3ZGP

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

Summary for 3ZGP

• Entry DOI: 10.2210/pdb3zgp/pdb
• Related: 3ZG4
• NMR Information: BMRB: 18911
• Descriptor: ERFK/YBIS/YCFS/YNHG, (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 (2 entities in total)
• Functional Keywords: transferase, transpeptidation, peptidoglycan biosynthesis, antibiotic resistance
• Biological source: ENTEROCOCCUS FAECIUM
• Total number of polymer chains: 1
• Total formula weight: 15049.68

Authors

Lecoq, L.,Triboulet, S.,Dubee, V.,Bougault, C.,Hugonnet, J.E.,Arthur, M.,Simorre, J.P. (deposition date: 2012-12-18, release date: 2013-04-24, Last modification date: 2024-11-06)

Primary citation

Lecoq, L.,Triboulet, S.,Dubee, V.,Bougault, C.,Hugonnet, J.E.,Arthur, M.,Simorre, J.P.
The Structure of Enterococcus Faecium L,D---Transpeptidase Acylated by Ertapenem Provides Insight Into the Inactivation Mechanism.
Acs Chem.Biol., 8:1140-1146, 2013

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.

PubMed: 23574509
DOI: 10.1021/cb4001603

Experimental method

SOLUTION NMR