Characterization of dihydrodipicolinate reductase from Thermotoga maritima reveals evolution of substrate binding kinetics

Journal of Biochemistry

Volumn 143, Issue 5, 2008, Pages 617-623

  Pearce, F Grant ^a   Sprissler, Clara ^a   Gerrard, Juliet A ^a  

^a UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

Dihydrodipicolinate reductase; Lysine biosynthesis; Pyridine nucleotide specificity; Thermophilic enzymes; Thermotoga maritima

Indexed keywords

DIHYDRODIPICOLINATE; DIHYDRODIPICOLINATE REDUCTASE; PICOLINIC ACID DERIVATIVE;

ARTICLE; BINDING KINETICS; ENZYME ANALYSIS; ENZYME SUBSTRATE; EVOLUTION; NONHUMAN; THERMOTOGA MARITIMA;

BACTERIAL PROTEINS; BINDING SITES; DIHYDRODIPICOLINATE REDUCTASE; ENZYME STABILITY; EVOLUTION; KINETICS; MODELS, MOLECULAR; NAD; NADP; PROTEIN BINDING; TEMPERATURE; THERMOTOGA MARITIMA;

ESCHERICHIA COLI; MYCOBACTERIUM TUBERCULOSIS; THERMOTOGA MARITIMA;

EID: 43449113875     PISSN: 0021924X     EISSN: 17562651     Source Type: Journal    
DOI: 10.1093/jb/mvn012     Document Type: Article

References (30)

