5UWV

Crystal structure of Mycobacterium abscessus L,D-transpeptidase 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mycobacterium abscessus l,d-Transpeptidases Are Susceptible to Inactivation by Carbapenems and Cephalosporins but Not Penicillins.

Kumar, P.Chauhan, V.Silva, J.R.A.Lameira, J.d'Andrea, F.B.Li, S.G.Ginell, S.L.Freundlich, J.S.Alves, C.N.Bailey, S.Cohen, K.A.Lamichhane, G.

(2017) Antimicrob. Agents Chemother. 61: --

  • DOI: 10.1128/AAC.00866-17

  • PubMed Abstract: 
  • As a growing number of clinical isolates of <i>Mycobacterium abscessus </i> are resistant to most antibiotics, new treatment options that are effective against these drug-resistant strains are desperately needed. The majority of the linkages in the ...

    As a growing number of clinical isolates of Mycobacterium abscessus are resistant to most antibiotics, new treatment options that are effective against these drug-resistant strains are desperately needed. The majority of the linkages in the cell wall peptidoglycan of M. abscessus are synthesized by nonclassical transpeptidases, namely, the l,d-transpeptidases. Emerging evidence suggests that these enzymes represent a new molecular vulnerability in this pathogen. Recent studies have demonstrated that inhibition of these enzymes by the carbapenem class of β-lactams determines their activity against Mycobacterium tuberculosis Here, we studied the interactions of β-lactams with two l,d-transpeptidases in M. abscessus , namely, Ldt Mab1 and Ldt Mab2 , and found that both the carbapenem and cephalosporin, but not penicillin, subclasses of β-lactams inhibit these enzymes. Contrary to the commonly held belief that combination therapy with β-lactams is redundant, doripenem and cefdinir exhibit synergy against both pansusceptible M. abscessus and clinical isolates that are resistant to most antibiotics, which suggests that dual-β-lactam therapy has potential for the treatment of M. abscessus Finally, we solved the first crystal structure of an M. abscessus l,d-transpeptidase, Ldt Mab2 , and using substitutions of critical amino acids in the catalytic site and computational simulations, we describe the key molecular interactions between this enzyme and β-lactams, which provide an insight into the molecular basis for the relative efficacy of different β-lactams against M. abscessus .


    Organizational Affiliation

    Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Taskforce To Study Resistance Emergence and Antimicrobial Development Technology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Departments of Pharmacology, Physiology and Neuroscience, and Medicine, Rutgers University, Newark, New Jersey, USA.,Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil.,Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA.,Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA.,Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém, Pará, Brazil.,Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA lamichhane@jhu.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L,D-TRANSPEPTIDASE 2
B, A, D, E, C, F
368Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543)Mutation(s): 0 
Find proteins for B1MMQ4 (Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543))
Go to UniProtKB:  B1MMQ4
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 94.239α = 90.00
b = 130.937β = 92.51
c = 135.664γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-3000data reduction
HKL-3000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesDP2OD008459

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence
  • Version 1.2: 2017-10-04
    Type: Database references