Structural studies of thiamin monophosphate kinase in complex with substrates and products

Biochemistry

Volumn 47, Issue 12, 2008, Pages 3810-3821

  McCulloch, Kathryn M ^a   Kinsland, Cynthia ^a   Begley, Tadhg P ^a   Ealick, Steven E ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

THIAMIN MONOPHOSPHATE KINASE; THIAMIN PYROPHOSPHATE (TPP);

BINDING ENERGY; BIOSYNTHESIS; CATALYSIS; PHOSPHORYLATION; VITAMINS;

ENZYME ACTIVITY;

ADENOSINE TRIPHOSPHATE; PHOSPHOTRANSFERASE; THIAMIN MONOPHOSPHATE KINASE; THIAMINE; THIAMINE PHOSPHATE; UNCLASSIFIED DRUG;

AQUIFEX AEOLICUS; ARTICLE; BINDING SITE; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME MECHANISM; ENZYME PHOSPHORYLATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; NONHUMAN; PRIORITY JOURNAL;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; BACTERIA; BINDING SITES; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHOSPHOTRANSFERASES (PHOSPHATE GROUP ACCEPTOR); PROTEIN CONFORMATION; SEQUENCE ALIGNMENT;

AQUIFEX AEOLICUS;

EID: 41149144136     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi800041h     Document Type: Article

References (35)

1. Settembre, E., Begley, T. P., and Ealick, S. E. (2003) Structural biology of enzymes of the thiamin biosynthesis pathway. Curr. Opin. Struct. Biol. 13, 739-747.
2. Jordan, F. (2003) Current mechanistic understanding of thiamin diphosphate-dependent enzymatic reactions. Nat. Prod. Rep. 20, 184-201.
3. Begley, T. P., Downs, D. M., Ealick, S. E., McLafferty, F. W., Van Loon, A. P., Taylor, S., Campobasso, N., Chiu, H. J., Kinsland, C., Reddick, J. J., and Xi, J. (1999) Thiamin biosynthesis in prokaryotes. Arch. Microbiol. 171, 293-300.
4. Webb, E., and Downs, D. (1997) Characterization of thiL, encoding thiamin-monophosphate kinase, in Salmonella typhimurium. J. Biol. Chem. 272, 15702-15707.
5. Li, C., Kappock, T. J., Stubbe, J., Weaver, T. M., and Ealick, S. E. (1999) X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 Å resolution. Structure 7, 1155-1166.
6. Anand, R., Hoskins, A. A., Stubbe, J., and Ealick, S. E. (2004) Domain Organization of Salmonella typhimurium Formylglycinamide Ribonucleotide Amidotransferase Revealed by X-ray Crystallography. Biochemistry 43, 10328-10342.
7. Jayaraj, S., Reid, R., and Santi, D. V. (2005) GeMS: An advanced software package for designing synthetic genes. Nucleic Acids Res. 33, 3011-3016.
8. Kodumal, S. J., Patel, K. G., Reid, R., Menzella, H. G., Welch, M., and Santi, D. V. (2004) Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc. Natl. Acad. Sci. U.S.A. 101, 15573-15578.
9. Kodumal, S. J., and Santi, D. V. (2004) DNA ligation by selection. BioTechniques 37, 34.
10. Sambrook, J., Fritsch, G. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Guide, Cold Spring Harbor Laboratory Press, Plainview, NY.
11. Matthews, B. W. (1968) Solvent content of protein crystals. J. Mol. Biol. 33, 491-497.
12. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
13. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
14. Emsley, P., and Cowtan, K. (2004) Coot: Model-Building Tools fo Molecular Graphics. Acta Crystallogr. D60, 2126-2132.
15. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D54, 905-921.
16. DeLano, W. L. (2002) The PyMOL Molecular Graphics System, DeLano Scientific, San Carlos, CA.
17. Krissinel, E., and Henrick, K. (2005) Detection of Protein Assemblies in Crystals, CompLife 2005, pp 163-174, Springer-Verlag, Berlin.
18. Morar, M., Anand, R., Hoskins, A. A., Stubbe, J., and Ealick, S. E. (2006) Complexed structures of formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima describe a novel ATP binding protein superfamily. Biochemistry 45, 14880-14895.
19. Watanabe, S., Matsumi, R., Arai, T., Atomi, H., Imanaka, T., and Miki, K. (2007) Crystal structures of [NiFe] hydrogenase maturation proteins HypC, HypD, and HypE: Insights into cyanation reaction by thiol redox signaling. Mol. Cell 27, 29-40.
20. Holm, L., and Sander, C. (1998) Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 26, 316-319.
21. Blokesch, M., Paschos, A., Bauer, A., Reissmann, S., Drapal, N., and Bock, A. (2004) Analysis of the transcarbamoylation-dehydration reaction catalyzed by the hydrogenase maturation proteins HypF and HypE. Eur. J. Biochem. 271, 3428-3436.
22. Holm, L., and Park, J. (2000) DaliLite workbench for protein structure comparison. Bioinformatics 16, 566-567.
23. Madej, T., Gibrat, J. F., and Bryant, S. H. (1995) Threading a database of protein cores. Proteins 23, 356-369.
24. Sinha, S., Rappu, P., Lange, S. C., Mantsala, P., Zalkin, H., and Smith, J. L. (1999) Crystal structure of Bacillus subtilis YabJ, a purine regulatory protein and member of the highly conserved YjgF family. Proc. Natl. Acad. Sci. U.S.A. 96, 13074-13079.
25. Volz, K. (1999) A test case for structure-based functional assignment: The 1.2 Å crystal structure of the yjgF gene product from Escherichia coli. Protein Sci. 8, 2428-2437.
26. Malandrinos, G., Louloudi, M., and Hadjiliadis, N. (2006) Thiamine models and perspectives on the mechanism of action of thiamine-dependent enzymes. Chem. Soc. Rev. 35, 684-692.
27. Dyda, F., Furey, W., Swaminathan, S., Sax, M., Farrenkopf, B., and Jordan, F. (1993) Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4-Å resolution. Biochemistry 32, 6165-6170.
28. Wikner, C., Nilsson, U., Meshalkina, L., Udekwu, C., Lindqvist, Y., and Schneider, G. (1997) Identification of catalytically important residues in yeast transketolase. Biochemistry 36, 15643-15649.
29. Peapus, D. H., Chiu, H. J., Campobasso, N., Reddick, J. J., Begley, T. P., and Ealick, S. E. (2001) Structural characterization of the enzyme-substrate, enzyme-intermediate, and enzyme-product complexes of thiamin phosphate synthase. Biochemistry 40, 10103-10114.
30. Mullins, L. S., Hong, S.-B., Gibson, G. E., Walker, H., Stadtman, T. C., and Raushel, F. M. (1997) Identification of a Phosphorylated Enzyme Intermediate in the Catalytic Mechanism for Selenophosphate Synthetase. J. Am. Chem. Soc. 119, 6684-6685.
31. Walker, H., Ferretti, J. A., and Stadtman, T. C. (1998) Isotope exchange studies on the Escherichia coli selenophosphate synthetase mechanism. Proc. Natl. Acad. Sci. U.S.A. 95, 2180-2185.
32. Schendel, F. J., Mueller, E., Stubbe, J., Shiau, A., and Smith, J. M. (1989) Formylglycinamide ribonucleotide synthetase from Escherichia coli: Cloning, sequencing, overproduction, isolation, and characterization. Biochemistry 28, 2459-2471.
33. Prasher, D. C., Carr, M. C., Ives, D. H., Tsai, T. C., and Frey, P. A. (1982) Nucleoside phosphotransferase from barley. Characterization and evidence for ping pong kinetics involving phosphoryl enzyme. J. Biol. Chem. 257, 4931-4939.
34. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
35. Gouet, P., Courcelle, E., Stuart, D. I., and Metoz, F. (1999) ESPript: Analysis of multiple sequence alignments in PostScript. Bioinformatics 15, 305-308.