees C. The transition was reversible below 39 degrees C and independent of solution pH (pH 6.8-7.8). It was also independent of the oxygenation state of hemoglobin, since a sample that was extensively deoxygenated with N2 showed a similar transition by CD. These findings suggest that a structural change in hemoglobin may enable the cellular passage phenomenon as well as the temperature-dependent decrease in viscosity of RBC solutions.
Published: 2004
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29. Crystal structure of an orphan protein (TM0875) from Thermotoga maritima at 2.00-A resolution reveals a new fold.

Author: Bakolitsa C, Schwarzenbacher R, McMullan D, Brinen LS, Canaves JM, Dai X, Deacon AM, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Multiprotein Complexes, Protein Structure, Secondary, Sequence Homology, Structural Homology, Protein, Bacterial Proteins chemistry, Thermotoga maritima chemistry
Published: 2004
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30. Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution.

Author: Levin I, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Biorac T, Cambell J, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Reyes R, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Animals, Binding Sites, Crystallography, X-Ray, Mice, Models, Molecular, Molecular Sequence Data, NADP metabolism, Oxidoreductases metabolism, Protein Structure, Secondary, Protein Structure, Tertiary, Quinone Reductases chemistry, Structural Homology, Protein, Oxidoreductases chemistry
Published: 2004
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31. Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution.

Author: Jaroszewski L, Schwarzenbacher R, von Delft F, McMullan D, Brinen LS, Canaves JM, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Levin I, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Reyes R, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Binding Sites, Crystallization, Manganese analysis, Models, Molecular, Molecular Sequence Data, Multiprotein Complexes, Oxidoreductases chemistry, Protein Structure, Secondary, Protein Structure, Tertiary, Structural Homology, Protein, Bacterial Proteins chemistry, Thermotoga maritima chemistry
Published: 2004
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32. Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution.

Author: Xu Q, Schwarzenbacher R, Page R, Sims E, Abdubek P, Ambing E, Biorac T, Brinen LS, Cambell J, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Quijano K, Reyes R, Rezezadeh F, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Conserved Sequence, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Multienzyme Complexes, Protein Structure, Secondary, Protein Structure, Tertiary, Structural Homology, Protein, Saccharomyces cerevisiae enzymology, Ureohydrolases chemistry
Published: 2004
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33. Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution.

Author: McMullan D, Schwarzenbacher R, Jaroszewski L, von Delft F, Klock HE, Vincent J, Quijano K, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Koesema E, Kreusch A, Kuhn P, Levin I, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Reyes R, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Lesley SA, and Wilson IA
Subjects: Amino Acid Sequence, Binding Sites, Conserved Sequence, Crystallization, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Sequence Data, Protein Structure, Secondary, Structural Homology, Protein, Bacterial Proteins chemistry, Thermotoga maritima enzymology
Published: 2004
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34. Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 A resolution.

Author: Heine A, Canaves JM, von Delft F, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Page R, Robb A, Rodrigues K, Schwarzenbacher R, Selby TL, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Bacterial Proteins metabolism, Binding Sites, Crystallography, X-Ray, Cysteine Synthase metabolism, Ligands, Models, Molecular, Molecular Sequence Data, Phosphates metabolism, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Bacterial Proteins chemistry, Cysteine Synthase chemistry, Thermotoga maritima enzymology
Published: 2004
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35. Crystal structure of a methionine aminopeptidase (TM1478) from Thermotoga maritima at 1.9 A resolution.

Author: Spraggon G, Schwarzenbacher R, Kreusch A, McMullan D, Brinen LS, Canaves JM, Dai X, Deacon AM, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kuhn P, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Rezezadeh F, Robb A, Sims E, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Lesley SA, and Wilson IA
Subjects: Amino Acid Sequence, Binding Sites, Crystallography, X-Ray, Methionyl Aminopeptidases, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Structure, Tertiary, Aminopeptidases chemistry, Bacterial Proteins chemistry, Thermotoga maritima enzymology
Published: 2004
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36. Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution.

