The structure of ll-diaminopimelate aminotransferase from Chlamydia trachomatis: Implications for its broad substrate specificity

Journal of Molecular Biology

Volumn 411, Issue 3, 2011, Pages 649-660

  Watanabe, Nobuhiko ^a   Clay, Matthew D ^b   Van Belkum, Marco J ^a   Fan, Chenguang ^a   Vederas, John C ^a   James, Michael N G ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b St Mary's University College   (Canada)

Author keywords

aminotransferase; Chlamydia; diaminopimelate; lysine biosynthesis; pyridoxal 5 phosphate

Indexed keywords

AMINOTRANSFERASE; DIAMINOPIMELATE AMINOTRANSFERASE; PYRIDOXAL 5 PHOSPHATE; UNCLASSIFIED DRUG;

ARTICLE; CHLAMYDIA TRACHOMATIS; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME SPECIFICITY; ENZYME STRUCTURE; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

ARABIDOPSIS THALIANA; CHLAMYDIA; CHLAMYDIA TRACHOMATIS;

EID: 79960900768     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.06.023     Document Type: Article

References (41)

1. Mandavilli A. Virtually incurable TB warns of impending disaster Nat. Med. 13 2007 271 (Pubitemid 46376664)
2. Kumarasamy K.K., Toleman M.A., Walsh T.R., Bagaria J., Butt F., and Balakrishnan R. Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study Lancet, Infect. Dis. 10 2010 597 602
3. Somani J., Bhullar V.B., Workowski K.A., Farshy C.E., and Black C.M. Multiple drug-resistant Chlamydia trachomatis associated with clinical treatment failure J. Infect. Dis. 181 2000 1421 1427 (Pubitemid 30252548)
4. Manavi K. A review on infection with Chlamydia trachomatis Best Pract. Res., Clin. Obstet. Gynaecol. 20 2006 941 951 (Pubitemid 44824841)
5. Belland R., Ojcius D.M., and Byrne G.I. Focus: chlamydia Nat. Rev., Microbiol. 2 2004 530 531
6. Thylefors B., Négrel A.D., Pararajasegaram R., and Dadzie K.Y. Global data on blindness Bull. World Health Organ. 73 1995 115 121
7. McCoy A.J., Adams N.E., Hudson A.O., Gilvarg C., Leustek T., and Maurelli A.T. l,l-Diaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate/lysine Proc. Natl Acad. Sci. USA 103 2006 17909 17914 (Pubitemid 44852259)
8. Hutton C.A., Perugini M.A., and Gerrard J.A. Inhibition of lysine biosynthesis: an evolving antibiotic strategy Mol. BioSyst. 3 2007 458
9. Scapin G., and Blanchard J.S. Enzymology of bacterial lysine biosynthesis Adv. Enzymol. Relat. Areas Mol. Biol. 72 1998 279 324
10. Vederas J.C. Diaminopimelate and lysine biosynthesis-an antimicrobial target in bacteria Can. J. Chem. 84 2006 1197 1207 (Pubitemid 46360963)
11. Cox R.J., Sutherland A., and Vederas J.C. Bacterial diaminopimelate metabolism as a target for antibiotic design Bioorg. Med. Chem. 8 2000 843 871 (Pubitemid 30336382)
12. Gillner D., Armoush N., Holz R.C., and Becker D.P. Inhibitors of bacterial N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) and demonstration of in vitro antimicrobial activity Bioorg. Med. Chem. Lett. 19 2009 6350 6352
13. van Heijenoort J. Recent advances in the formation of the bacterial peptidoglycan monomer unit Nat. Prod. Rep. 18 2001 503 519 (Pubitemid 33016991)
14. Watanabe N., Cherney M.M., van Belkum M.J., Marcus S.L., Flegel M.D., and Clay M.D. Crystal structure of ll-diaminopimelate aminotransferase from Arabidopsis thaliana: a recently discovered enzyme in the biosynthesis of l-lysine by plants and Chlamydia J. Mol. Biol. 371 2007 685 702 (Pubitemid 47087824)
15. Watanabe N., Clay M.D., van Belkum M.J., Cherney M.M., Vederas J.C., and James M.N.G. Mechanism of substrate recognition and PLP-induced conformational changes in ll-diaminopimelate aminotransferase from Arabidopsis thaliana J. Mol. Biol. 384 2008 1314 1329
16. Hudson A.O., Singh B.K., Leustek T., and Gilvarg C. An ll-diaminopimelate aminotransferase defines a novel variant of the lysine biosynthesis pathway in plants Plant Physiol. 140 2006 292 301 (Pubitemid 43956322)
17. Schneider G., Käck H., and Lindqvist Y. The manifold of vitamin B6 dependent enzymes Structure 8 2000 R1 R6
18. Eliot A.C., and Kirsch J.F. Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations Annu. Rev. Biochem. 73 2004 383 415 (Pubitemid 39050374)
19. Cohen G.E. ALIGN: a program to superimpose protein coordinates, accounting for insertions and deletions J. Appl. Crystallogr. 30 1997 1160 1161
20. Islam M.M., Goto M., Miyahara I., Ikushiro H., Hirotsu K., and Hayashi H. Binding of C5-dicarboxylic substrate to aspartate aminotransferase: implications for the conformational change at the transaldimination step Biochemistry 44 2005 8218 8229 (Pubitemid 40799902)
21. Jäger J., Moser M., Sauder U., and Jansonius J.N. Crystal structures of Escherichia coli aspartate aminotransferase in two conformations. Comparison of an unliganded open and two liganded closed forms J. Mol. Biol. 239 1994 285 305
22. Malashkevich V.N., Strokopytov B.V., Borisov V.V., Dauter Z., Wilson K.S., and Torchinsky Y.M. Crystal structure of the closed form of chicken cytosolic aspartate aminotransferase at 1.9 Å resolution J. Mol. Biol. 247 1995 111 124
23. Rhee S., Silva M.M., Hyde C.C., Rogers P.H., Metzler C.M., Metzler D.E., and Arnone A. Refinement and comparisons of the crystal structures of pig cytosolic aspartate aminotransferase and its complex with 2-methylaspartate J. Biol. Chem. 272 1997 17293
24. Marković-Housley Z., Schirmer T., Hohenester E., Khomutov A.R., Khomutov R.M., and Karpeisky M.Y. Crystal structures and solution studies of oxime adducts of mitochondrial aspartate aminotransferase Eur. J. Biochem. 236 1996 1025 1032 (Pubitemid 26112928)
25. Hudson A.O., Gilvarg C., and Leustek T. Biochemical and phylogenetic characterization of a novel diaminopimelate biosynthesis pathway in prokaryotes identifies a diverged form of ll-diaminopimelate aminotransferase J. Bacteriol. 190 2008 3256 3263 (Pubitemid 351581421)
26. Chow M.A., McElroy K.E., Corbett K.D., Berger J.M., and Kirsch J.F. Narrowing substrate specificity in a directly evolved enzyme: the A293D mutant of aspartate aminotransferase Biochemistry 43 2004 12780 12787 (Pubitemid 39331797)
27. Onuffer J.J., and Kirsch J.F. Redesign of the substrate specificity of Escherichia coli aspartate aminotransferase to that of Escherichia coli tyrosine aminotransferase by homology modeling and site-directed mutagenesis Protein Sci. 4 1995 1750 1757
28. Malashkevich V.N., Onuffer J.J., Kirsch J.F., and Jansonius J.N. Alternating arginine-modulated substrate specificity in an engineered tyrosine aminotransferase Nat. Struct. Biol. 2 1995 548 553
29. Okamoto A., Nakai Y., Hayashi H., Hirotsu K., and Kagamiyama H. Crystal structures of Paracoccus denitrificans aromatic amino acid aminotransferase: a substrate recognition site constructed by rearrangement of hydrogen bond network J. Mol. Biol. 280 1998 443 461 (Pubitemid 28327282)
30. Okamoto A., Ishii S., Hirotsu K., and Kagamiyama H. The active site of Paracoccus denitrificans aromatic amino acid aminotransferase has contrary properties: flexibility and rigidity Biochemistry 38 1999 1176 1184
31. Hayashi H., Kuramitsu S., Inoue Y., Morino Y., and Kagamiyama H. [Arg292 → Val] or [Arg292 → Leu] mutation enhances the reactivity of Escherichia coli aspartate aminotransferase with aromatic amino acids Biochem. Biophys. Res. Commun. 159 1989 337 342 (Pubitemid 19087650)
32. Okamoto A., Higuchi T., Hirotsu K., Kuramitsu S., and Kagamiyama H. X-ray crystallographic study of pyridoxal 5′-phosphate-type aspartate aminotransferases from Escherichia coli in open and closed form J. Biochem. (Tokyo) 116 1994 95 107
33. Studier F.W. Protein production by auto-induction in high density shaking cultures Protein Expression Purif. 41 2005 207 234
34. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol 276 1997 307 326 (Pubitemid 27085611)
35. Long F., Vagin A.A., Young P., and Murshudov G.N. BALBES: a molecular-replacement pipeline Acta Crystallogr., Sect. D: Biol. Crystallogr. 64 2008 125 132 (Pubitemid 350308686)
36. Collaborative Computational Project, Number 4 The CCP4 suite: programs for protein crystallography Acta Crystallogr., Sect. D: Biol. Crystallogr. 50 1994 760 763
37. Murshudov G.N., Vagin A.A., Lebedev A., Wilson K.S., and Dodson E.J. Efficient anisotropic refinement of macromolecular structures using FFT Acta Crystallogr., Sect. D: Biol. Crystallogr. 55 1999 247 255 (Pubitemid 29053823)
38. McRee D.E. XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density J. Struct. Biol. 125 1999 156 165 (Pubitemid 29402600)
39. Perrakis A., Morris R., and Lamzin V.S. Automated protein model building combined with iterative structure refinement Nat. Struct. Biol. 6 1999 458 463 (Pubitemid 29218016)
40. McCoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., and Read R.J. Phaser crystallographic software J. Appl. Crystallogr. 40 2007 658 674 (Pubitemid 47080256)
41. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26 1993 283 291