2WAD

PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pbp Active Site Flexibility as the Key Mechanism for Beta-Lactam Resistance in Pneumococci

Contreras-Martel, C.Dahout-Gonzalez, C.Dos-Santos-Martins, A.Kotnik, M.Dessen, A.

(2009) J.Mol.Biol. 387: 899

  • DOI: 10.1016/j.jmb.2009.02.024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Penicillin-binding proteins (PBPs), the main targets of beta-lactam antibiotics, are membrane-associated enzymes that catalyze the two last steps in the biosynthesis of peptidoglycan. In Streptococcus pneumoniae, a major human pathogen, the surge in ...

    Penicillin-binding proteins (PBPs), the main targets of beta-lactam antibiotics, are membrane-associated enzymes that catalyze the two last steps in the biosynthesis of peptidoglycan. In Streptococcus pneumoniae, a major human pathogen, the surge in resistance to such antibiotics is a direct consequence of the proliferation of mosaic PBP-encoding genes, which give rise to proteins containing tens of mutations. PBP2b is a major drug resistance target, and its modification is essential for the development of high levels of resistance to piperacillin. In this work, we have solved the crystal structures of PBP2b from a wild-type pneumococcal strain, as well as from a highly drug-resistant clinical isolate displaying 58 mutations. Although mutations are present throughout the entire PBP structure, those surrounding the active site influence the total charge and the polar character of the region, while those in close proximity to the catalytic nucleophile impart flexibility onto the beta3/beta4 loop area, which encapsulates the cleft. The wealth of structural data on pneumococcal PBPs now underlines the importance of high malleability in active site regions of drug-resistant strains, suggesting that active site "breathing" could be a common mechanism employed by this pathogen to prevent targeting by beta-lactams.


    Related Citations: 
    • Biochemical Characterization of Streptococcus Pneumoniae Penicillin-Binding Protein 2B and its Implication in Beta-Lactam Resistance
      Pagliero, E.,Chesnel, L.,Hopkins, J.,Croize, J.,Dideberg, O.,Vernet, T.,Di-Guilmi, A.
      (2004) Antimicrob.Agents Chemother. 48: 1848


    Organizational Affiliation

    Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075 (CEA, CNRS, UJF, PSB), Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PENICILLIN-BINDING PROTEIN 2B
A, B, C
680Streptococcus pneumoniaeMutation(s): 0 
Gene Names: penA
Find proteins for B0B6I9 (Streptococcus pneumoniae)
Go to UniProtKB:  B0B6I9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 128.788α = 90.00
b = 128.788β = 90.00
c = 123.139γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
autoSHARPphasing
XSCALEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2014-02-19
    Type: Database references