Author: Levin I, Schwarzenbacher R, Page R, Abdubek P, Ambing E, Biorac T, Brinen LS, Campbell J, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Quijano K, Reyes R, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Binding Sites, Crystallography, X-Ray, Exonucleases chemistry, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Folding, Protein Structure, Secondary, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Siphoviridae enzymology, Viral Proteins chemistry, Archaeal Proteins chemistry, Archaeoglobus fulgidus chemistry
Published: 2004
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37. Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 A resolution.

Author: Schwarzenbacher R, von Delft F, Jaroszewski L, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Bacterial Proteins genetics, Bacterial Proteins metabolism, Carboxy-Lyases genetics, Carboxy-Lyases metabolism, Crystallography, X-Ray, Ligands, Models, Molecular, Molecular Sequence Data, Multigene Family, Oxalates metabolism, Protein Conformation, Protein Structure, Secondary, Proteome, Recombinant Fusion Proteins chemistry, Thermotoga maritima genetics, Bacterial Proteins chemistry, Carboxy-Lyases chemistry, Thermotoga maritima enzymology
Published: 2004
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38. Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution.

Author: Santelli E, Schwarzenbacher R, McMullan D, Biorac T, Brinen LS, Canaves JM, Cambell J, Dai X, Deacon AM, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA
Subjects: Crystallization, Crystallography, X-Ray, Models, Molecular, Protein Structure, Secondary, Protein Structure, Tertiary, Reproducibility of Results, Phosphoric Diester Hydrolases chemistry, Thermotoga maritima enzymology
Published: 2004
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39. Crystal structure of a ribose-5-phosphate isomerase RpiB (TM1080) from Thermotoga maritima at 1.90 A resolution.

Author: Xu Q, Schwarzenbacher R, McMullan D, von Delft F, Brinen LS, Canaves JM, Dai X, Deacon AM, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, and Wilson IA
Subjects: Crystallization, Crystallography, X-Ray, Models, Molecular, Protein Structure, Secondary, Reproducibility of Results, Aldose-Ketose Isomerases chemistry, Thermotoga maritima enzymology
Published: 2004
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40. Predicted role for the archease protein family based on structural and sequence analysis of TM1083 and MTH1598, two proteins structurally characterized through structural genomics efforts.

Author: Canaves JM
Subjects: Amino Acid Motifs, Amino Acid Sequence, Animals, Archaea chemistry, Archaea genetics, Bacteria chemistry, Bacteria genetics, Binding Sites, Computational Biology, Conserved Sequence, Gene Expression Profiling, Humans, Models, Molecular, Molecular Chaperones chemistry, Molecular Chaperones genetics, Molecular Chaperones metabolism, Molecular Sequence Data, Multigene Family, Open Reading Frames genetics, Protein Structure, Tertiary, Proteins genetics, Proteomics, Sequence Alignment, Sequence Homology, Structure-Activity Relationship, Genomics, Proteins chemistry, Proteins metabolism, Structural Homology, Protein
Abstract: Recently, the structures of two proteins belonging to the archease family, TM1083 from Thermotoga maritima and MTH1598 from Methanobacterium thermoautotrophicum, have been solved independently by two Protein Structure Initiative structural genomics pilot centers using X-ray crystallography and NMR, respectively. The archease protein family is a good example of one of the paradoxes of structural genomics: Approximately one third of protein structures produced by structural genomics centers have no known function and are still annotated as "hypothetical proteins" in the Protein Data Bank. In the case of archeases, despite the existence of two protein structures and abundant sequence information, there is still no function assigned to this protein family. Here, our group predicts, based on structural similarity, sequence conservation, and gene context analyses, that members of this protein family might function as chaperones or modulators of proteins involved in DNA/RNA processing. The conservation of genomic context for this protein family is constant from Archaea and Bacteria to humans, and suggests that unannotated open reading frames contiguous to them could be novel RNA/DNA binding proteins., (Copyright 2004 Wiley-Liss, Inc.)
Published: 2004
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41. PCR primer selection tool optimized for high-throughput proteomics and structural genomics.

