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Structure and Inhibitor Specificity of L,D-Transpeptidase (LdtMt2) from Mycobacterium tuberculosis and Antibiotic Resistance: Calcium Binding Promotes Dimer Formation

  • Research Article
  • Theme: Better Drugs for Better Life: Drug Discovery and Development Colloquium 2017
  • Published:
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Abstract

The final step of peptidoglycan (PG) synthesis in all bacteria is the formation of cross-linkage between PG-stems. The cross-linking between amino acids in different PG chains gives the peptidoglycan cell wall a 3-dimensional structure and adds strength and rigidity to it. There are two distinct types of cross-linkages in bacterial cell walls. D,D-transpeptidase (D,D-TPs) generate the classical 4➔3 cross-linkages and the L,D-transpeptidase (L,D-TPs) generate the 3➔3 non-classical peptide cross-linkages. The present study is aimed at understanding the nature of drug resistance associated with L,D-TP and gaining insights for designing novel antibiotics against multi-drug resistant bacteria. Penicillin and cephalosporin classes of β-lactams cannot inhibit L,D-TP function; however, carbapenems inactivate its function. We analyzed the structure of L,D-TP of Mycobacterium tuberculosis in the apo form and in complex with meropenem and imipenem. The periplasmic region of L,D-TP folds into three domains. The catalytic residues are situated in the C-terminal domain. The acylation reaction occurs between carbapenem antibiotics and the catalytic Cys-354 forming a covalent complex. This adduct formation mimics the acylation of L,D-TP with the donor PG-stem. A novel aspect of this study is that in the crystal structures of the apo and the carbapenem complexes, the N-terminal domain has a muropeptide unit non-covalently bound to it. Another interesting observation is that the calcium complex crystallized as a dimer through head and tail interactions between the monomers.

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Acknowledgements

The authors thank Dr. Henry Bellamy, CAMD, for SAD data collection, and SSRL for high resolution data collection. Dr. Kuppan Gokulan is supported by the FDA Commissioner Fellowship Program. The authors would like to thank Dr. Kevin Young (UAMS), and Dr. Sutherland (NCTR) for their helpful review and critique of the manuscript.

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Authors and Affiliations

  1. Division of Microbiology, National Center for Toxicological Research, US-FDA, 3900 NCTR Road, Jefferson, Arkansas, 72079, USA

    Kuppan Gokulan, Sangeeta Khare, Carl E. Cerniglia & Steven L. Foley

  2. Department of Physiology & Biophysics, University of Arkansas for Medical Sciences, #750, 4301 W. Markham St, Little Rock, Arkansas, 72205-7199, USA

    Kottayil I. Varughese

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  1. Kuppan Gokulan
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  2. Sangeeta Khare
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Correspondence to Kuppan Gokulan or Kottayil I. Varughese.

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Gokulan, K., Khare, S., Cerniglia, C.E. et al. Structure and Inhibitor Specificity of L,D-Transpeptidase (LdtMt2) from Mycobacterium tuberculosis and Antibiotic Resistance: Calcium Binding Promotes Dimer Formation. AAPS J 20, 44 (2018). https://doi.org/10.1208/s12248-018-0193-x

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