1. Coulter, C.V., Gerrard, J.A., Kraunsoe, J.A.E., and Pratt, A.J. (1999) Escherichia coli dihydrodipicolinate synthase and dihydrodipicolinate reductase: kinetic and inhibition studies of two putative herbicide targets. Pesticide Sci. 55, 887-895
2. Cox, R., Sutherland, A., and Vederas, J. (2000) Bacterial diaminopimelate metabolism as a target for antibiotic design. Bioorg. Med. Chem. 8, 843-871
3. Tamir, H. and Gilvarg, C. (1974) Dihydrodipicolinic acid reductase. J. Biol. Chem. 249, 3034-3040
4. Reddy, S.G., Sacchettini, J.C., and Blanchard, J.S. (1995) Expression, purification, and characterization of Escherichia coli dihydrodipicolinate reductase. Biochemistry 34, 3492-3501
5. Blickling, S., Renner, C., Laber, B., Pohlenz, H., Holak, T., and Huber, R. (1997) Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy. Biochemistry 36, 24-33
6. Reddy, S.G., Scapin, G., and Blanchard, J.S. (1996) Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes. Biochemistry 35, 13294-13302
7. Cirilli, M., Zheng, R., Scapin, G., and Blanchard, J.S. (2003) The three-dimensional structures of the Mycobacterium tuberculosis dihydrodipicolinate reductase-NADH-2,6-PDC and -NADPH-2,6-PDC complexes. Structural and mutagenic analysis of relaxed nucleotide specificity. Biochemistry 42, 10644-10650
8. Scapin, G., Reddy, S.G., Zheng, R., and Blanchard, J.S. (1997) Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate. Biochemistry 36, 15081-15088
9. Scapin, G., Blanchard, J.S., and Sacchettini, J.C. (1995) Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase. Biochemistry 34, 3502-3512
10. Achenbach-Richter, L., Gupta, R., Stetter, K.O., and Woese, C.R. (1989) Were the original Eubacteria thermophiles? Syst. Appl. Microbiol. 9, 34-39
11. Hudson, A.O., Bless, C., Macedo, P., Chatterjee, S.P., Singh, B.K., Gilvarg, C., and Leustek, T. (2005) Biosynthesis of lysine in plants: evidence for a variant of the known bacterial pathways. Biochim. Biophys. Acta 1721, 27-36
12. Paiva, A.M., Vanderwall, D.E., Blanchard, J.S., Kozarich, J.W., Williamson, J.M., and Kelly, T.M. (2001) Inhibitors of dihydrodipicolinate reductase, a key enzyme of the diaminopimelate pathway of Mycobacterium tuberculosis. Biochim Biophys Acta 1545, 67-77
13. Tsujimoto, N., Gunji, Y., Ogawa-Miyata, Y., Shimaoka, M., and Yasueda, H. (2006) L-Lysine biosynthetic pathway of Methylophilus methylotrophus and construction of an L-lysine producer. J. Biotechnol. 124, 327-337
14. Pearce, F.G., Perugini, M.A., McKerchar, H.J., and Gerrard, J.A. (2006) Dihydrodipicolinate synthase from Thermotoga maritima. Biochem. J. 400, 359-366
15. Bradford, M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248
16. Roberts, S.J., Morris, J.C., Dobson, R.C.J., and Gerrard, J.A. (2003) The preparation of (S)-aspartate semi-aldehyde appropriate for use in biochemical studies. Bioorg. Med. Chem. Lett. 13, 265-267
17. Nelson, K.E., Clayton, R.A., Gill, S.R., Gwinn, M.L., Dodson, R.J., Haft, D.H., Hickey, E.K., Peterson, J.D., Nelson, W.C., Ketchum, K.A., McDonald, L., Utterback, T.R., Malek, J.A., Linher, K.D., Garrett, M.M., Stewart, A.M., Cotton, M.D., Pratt, M.S., Phillips, C.A., Richardson, D., Heidelberg, J., Sutton, G.G., Fleischmann, R.D., Eisen, J.A., White, O., Salzberg, S.L., Smith, H.O., Venter, J.C., and Fraser, C.M. (1999) Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 399, 323-329
18. Ericsson, U.B., Hallberg, B.M., DeTitta, G.T., Dekker, N., and Nordlund, P. (2006) Thermofluor-based high-throughput stability optimization of proteins for structural studies. Anal. Biochem. 357, 289-298
19. Cornish-Bowden, A. (1999) Fundamentals of Enzyme Kinetics. Portland Press Ltd, London
20. Coulter, C.V., Gerrard, J.A., Kraunsoe, J.A.E., and Pratt, A.J. (1996) (S)-Aspartate semi-aldehyde: synthetic and structural studies. Tetrahedron 52, 7127-7136
21. Robinson-Rechavi, M., Alibes, A., and Godzik, A. (2006) Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima. J. Mol. Biol. 356, 547-557
22. Robinson-Rechavi, M. and Godzik, A. (2005) Structural genomics of Thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability. Structure 13, 857-860
23. Walden, H., Bell, G.S., Russell, R.J.M., Siebers, B., Hensel, R., and Taylor, G.L. (2001) Tiny TIM: a small, tetrameric, hyperthermostable triosephosphate isomerase. J. Mol. Biol. 306, 745-757
24. Matulis, D., Kranz, J.K., Salemme, F.R., and Todd, M.J. (2005) Thermodynamic stability of carbonic anhydrase: measurements of binding affinity and stoichiometry using ThermoFluor. Biochemistry 44, 5258-5266
25. Daniel, R.M. (1996) The upper limits of enzyme thermal stability. Enzyme Microb. Tech. 19, 74-79
26. Wrba, A., Schweiger, A., Schultes, V., Jaenicke, R., and Zavodszky, P. (1990) Extremely thermostable D-glyceraldehyde-3-phosphate dehydrogenase from the eubacterium Thermotoga maritima. Biochemistry 29, 7584-7592
27. Varley, P.G. and Pain, R.H. (1991) Relation between stability, dynamics and enzyme-activity in 3-phosphoglycerate kinases from yeast and Thermus thermophilus. J. Mol. Biol. 220, 531-538
28. Huber, R., Langworthy, T.A., Konig, H., Thomm, M., Woese, C.R., Sleytr, U.B., and Stetter, K.O. (1986) Thermotoga maritima sp represents a new genus of unique extremely thermophilic eubacteria growing up to 90 degrees C. Arch. Microbiol. 144, 324-333
29. Rodionov, D.A., Vitreschak, A.G., Mironov, A.A., and Gelfand, M.S. (2003) Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res. 31, 6748-6757
30. DeLano, W.L. (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org