Author: Canaves JM, Morse A, and West B
Subjects: DNA Primers chemical synthesis, Database Management Systems, Genomics methods, Information Storage and Retrieval, Quality Control, User-Computer Interface, DNA Primers chemistry, DNA Primers genetics, Polymerase Chain Reaction methods, Proteomics methods, Sequence Analysis, DNA methods, Software
Published: 2004
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42. Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution.

Author: Spraggon G, Schwarzenbacher R, Kreusch A, Lee CC, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kuhn P, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Lesley SA, and Wilson IA
Subjects: Amino Acid Sequence, Crystallography, X-Ray, Molecular Sequence Data, Bacterial Proteins chemistry, Models, Molecular, Peptide Synthases chemistry, Thermotoga maritima enzymology
Published: 2004
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43. Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution.

Author: Schwarzenbacher R, Jaroszewski L, von Delft F, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Crystallography, X-Ray, Molecular Sequence Data, Aspartate Aminotransferases chemistry, Bacterial Proteins chemistry, Models, Molecular, Thermotoga maritima enzymology
Published: 2004
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44. Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 A resolution.

Author: Schwarzenbacher R, Jaroszewski L, von Delft F, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Crystallography, X-Ray, Dimerization, Molecular Sequence Data, Bacterial Proteins chemistry, Models, Molecular, Pentosyltransferases chemistry, Thermotoga maritima enzymology
Published: 2004
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45. Crystal structure of a phosphoribosylaminoimidazole mutase PurE (TM0446) from Thermotoga maritima at 1.77-A resolution.

Author: Schwarzenbacher R, Jaroszewski L, von Delft F, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Crystallization, Crystallography, X-Ray, Intramolecular Transferases metabolism, Models, Molecular, Molecular Sequence Data, Protein Conformation, Reproducibility of Results, Imidazoles metabolism, Intramolecular Transferases chemistry, Thermotoga maritima enzymology
Published: 2004
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46. Conformational differences among solution structures of the type Ialpha, IIalpha and IIbeta protein kinase A regulatory subunit homodimers: role of the linker regions.

Author: Vigil D, Blumenthal DK, Heller WT, Brown S, Canaves JM, Taylor SS, and Trewhella J
Subjects: Animals, Cattle, Cyclic AMP chemistry, Cyclic AMP pharmacology, Cyclic AMP-Dependent Protein Kinase RIIalpha Subunit, Cyclic AMP-Dependent Protein Kinase RIIbeta Subunit, Cyclic AMP-Dependent Protein Kinase RIalpha Subunit, Cyclic AMP-Dependent Protein Kinase RIbeta Subunit, Evolution, Molecular, Models, Molecular, Protein Conformation drug effects, Protein Isoforms chemistry, Protein Structure, Tertiary, Solutions, X-Ray Diffraction, Cyclic AMP-Dependent Protein Kinases chemistry, Protein Subunits chemistry
Abstract: The regulatory (R) subunits of the cAMP-dependent protein kinase (protein kinase A or PKA) are multi-domain proteins responsible for conferring cAMP-dependence and localizing PKA to specific subcellular locations. There are four isoforms of the R subunit in mammals that are similar in molecular mass and domain organization, but clearly serve different biological functions. Although high-resolution structures are available for the cAMP-binding domains and dimerization/docking domains of two isoforms, there are no high-resolution structures of any of the intact R subunit homodimer isoforms. The results of small-angle X-ray scattering studies presented here indicate that the RIalpha, RIIalpha, and RIIbeta homodimers differ markedly in overall shape, despite extensive sequence homology and similar molecular masses. The RIIalpha and RIIbeta homodimers have very extended, rod-like shapes, whereas the RIalpha homodimer likely has a compact Y-shape. Based on a comparison of the R subunit sequences, we predict that the linker regions are the likely cause of these large differences in shape among the isoforms. In addition, we show that cAMP binding does not cause large conformational changes in type Ialpha or IIalpha R subunit homodimers, suggesting that the activation of PKA by cAMP involves only local conformational changes in the R subunits.
Published: 2004
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47. Crystal structure of an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 A resolution.

