3ZGP

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 2.0 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.Triboulet, S.Dubee, V.Bougault, C.Hugonnet, J.E.Arthur, M.Simorre, J.P.

(2013) ACS Chem Biol 8: 1140-1146

  • DOI: https://doi.org/10.1021/cb4001603
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1RG
Query on 1RG

Download Ideal Coordinates CCD File 
B [auth A](4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid
C22 H27 N3 O7 S
PGRRQYXTRXQDDJ-SKHPLXCOSA-N
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 1.2: 2014-02-12
    Changes: Atomic model, Derived calculations, Non-polymer description, Other
  • Version 1.3: 2018-01-24
    Changes: Data collection, Database references
  • Version 2.0: 2023-06-14
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other