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 1.3 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: 10.1021/cb4001603
  • Primary Citation of Related Structures:  3ZG4

  • 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 e ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ERFK/YBIS/YCFS/YNHG
A
129Enterococcus faecium DON/A
Find proteins for Q3Y185 (Enterococcus faecium DO)
Go to UniProtKB:  Q3Y185
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1RG
Query on 1RG

Download SDF File 
Download CCD File 
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
ERTAPENEM, bound form PRE-ISOMERIZED
C22 H27 N3 O7 S
PGRRQYXTRXQDDJ-SKHPLXCOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1700 
  • Conformers Submitted: 20 
  • Selection Criteria: TOTAL ENERGY 
  • Olderado: 3ZGP Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references
  • Version 1.2: 2014-02-12
    Type: Atomic model, Derived calculations, Non-polymer description, Other
  • Version 1.3: 2018-01-24
    Type: Data collection, Database references