Active site restructuring regulates ligand recognition in class A penicillin-binding proteins

Experimental Data Snapshot

  • Resolution: 2.39 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.168 

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Active Site Restructuring Regulates Ligand Recognition in Class a Penicillin-Binding Proteins

Macheboeuf, P.Di Guilmi, A.M.Job, V.Vernet, T.Dideberg, O.Dessen, A.

(2005) Proc Natl Acad Sci U S A 102: 577

  • DOI: https://doi.org/10.1073/pnas.0407186102
  • Primary Citation of Related Structures:  
    2BG1, 2UWX, 2XD1

  • PubMed Abstract: 

    Bacterial cell division is a complex, multimolecular process that requires biosynthesis of new peptidoglycan by penicillin-binding proteins (PBPs) during cell wall elongation and septum formation steps. Streptococcus pneumoniae has three bifunctional (class A) PBPs that catalyze both polymerization of glycan chains (glycosyltransfer) and cross-linking of pentapeptidic bridges (transpeptidation) during the peptidoglycan biosynthetic process. In addition to playing important roles in cell division, PBPs are also the targets for beta-lactam antibiotics and thus play key roles in drug-resistance mechanisms. The crystal structure of a soluble form of pneumococcal PBP1b (PBP1b*) has been solved to 1.9 A, thus providing previously undescribed structural information regarding a class A PBP from any organism. PBP1b* is a three-domain molecule harboring a short peptide from the glycosyltransferase domain bound to an interdomain linker region, the transpeptidase domain, and a C-terminal region. The structure of PBP1b* complexed with beta-lactam antibiotics reveals that ligand recognition requires a conformational modification involving conserved elements within the cleft. The open and closed structures of PBP1b* suggest how class A PBPs may become activated as novel peptidoglycan synthesis becomes necessary during the cell division process. In addition, this structure provides an initial framework for the understanding of the role of class A PBPs in the development of antibiotic resistance.

  • Organizational Affiliation

    Laboratoires de Cristallographie Macromoléculaire, Centre National de la Recherche Scientifique/Commissariat à l'Energie Atomique/Université Joseph Fourier, 41 Rue Jules Horowitz, 38027 Grenoble, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PENICILLIN-BINDING PROTEIN 1B494Streptococcus pneumoniae R6Mutation(s): 2 
EC: (PDB Primary Data), 2.3.2 (PDB Primary Data)
Find proteins for Q7CRA4 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q7CRA4 
Go to UniProtKB:  Q7CRA4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7CRA4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.39 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.168 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.52α = 90
b = 148.65β = 90
c = 98.02γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-03
    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