3ZG4 | pdb_00003zg4

NMR structure of the catalytic domain from E. faecium L,D- transpeptidase


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1700 
  • Conformers Submitted: 20 
  • Selection Criteria: TOTAL ENERGY 

wwPDB Validation 3D Report Full Report

Validation slider image for 3ZG4

This is version 2.2 of the entry. See complete history

Literature

The Structure of Enterococcus Faecium L,D---Transpeptidase Acylated by Ertapenem Provides Insight Into the Inactivation Mechanism.

Lecoq, L.Dubee, V.Triboulet, S.Bougault, C.Hugonnet, J.E.Arthur, M.Simorre, J.P.

(2013) ACS Chem Biol 8: 1140

  • DOI: https://doi.org/10.1021/cb4001603
  • Primary Citation Related Structures: 
    3ZG4, 3ZGP

  • PubMed Abstract: 

    The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a biopolymer highly cross-linked through d,d-transpeptidation. Peptidoglycan cross-linking is catalyzed by penicillin-binding proteins (PBPs) that are the essential target of β-lactam antibiotics. PBPs are functionally replaced by l,d-transpeptidases (Ldts) in ampicillin-resistant mutants of Enterococcus faecium and in wild-type Mycobacterium tuberculosis. Ldts are inhibited in vivo by a single class of β-lactams, the carbapenems, which act as a suicide substrate. We present here the first structure of a carbapenem-acylated l,d-transpeptidase, E. faecium Ldtfm acylated by ertapenem, which revealed key contacts between the carbapenem core and residues of the catalytic cavity of the enzyme. Significant reorganization of the antibiotic conformation occurs upon enzyme acylation. These results, together with the analysis of protein-to-carbapenem proton transfers, provide new insights into the mechanism of Ldt acylation by carbapenems.


  • Organizational Affiliation
    • CEA, Institut de Biologie Structurale Jean-Pierre Ebel , UMR 5075, Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 14.57 kDa 
  • Atom Count: 1,027 
  • Modeled Residue Count: 129 
  • Deposited Residue Count: 129 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ERFK/YBIS/YCFS/YNHG129Enterococcus faeciumMutation(s): 0 
EC: 2.3.2.12
UniProt
Find proteins for Q3Y185 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO))
Explore Q3Y185 
Go to UniProtKB:  Q3Y185
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3Y185
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1700 
  • Conformers Submitted: 20 
  • Selection Criteria: TOTAL ENERGY 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 2.0: 2021-06-23
    Changes: Atomic model, Data collection, Other
  • Version 2.1: 2023-06-14
    Changes: Database references, Other
  • Version 2.2: 2024-06-19
    Changes: Data collection, Database references