Crystal Structure of an Enterococcus faecium peptidoglycan binding protein at 2.4 A resolution

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

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Crystal Structure of a Novel beta-Lactam-insensitive Peptidoglycan Transpeptidase.

Biarrotte-Sorin, S.Hugonnet, J.E.Delfosse, V.Mainardi, J.L.Gutmann, L.Arthur, M.Mayer, C.

(2006) J Mol Biol 359: 533-538

  • DOI: https://doi.org/10.1016/j.jmb.2006.03.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    During the final stages of cell-wall synthesis in bacteria, penicillin-binding proteins (PBPs) catalyse the cross-linking of peptide chains from adjacent glycan strands of nascent peptidoglycan. We have recently shown that this step can be bypassed by an L,D-transpeptidase, which confers high-level beta-lactam-resistance in Enterococcus faecium. The resistance bypass leads to replacement of D-Ala4-->D-Asx-L-Lys3 cross-links generated by the PBPs by L-Lys3-->D-Asx-L-Lys3 cross-links generated by the L,D-transpeptidase. As the first structure of a member of this new transpeptidase family, we have determined the crystal structure of a fragment of the L,D-transpeptidase from E.faecium (Ldt(fm217)) at 2.4A resolution. Ldt(fm217) consists of two domains, the N-terminal domain, a new mixed alpha-beta fold, and the ErfK_YbiS_YhnG C-terminal domain, a representative of the mainly beta class of protein structures. Residue Cys442 of the C-terminal domain has been proposed to be the catalytic residue implicated in the cleavage of the L-Lys-D-Ala peptide bond. Surface analysis of Ldt(fm217) reveals that residue Cys442 is localized in a buried pocket and is accessible by two paths on different sides of the protein. We propose that the two paths to the catalytic residue Cys442 are the binding sites for the acceptor and donor substrates of the L,D-transpeptidase.

  • Organizational Affiliation

    INSERM, U655-LRMA, Université Pierre et Marie Curie-Paris 6, Université Paris-Descartes, Faculté de Médecine Pitié Salpêtrière and Centre de Recherches Biomédicales des Cordeliers, 91 boulevard de l'Hôpital, 75634 Paris Cedex 13, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L,D-transpeptidase250Enterococcus faeciumMutation(s): 0 
Gene Names: ldtfm
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.976α = 90
b = 115.976β = 90
c = 68.275γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations