1HD8

Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of a Deacylation-Defective Mutant of Penicillin-Binding Protein 5 at 2.3-A Resolution

Davies, C.White, S.W.Nicholas, R.A.

(2001) J Biol Chem 276: 616

  • DOI: 10.1074/jbc.M004471200
  • Primary Citation of Related Structures:  
    1HD8

  • PubMed Abstract: 
  • Penicillin-binding protein 5 (PBP 5) of Escherichia coli functions as a d-alanine carboxypeptidase, cleaving the C-terminal d-alanine residue from cell wall peptides. Like all PBPs, PBP 5 forms a covalent acyl-enzyme complex with beta-lactam antibiot ...

    Penicillin-binding protein 5 (PBP 5) of Escherichia coli functions as a d-alanine carboxypeptidase, cleaving the C-terminal d-alanine residue from cell wall peptides. Like all PBPs, PBP 5 forms a covalent acyl-enzyme complex with beta-lactam antibiotics; however, PBP 5 is distinguished by its high rate of deacylation of the acyl-enzyme complex (t(12) approximately 9 min). A Gly-105 --> Asp mutation in PBP 5 markedly impairs this beta-lactamase activity (deacylation), with only minor effects on acylation, and promotes accumulation of a covalent complex with peptide substrates. To gain further insight into the catalytic mechanism of PBP 5, we determined the three-dimensional structure of the G105D mutant form of soluble PBP 5 (termed sPBP 5') at 2.3 A resolution. The structure is composed of two domains, a penicillin binding domain with a striking similarity to Class A beta-lactamases (TEM-1-like) and a domain of unknown function. In addition, the penicillin-binding domain contains an active site loop spatially equivalent to the Omega loop of beta-lactamases. In beta-lactamases, the Omega loop contains two amino acids involved in catalyzing deacylation. This similarity may explain the high beta-lactamase activity of wild-type PBP 5. Because of the low rate of deacylation of the G105D mutant, visualization of peptide substrates bound to the active site may be possible.


    Related Citations: 
    • Relations between Beta-Lactamases and Penicillin-Binding Proteins: Beta-Lactamase Activity of Penicillin-Binding Protein 5 from Escherichia Coli
      Nicholas, R.A., Strominger, J.L.
      (1988) Rev Infect Dis 10: 733
    • An Amino Acid Substitution that Blocks the Deacylation Step in the Enzyme Mechanism of Penicillin-Binding Protein 5 of Escherichia Coli
      Broome-Smith, J., Spratt, B.G.
      (1984) FEBS Lett 165: 185

    Organizational Affiliation

    School of Biological Sciences, University of Sussex, Falmer, Brighton BN1 9QG, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PENICILLIN-BINDING PROTEIN 5A363Escherichia coliMutation(s): 1 
Gene Names: dacA
EC: 3.4.16.4 (PDB Primary Data), 3.5.2.6 (UniProt)
Find proteins for P0AEB2 (Escherichia coli (strain K12))
Explore P0AEB2 
Go to UniProtKB:  P0AEB2
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.207 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.83α = 90
b = 50.83β = 90
c = 140.29γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance