Targeting the cell wall of mycobacterium tuberculosis: Structure and mechanism of L,D-transpeptidase 2

Structure

Volumn 20, Issue 12, 2012, Pages 2103-2115

  Erdemli, Sabri B ^a   Gupta, Radhika ^a   Bishai, William R ^a   Lamichhane, Gyanu ^a   Amzel, L Mario ^a   Bianchet, Mario A ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; BETA LACTAMASE; CARBAPENEM; CYSTEINE; ERTAPENEM; IMIPENEM; L,D TRANSPEPTIDASE 2; MEROPENEM; PEPTIDOGLYCAN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL CELL WALL; CATALYSIS; CHEMICAL MODIFICATION; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME KINETICS; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE; LIGAND BINDING; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANTIBIOTICS, ANTITUBERCULAR; BACTERIAL PROTEINS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; IMIPENEM; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; MYCOBACTERIUM TUBERCULOSIS; PEPTIDOGLYCAN; PEPTIDYL TRANSFERASES; PROTEIN BINDING; SEQUENCE HOMOLOGY, AMINO ACID; THERMODYNAMICS; THIENAMYCINS;

CORYNEBACTERINEAE; MYCOBACTERIUM TUBERCULOSIS;

EID: 84870500858     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2012.09.016     Document Type: Article

References (39)

1. L.M. Amzel, and R.J. Poljak Three-dimensional structure of immunoglobulins Annu. Rev. Biochem. 48 1979 961 997
2. H. Barreteau, A. Kovac, A. Boniface, M. Sova, S. Gobec, and D. Blanot Cytoplasmic steps of peptidoglycan biosynthesis FEMS Microbiol. Rev. 32 2008 168 207
3. A. Bateman, and M. Bycroft The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD) J. Mol. Biol. 299 2000 1113 1119
4. J.C. Betts, P.T. Lukey, L.C. Robb, R.A. McAdam, and K. Duncan Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling Mol. Microbiol. 43 2002 717 731
5. S. Biarrotte-Sorin, J.E. Hugonnet, V. Delfosse, J.L. Mainardi, L. Gutmann, M. Arthur, and C. Mayer Crystal structure of a novel beta-lactam-insensitive peptidoglycan transpeptidase J. Mol. Biol. 359 2006 533 538
6. J. Bielnicki, Y. Devedjiev, U. Derewenda, Z. Dauter, A. Joachimiak, and Z.S. Derewenda B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes Proteins 62 2006 144 151
7. W. Bishai Lipid lunch for persistent pathogen Nature 406 2000 683 685
8. G. Bonfiglio, G. Russo, and G. Nicoletti Recent developments in carbapenems Expert Opin. Investig. Drugs 11 2002 529 544
9. F. Cava, M.A. de Pedro, H. Lam, B.M. Davis, and M.K. Waldor Distinct pathways for modification of the bacterial cell wall by non-canonical D-amino acids EMBO J. 30 2011 3442 3453
10. Collaborative Computational Project, Number 4 The CCP4 suite: programs for protein crystallography Acta Crystallogr. D Biol. Crystallogr. 50 1994 760 763
11. G. Dodson, and A. Wlodawer Catalytic triads and their relatives Trends Biochem. Sci. 23 1998 347 352
12. V. Dubée, S. Triboulet, J.L. Mainardi, M. Ethève- Quelquejeu, L. Gutmann, A. Marie, L. Dubost, J.E. Hugonnet, and M. Arthur Inactivation of Mycobacterium tuberculosis l,d-transpeptidase LdtMt by carbapenems and cephalosporins Antimicrob. Agents Chemother. 56 2012 4189 4195
13. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132
14. A.S. Fauci NIAID Tuberculosis Working Group Multidrug-resistant and extensively drug-resistant tuberculosis: the National Institute of Allergy and Infectious Diseases Research agenda and recommendations for priority research J. Infect. Dis. 197 2008 1493 1498
15. C. Goffin, and J.M. Ghuysen Biochemistry and comparative genomics of SxxK superfamily acyltransferases offer a clue to the mycobacterial paradox: presence of penicillin-susceptible target proteins versus lack of efficiency of penicillin as therapeutic agent Microbiol. Mol. Biol. Rev. 66 2002 702 738
16. R. Gupta, M. Lavollay, J.L. Mainardi, M. Arthur, W.R. Bishai, and G. Lamichhane The Mycobacterium tuberculosis protein LdtMt2 is a nonclassical transpeptidase required for virulence and resistance to amoxicillin Nat. Med. 16 2010 466 469
17. J.E. Hugonnet, L.W. Tremblay, H.I. Boshoff, C.E. Barry 3rd, and J.S. Blanchard Meropenem-clavulanate is effective against extensively drug-resistant Mycobacterium tuberculosis Science 323 2009 1215 1218
18. A. Jindani, C.J. Doré, and D.A. Mitchison Bactericidal and sterilizing activities of antituberculosis drugs during the first 14 days Am. J. Respir. Crit. Care Med. 167 2003 1348 1354
19. I. Keren, S. Minami, E. Rubin, and K. Lewis Characterization and transcriptome analysis of Mycobacterium tuberculosis persisters MBio 2 2011 e00100 e00111
20. E. Krissinel Macromolecular complexes in crystals and solutions Acta Crystallogr. D Biol. Crystallogr. 67 2011 376 385
21. M. Lavollay, M. Arthur, M. Fourgeaud, L. Dubost, A. Marie, N. Veziris, D. Blanot, L. Gutmann, and J.L. Mainardi The peptidoglycan of stationary-phase Mycobacterium tuberculosis predominantly contains cross-links generated by L,D-transpeptidation J. Bacteriol. 190 2008 4360 4366
22. M. Lavollay, M. Fourgeaud, J.L. Herrmann, L. Dubost, A. Marie, L. Gutmann, M. Arthur, and J.L. Mainardi The peptidoglycan of Mycobacterium abscessus is predominantly cross-linked by L,D-transpeptidases J. Bacteriol. 193 2011 778 782
23. K. Lewis Persister cells, dormancy and infectious disease Nat. Rev. Microbiol. 5 2007 48 56
24. J.L. Mainardi, M. Fourgeaud, J.E. Hugonnet, L. Dubost, J.P. Brouard, J. Ouazzani, L.B. Rice, L. Gutmann, and M. Arthur A novel peptidoglycan cross-linking enzyme for a beta-lactam-resistant transpeptidation pathway J. Biol. Chem. 280 2005 38146 38152
25. J.L. Mainardi, J.E. Hugonnet, F. Rusconi, M. Fourgeaud, L. Dubost, A.N. Moumi, V. Delfosse, C. Mayer, L. Gutmann, L.B. Rice, and M. Arthur Unexpected inhibition of peptidoglycan LD-transpeptidase from Enterococcus faecium by the beta-lactam imipenem J. Biol. Chem. 282 2007 30414 30422
26. M. Matsuhashi [Biosynthesis in the bacterial cell wall] Tanpakushitsu Kakusan Koso 11 1966 875 886
27. Medical Section of the American Lung Association Diagnosis and treatment of disease caused by nontuberculous mycobacteria. This official statement of the American Thoracic Society was approved by the Board of Directors, March 1997. Medical Section of the American Lung Association Am. J. Respir. Crit. Care Med. 156 1997 S1 S25
28. J. Monks, and S.G. Waley Imipenem as substrate and inhibitor of beta-lactamases Biochem. J. 253 1988 323 328
29. G.N. Murshudov, P. Skubák, A.A. Lebedev, N.S. Pannu, R.A. Steiner, R.A. Nicholls, M.D. Winn, F. Long, and A.A. Vagin REFMAC5 for the refinement of macromolecular crystal structures Acta Crystallogr. D Biol. Crystallogr. 67 2011 355 367
30. S.T. Nolan, and G. Lamichhane Protective efficacy of BCG overexpressing an L,D-transpeptidase against M. tuberculosis infection PLoS One 5 2010 e13773
31. C.H. O'Callaghan, A. Morris, S.M. Kirby, and A.H. Shingler Novel method for detection of beta-lactamases by using a chromogenic cephalosporin substrate Antimicrob. Agents Chemother. 1 1972 283 288
32. T.V. O'Halloran, S.J. Lippard, T.J. Richmond, and A. Klug Multiple heavy-atom reagents for macromolecular X-ray structure determination. Application to the nucleosome core particle J. Mol. Biol. 194 1987 705 712
33. J. Peltier, P. Courtin, I. El Meouche, L. Lemée, M.P. Chapot-Chartier, and J.L. Pons Clostridium difficile has an original peptidoglycan structure with a high level of N-acetylglucosamine deacetylation and mainly 3-3 cross-links J. Biol. Chem. 286 2011 29053 29062
34. J.L. Risler, M.O. Delorme, H. Delacroix, and A. Henaut Amino acid substitutions in structurally related proteins. A pattern recognition approach. Determination of a new and efficient scoring matrix J. Mol. Biol. 204 1988 1019 1029
35. S. Triboulet, M. Arthur, J.L. Mainardi, C. Veckerlé, V. Dubée, A. Nguekam-Moumi, L. Gutmann, L.B. Rice, and J.E. Hugonnet Inactivation kinetics of a new target of β-lactam antibiotics J. Biol. Chem. 286 2011 22777 22784
36. E. Tuomanen, and R. Cozens Changes in peptidoglycan composition and penicillin-binding proteins in slowly growing Escherichia coli J. Bacteriol. 169 1987 5308 5310
37. W. Vollmer, and J.V. Höltje The architecture of the murein (peptidoglycan) in gram-negative bacteria: vertical scaffold or horizontal layer(s)? J. Bacteriol. 186 2004 5978 5987
38. C. Vonrhein, E. Blanc, P. Roversi, and G. Bricogne Automated structure solution with autoSHARP Methods Mol. Biol. 364 2007 215 230
39. J. Wietzerbin, B.C. Das, J.F. Petit, E. Lederer, M. Leyh-Bouille, and J.M. Ghuysen Occurrence of D-alanyl-(D)-meso-diaminopimelic acid and meso-diaminopimelyl-meso-diaminopimelic acid interpeptide linkages in the peptidoglycan of Mycobacteria Biochemistry 13 1974 3471 3476