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 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1128/AAC.00866-17
  • Primary Citation of Related Structures:  
    5UWV

  • PubMed Abstract: 

    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

    Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L,D-TRANSPEPTIDASE 2368Mycobacteroides abscessus ATCC 19977Mutation(s): 0 
Gene Names: MAB_1530
UniProt
Find proteins for B1MMQ4 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948))
Explore B1MMQ4 
Go to UniProtKB:  B1MMQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1MMQ4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.239α = 90
b = 130.937β = 92.51
c = 135.664γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.2: 2017-10-04
    Changes: Database references
  • Version 1.3: 2019-08-14
    Changes: Data collection, Structure summary
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description