Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 Å resolution reveals a new fold

Proteins: Structure, Function and Genetics

Volumn 65, Issue 1, 2006, Pages 243-248

  Schwarzenbacher, Robert ^a,c   McMullan, Daniel ^a,d   Krishna, S Sri ^a,b,c   Xu, Qingping ^a,e   Miller, Mitchell D ^a,e   Canaves, Jaume M ^a,c   Elsliger, Marc André ^a,f   Floyd, Ross ^a,e   Grzechnik, Slawomir K ^a,c   Jaroszewski, Lukasz ^a,b,c   Klock, Heath E ^a,d   Koesema, Eric ^a,d   Kovarik, John S ^a,e   Kreusch, Andreas ^a,d   Kuhn, Peter ^a,f   McPhillips, Timothy M ^a,e   Morse, Andrew T ^a,c   Quijano, Kevin ^a,d   Spraggon, Glen ^a,d   Stevens, Raymond C ^a,f   Van Den Bedem, Henry ^a,e   Wolf, Guenter ^a,e   Hodgson, Keith O ^a,e   Wooley, John ^a,c   Deacon, Ashley M ^a,e   Godzik, Adam ^a,b,c   Lesley, Scott A ^a,d,f   Wilson, Ian A ^a,f   more..

^a Joint Center for Structural Genomics   (United States)

^b BURNHAM INSTITUTE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^e SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^f SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; GLYCERATE KINASE; PHOSPHOTRANSFERASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; CRYSTAL STRUCTURE; ENZYME ANALYSIS; ENZYME STRUCTURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; STRUCTURE ANALYSIS; THERMOTOGA MARITIMA; TM1585 GENE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; MOLECULAR SEQUENCE DATA; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); PROTEIN FOLDING; THERMOTOGA MARITIMA;

THERMOTOGA MARITIMA;

EID: 33748286212     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21058     Document Type: Article

References (25)

1. Ichihara A, Greenberg DM. Studies on the purification and properties of D-glyceric acid kinase of liver. J Biol Chem 1957;225: 949-958.
2. Doughty CC, Hayashi JA, Guenther HL. Purification and properties of D-glycerate 3-kinase from Escherichia coli. J Biol Chem 1966;241:568-572.
3. Cheek S, Ginalski K, Zhang H, Grishin NV. A comprehensive update of the sequence and structure classification of kinases. BMC Struct Biol 2005;5:6.
4. Chistoserdova L, Lidstrom ME. Identification and mutation of a gene required for glycerate kinase activity from a facultative methylotroph, Methylobacterium extorquens AM1. J Bacteriol 1997;179:4946-4948.
5. Crouzet P, Otten L. Sequence and mutational analysis of a tartrate utilization operon from Agrobacterium vitis. J Bacteriol 1995;177:6518-6526.
6. Bonham JR, Stephenson TJ, Carpenter KH, Rattenbury JM, Cromby CH, Pollitt RJ, Hull D. D(+)-glyceric aciduria: etiology and clinical consequences. Pediatr Res 1990;28:38-41.
7. Duran M, Beemer FA, Bruinvis L, Ketting D, Wadman SK. D-glyceric acidemia: an inborn error associated with fructose metabolism. Pediatr Res 1987;21:502-506.
8. Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, et al. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci USA 2002;99:11664-11669.
9. Santarsiero BD, Yegian DT, Lee CC, Spraggon G, Gu J, Scheibe D, Uber DC, Cornell EW, Nordmeyer RA, Kolbe WF, et al. An approach to rapid protein crystallization using nanodroplets. J Appl Crystallogr 2002;35:278-281.
10. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl Cryst 1993;26:795-800.
11. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994;50:760-763.
12. Terwilliger TC, Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 1999;55:849-861.
13. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004;60:2126-2132.
14. Winn MD, Murshudov GN, Papiz MZ. Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol 2003;374:300-321.
15. Yang H, Guranovic V, Dutta S, Feng Z, Berman HM, Westbrook JD. Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr D Biol Crystallogr 2004;60:1833-1839.
16. Davis IW, Murray LW, Richardson JS, Richardson DC. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 2004;32: W615-619.
17. Vaguine AA, Richelle J, Wodak SJ. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D Biol Crystallogr 1999;55:191-205.
18. Vriend G. WHAT IF: a molecular modeling and drug design program. J Mol Graph 1990;8:52-56, 29.
19. Henrick K, Thornton JM. PQS: a protein quaternary structure file server. Trends Biochem Sci 1998;23:358-361.
20. Matthews BW. Solvent content of protein crystals. J Mol Biol 1968;33:491-497.
21. Holm L, Sander C. Dali: a network tool for protein structure comparison. Trends Biochem Sci 1995;20:478-480.
22. Moser J, Schubert WD, Beier V, Bringemeier I, Jahn D, Heinz DW. V-shaped structure of glutamyl-tRNA reductase, the first enzyme of tRNA-dependent tetrapyrrole biosynthesis. Embo J 2001;20:6583-6590.
23. Schubert HL, Wilson KS, Raux E, Woodcock SC, Warren MJ. The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase. Nat Struct Biol 1998;5:585-592.
24. Kinch LN, Qi Y, Hubbard TJ, Grishin NV. CASP5 target classification. Proteins 2003;Suppl 6:340-351.
25. Tickle IJ, Laskowski RA, Moss DS. Error estimates of protein structure coordinates and deviations from standard geometry by full-matrix refinement of gammaB- and betaB2-crystallin. Acta Crystallogr D Biol Crystallogr 1998;54:243-252.