2JE5

STRUCTURAL AND MECHANISTIC BASIS OF PENICILLIN BINDING PROTEIN INHIBITION BY LACTIVICINS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Mechanistic Basis of Penicillin-Binding Protein Inhibition by Lactivicins

Macheboeuf, P.Fisher, D.S.Brown, T.J.Zervosen, A.Luxen, A.Joris, B.Dessen, A.Schofield, C.J.

(2007) Nat.Chem.Biol. 3: 565

  • DOI: 10.1038/nchembio.2007.21
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Beta-lactam antibiotics, including penicillins and cephalosporins, inhibit penicillin-binding proteins (PBPs), which are essential for bacterial cell wall biogenesis. Pathogenic bacteria have evolved efficient antibiotic resistance mechanisms that, i ...

    Beta-lactam antibiotics, including penicillins and cephalosporins, inhibit penicillin-binding proteins (PBPs), which are essential for bacterial cell wall biogenesis. Pathogenic bacteria have evolved efficient antibiotic resistance mechanisms that, in Gram-positive bacteria, include mutations to PBPs that enable them to avoid beta-lactam inhibition. Lactivicin (LTV; 1) contains separate cycloserine and gamma-lactone rings and is the only known natural PBP inhibitor that does not contain a beta-lactam. Here we show that LTV and a more potent analog, phenoxyacetyl-LTV (PLTV; 2), are active against clinically isolated, penicillin-resistant Streptococcus pneumoniae strains. Crystallographic analyses of S. pneumoniae PBP1b reveal that LTV and PLTV inhibition involves opening of both monocyclic cycloserine and gamma-lactone rings. In PBP1b complexes, the ring-derived atoms from LTV and PLTV show a notable structural convergence with those derived from a complexed cephalosporin (cefotaxime; 3). The structures imply that derivatives of LTV will be useful in the search for new antibiotics with activity against beta-lactam-resistant bacteria.


    Organizational Affiliation

    Institut de Biologie Structurale Jean-Pierre Ebel Commissariat à l'énergie atomique - Centre National de La Recherche Scientifique - Université Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PENICILLIN-BINDING PROTEIN 1B
A, B
720Streptococcus pneumoniaeMutation(s): 7 
Gene Names: pbp1b (pbp1B)
Find proteins for O70038 (Streptococcus pneumoniae)
Go to UniProtKB:  O70038
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
L4C
Query on L4C

Download SDF File 
Download CCD File 
A, B
(2E)-2-{[(2S)-2-(ACETYLAMINO)-2-CARBOXYETHOXY]IMINO}PENTANEDIOIC ACID
LACTIVICIN
C10 H14 N2 O8
ULEFFWARYSNNRF-NYYVKIQXSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 98.540α = 90.00
b = 99.830β = 90.00
c = 152.160γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
AMoREphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance