Direct Evidence for a Glutamate Switch Necessary for Substrate Recognition: Crystal Structures of Lysine ε-Aminotransferase (Rv3290c) from Mycobacterium tuberculosis H37Rv

Journal of Molecular Biology

Volumn 362, Issue 5, 2006, Pages 877-886

  Mani Tripathi, Sarvind ^a   Ramachandran, Ravishankar ^a  

^a CENTRAL DRUG RESEARCH INSTITUTE   (India)

Author keywords

crystal structure; Glu243 switch; lysine aminotransferase; Mycobacterium tuberculosis; ketoglutarate

Indexed keywords

2 OXOGLUTARIC ACID; ARGININE; GLUTAMIC ACID; LYSINE; LYSINE 6 AMINOTRANSFERASE; PYRIDOXAMINE PHOSPHATE;

AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME BINDING; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; MOLECULAR CLONING; MUTATIONAL ANALYSIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL;

MYCOBACTERIUM TUBERCULOSIS;

EID: 33748605299     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.08.019     Document Type: Article

References (43)

1. Fujii T., Narita T., Agematu H., Agata N., and Isshiki K. Characterization of L-lysine 6-aminotransferase and its structural gene from Flavobacterium lutescens IFO3084. J. Biochem. 128 (2000) 391-397
2. Tobin M.B., Kovacevic S., Madduri K., Hoskins J.A., Skatrud P.L., Vining L.C., et al. Localization of the lysine ε-aminotransferase (lat) and δ-(L-α-aminoadipyl)-L-cysteinyl-d-valine synthetase(pcbAB) genes from Streptomyces clavuligerus and production of lysine ε-aminotransferase activity in Escherichia coli. J. Bacteriol. 173 (1991) 6223-6229
3. Mehta P.K., Hale T.I., and Christen P. Aminotransferases: demonstration of homology and division into evolutionary subgroups. Eur. J. Biochem. 214 (1993) 549-561
4. 6-dependent enzymes. Curr. Opin. Struct. Biol. 8 (1998) 759-769
5. Grishin N.V., Phillips M.A., and Goldsmith E.J. Modeling of the spatial structure of eukaryotic decarboxylases. Protein Sci. 4 (1995) 1291-1304
6. Hayashi H. Pyridoxal enzymes: mechanistic diversity and uniformity. J. Biochem. 118 (1995) 463-473
7. Shen B.W., Henning M., Hohenester E., Jansonius J.N., and Schirmer T. Crystal structure of human recombinant ornithine aminotransferase. J. Mol. Biol. 277 (1998) 81-102
8. Storici P., Biase D.D., Bossa F., Bruno S., Mozzarelli A., Peneff C., et al. Structures of γ-aminobutyric acid (GABA) aminotransferase, a pyridoxal 5′-phosphate, and [2Fe-2S] cluster containing enzymes, complexed with γ-ethynyl-GABA and with the antiepilepsy drug vigabatrin. J. Biol. Chem. 279 (2004) 363-373
9. John R.A. Pyridoxal phosphate-dependent enzymes. Biochim. Biophys. Acta 1248 (1995) 81-96
10. Velick S.F., and Vavra J. A kinetic and equilibrium analysis of the glutamic oxaloacetate transaminase mechanism. J. Biol. Chem. 237 (1962) 2109-2122
11. 1-piperidine-6-carboxylic acid. Biochemistry 7 (1968) 4102-4109
12. Soda K., and Misono H. L-lysine α-ketoglutarate aminotransferase. II. Purification, crystallization, and properties. Biochemistry 7 (1968) 4110-4119
13. Betts J.C., Luckey P.T., Robb L.C., McAdam R.A., and Duncan K. Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol. Microbiol. 43 (2002) 717-731
14. Voskuil M.I., Visconti K.C., and Schoolnik G.K. Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low oxygen dormancy. Tuberculosis 84 (2004) 218-227
15. Voskuil M.I. Mycobacterium tuberculosis gene expression during environment conditions associated with latency. Tuberculosis 84 (2004) 138-143
16. Khetan A., Hu W., and Sherman D.H. Heterogeneous distribution of lysine 6-aminotransferase during cephamycin C biosynthesis in Streptomyces clavuligerus demonstrated using green fluorescent protein as receptor. Microbiology 146 (2000) 1869-1880
17. Yagi T., Misono H., Tanizawa K., Yoshimura T., and Soda K. Characterization of the half and overall reactions catalyzed by L-lysine: 2-oxoglutarate 6-aminotransferase. J. Biochem. 109 (1991) 61-65
18. Hammer T., and Bode R. Purification and characterization of an inducible L-lysine: 2-oxoglutarate 6-aminotransferase from candida utilis. J. Basic Microbiol. 32 (1992) 21-27
19. Kern B.A., Hendlin D., and Inamine E. L-lysine ε-aminotransferase involved in cephamycin C synthesis in Streptomyces lactamdurans. Antimicrob. Agents Chemother. 17 (1980) 679-685
20. Tripathi S.M., and Ramachandran R. Overexpression, purification and crystallization of lysine ε-aminotransferase (Rv3290c) from Mycobacterium tuberculosis H37Rv. Acta Crystallog. sect. F 62 (2006) 572-575
21. Goto M., Omi R., Miyahara I., Hosono A., Mizuguchi H., Hayashi H., et al. Crystal structures of glutamine:phenylpyruvate aminotransferase from Thermus thermophilus HB8. J. Biol. Chem. 279 (2004) 16518-16525
22. Goto M., Miyahara I., Hayashi H., Kagamiyama H., and Hirotsu K. Crystal structure of branched-chain amino acid aminotrasnferase complexed with glutamate and glutarate: true reaction intermediate and double substrate recognition of the enzyme. Biochemistry 42 (2003) 3725-3733
23. Ford G.C., Eichele G., and Jansonius J.N. Three-Dimensional structure of a Pyridoxal-phosphate-dependent enzyme, mitochondrial aspartate aminotransferase. Proc. Natl Acad. Sci. USA 77 (1980) 2559-2563
24. Christen P., and Metzler D.E. Transaminases (1985), Wiley, New York
25. Jansonius J.N., and Vincent M.G. Structural basis for catalysis by aspartate aminotransferase. In: Jurnak F.A., and Mc Pherson A. (Eds). Biological Macromolecules and Assemblies vol 3 (1987), Wiley, New York 187-285
26. Storici P., Capitani G., Muller R., Schirmer T., and Jansonius J.N. Crystal structure of human ornithine aminotransferase complexed with the highly specific and potent inhibitor 5-fluoromethylornithine. J. Mol. Biol. 285 (1999) 297-309
27. Liu W., Peterson P.E., Langston J.A., Jin X., Zhou X., Fisher A.J., and Toney M.D. Kinetic and crystallographic analysis of active site mutants of Escherichia coli γ-aminobutyrate aminotransferase. Biochemistry 44 (2005) 2982-2992
28. Markova M., Peneff C., Hewlins M.J.E., Schirmer T., and John R.A. Detreminants of substrate specificity in ω-aminotransferases. J. Biol. Chem. 280 (2005) 36409-36416
29. Islam M.M., Goto M., Miyahara I., Ikushiro H., Hirotsu K., and Hayashi H. Binding of C5-dicarboxylic substrate to aspartate aminotransferase: implication for the conformational change at the transaldimination step. Biochemistry 44 (2005) 8218-8229
30. Islam M.M., Hayashi H., and Kagamiyama H. Reaction of aspartate aminotransferase with C5-dicarboxylic acids: comparison with the reaction with C4-dicarboxylic acids. J. Biochem. 134 (2003) 277-285
31. Haruyama K., Nakai T., Miyahara I., Hirotsu K., Mizuguchi H., Hayashi H., and Kagamiyama H. Structures of Escherichia coli histidinol-phosphate aminotransferase and its complexes with histidinol-phosphate and N-(5′-phosphopyridoxyl)-L-glutamate: double substrate recognition of the enzyme. Biochemistry 40 (2001) 4633-4644
32. Fernandez F.J., Vega M.C., Lehman F., Sandmeier E., Gehring H., Christen P., and Wilmanns M. Structural studies of the catalytic reaction pathway of a hyperthermophilic histidinol-phosphate aminotransferase. J. Biol. Chem. 279 (2004) 21478-21488
33. Leslie A.G.W. (1992). Joint CCP4 + ESF-EAMCB Newsletter on Protein Crystallography, No. 26.
34. Evans P.R. Proceedings of the CCP4 Study Weekend. Data Collection and Processing. In: Sawyer L., Issacs N., and Bailey S. (Eds) (1993), Daresbury Laboratory, Warrington, UK 114-1222
35. Collaborative Computing Project No. 4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D 50 (1994) 760-763
36. Navaza J. AMoRe: an automated package for molecular replacement. Crystallog. sect. A 50 (1994) 157-163
37. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the Maximum-Likelihood Method. Acta Crystallog. sect. D 53 (1997) 240-245
38. Jones T.A. A graphic model building and refinement system for macromolecules. J. Appl. Crystallog. 11 (1989) 268-272
39. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereo-chemical quality of protein structures. J. Appl. Crystallog. 26 (1993) 283-291
40. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24 (1991) 946-950
41. Merritt E.A., and Murphy M.E. Raster3D: a program for photorealistic molecular graphics. Acta Crystallog. sect. D 50 (1994) 869-873
42. Higgins D., Thompson J., Gibson T., Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22 (1994) 4673-4680
43. Gouet P., Robert X., and Courcelle E. ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucl. Acids Res. 31 (2003) 3320-3323