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 5UWV | pdb_00005uwv

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 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5UWV

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 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.

Macromolecule Content 

  • Total Structure Weight: 237.13 kDa 
  • Atom Count: 15,188 
  • Modeled Residue Count: 2,011 
  • Deposited Residue Count: 2,208 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
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