Author: Erlandsen H, Canaves JM, Elsliger MA, von Delft F, Brinen LS, Dai X, Deacon AM, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Robb A, Quijano K, Schwarzenbacher R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Bacterial Proteins genetics, Crystallography, X-Ray, Genes, Bacterial genetics, Models, Molecular, Molecular Sequence Data, Protein Structure, Tertiary, Reproducibility of Results, Thermotoga maritima genetics, Bacterial Proteins chemistry, Thermotoga maritima chemistry
Published: 2004
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48. Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution.

Author: Schwarzenbacher R, von Delft F, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA
Subjects: Amino Acid Sequence, Bacterial Proteins genetics, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, PII Nitrogen Regulatory Proteins, Protein Structure, Secondary, Reproducibility of Results, Thermotoga maritima genetics, Bacterial Proteins chemistry, Signal Transduction, Thermotoga maritima chemistry
Published: 2004
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49. Balanol analogues probe specificity determinants and the conformational malleability of the cyclic 3',5'-adenosine monophosphate-dependent protein kinase catalytic subunit.

Author: Akamine P, Madhusudan, Brunton LL, Ou HD, Canaves JM, Xuong NH, and Taylor SS
Subjects: Amino Acid Sequence, Animals, Binding Sites, Crystallography, X-Ray, Cyclic AMP-Dependent Protein Kinase Catalytic Subunits, Cyclic AMP-Dependent Protein Kinases antagonists & inhibitors, Hydrophobic and Hydrophilic Interactions, Isoenzymes antagonists & inhibitors, Isoenzymes chemistry, Mice, Molecular Sequence Data, Peptide Fragments antagonists & inhibitors, Peptide Fragments chemistry, Protein Binding, Protein Conformation, Protein Structure, Tertiary, Protein Subunits antagonists & inhibitors, Swine, Thermodynamics, Azepines chemistry, Catalytic Domain, Cyclic AMP-Dependent Protein Kinases chemistry, Enzyme Inhibitors chemistry, Hydroxybenzoates chemistry, Mitosporic Fungi chemistry, Protein Subunits chemistry
Abstract: The protein kinase family is a prime target for therapeutic agents, since unregulated protein kinase activities are linked to myriad diseases. Balanol, a fungal metabolite consisting of four rings, potently inhibits Ser/Thr protein kinases and can be modified to yield potent inhibitors that are selective-characteristics of a desirable pharmaceutical compound. Here, we characterize three balanol analogues that inhibit cyclic 3',5'-adenosine monophosphate-dependent protein kinase (PKA) more specifically and potently than calcium- and phospholipid-dependent protein kinase (PKC). Correlation of thermostability and inhibition potency suggests that better inhibitors confer enhanced protection against thermal denaturation. Crystal structures of the PKA catalytic (C) subunit complexed to each analogue show the Gly-rich loop stabilized in an "intermediate" conformation, disengaged from important phosphoryl transfer residues. An analogue that perturbs the PKA C-terminal tail has slightly weaker inhibition potency. The malleability of the PKA C subunit is illustrated by active site residues that adopt alternate rotamers depending on the ligand bound. On the basis of sequence homology to PKA, a preliminary model of the PKC active site is described. The balanol analogues serve to test the model and to highlight differences in the active site local environment of PKA and PKC. The PKA C subunit appears to tolerate balanol analogues with D-ring modifications; PKC does not. We attribute this difference in preference to the variable B helix and C-terminal tail. By understanding the details of ligand binding, more specific and potent inhibitors may be designed that differentiate among closely related AGC protein kinase family members.
Published: 2004
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50. Crystal structure of an iron-containing 1,3-propanediol dehydrogenase (TM0920) from Thermotoga maritima at 1.3 A resolution.

Author: Schwarzenbacher R, von Delft F, Canaves JM, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Page R, Robb A, Rodrigues K, Selby TL, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, and Wilson IA
Subjects: Alcohol Dehydrogenase, Amino Acid Sequence, Crystallography, X-Ray, Molecular Sequence Data, Alcohol Oxidoreductases chemistry, Bacterial Proteins chemistry, Iron-Binding Proteins chemistry, Models, Molecular, Thermotoga maritima enzymology
Published: 2004
Full Text: View/download PDF

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