2JE5 | pdb_00002je5

STRUCTURAL AND MECHANISTIC BASIS OF PENICILLIN BINDING PROTEIN INHIBITION BY LACTIVICINS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.298 (Depositor), 0.297 (DCC) 
  • R-Value Work: 
    0.260 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 
    0.262 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1038/nchembio.2007.21
  • Primary Citation Related Structures: 
    2JCH, 2JE5

  • 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, 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.

Macromolecule Content 

  • Total Structure Weight: 157.77 kDa 
  • Atom Count: 7,239 
  • Modeled Residue Count: 923 
  • Deposited Residue Count: 1,440 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PENICILLIN-BINDING PROTEIN 1B
A, B
720Streptococcus pneumoniae R6Mutation(s): 7 
UniProt
Find proteins for O70038 (Streptococcus pneumoniae)
Explore O70038 
Go to UniProtKB:  O70038
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO70038
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L4C

Query on L4C



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
(2E)-2-{[(2S)-2-(ACETYLAMINO)-2-CARBOXYETHOXY]IMINO}PENTANEDIOIC ACID
C10 H14 N2 O8
ULEFFWARYSNNRF-NYYVKIQXSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
I [auth B],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.298 (Depositor), 0.297 (DCC) 
  • R-Value Work:  0.260 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 0.262 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.54α = 90
b = 99.83β = 90
c = 152.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary