4K91 | pdb_00004k91

Crystal structure of Penicillin-Binding Protein 5 (PBP5) from Pseudomonas aeruginosa in apo state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.263 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4K91

This is version 1.1 of the entry. See complete history

Literature

Structural analysis of the role of Pseudomonas aeruginosa penicillin-binding protein 5 in beta-lactam resistance.

Smith, J.D.Kumarasiri, M.Zhang, W.Hesek, D.Lee, M.Toth, M.Vakulenko, S.Fisher, J.F.Mobashery, S.Chen, Y.

(2013) Antimicrob Agents Chemother 57: 3137-3146

  • DOI: https://doi.org/10.1128/AAC.00505-13
  • Primary Citation Related Structures: 
    4K91

  • PubMed Abstract: 

    Penicillin-binding protein 5 (PBP5) is one of the most abundant PBPs in Pseudomonas aeruginosa. Although its main function is that of a cell wall dd-carboxypeptidase, it possesses sufficient β-lactamase activity to contribute to the ability of P. aeruginosa to resist the antibiotic activity of the β-lactams. The study of these dual activities is important for understanding the mechanisms of antibiotic resistance by P. aeruginosa, an important human pathogen, and to the understanding of the evolution of β-lactamase activity from the PBP enzymes. We purified a soluble version of P. aeruginosa PBP5 (designated Pa sPBP5) by deletion of its C-terminal membrane anchor. Under in vitro conditions, Pa sPBP5 demonstrates both dd-carboxypeptidase and expanded-spectrum β-lactamase activities. Its crystal structure at a 2.05-Å resolution shows features closely resembling those of the class A β-lactamases, including a shortened loop spanning residues 74 to 78 near the active site and with respect to the conformations adopted by two active-site residues, Ser101 and Lys203. These features are absent in the related PBP5 of Escherichia coli. A comparison of the two Pa sPBP5 monomers in the asymmetric unit, together with molecular dynamics simulations, revealed an active-site flexibility that may explain its carbapenemase activity, a function that is absent in the E. coli PBP5 enzyme. Our functional and structural characterizations underscore the versatility of this PBP5 in contributing to the β-lactam resistance of P. aeruginosa while highlighting how broader β-lactamase activity may be encoded in the structural folds shared by the PBP and serine β-lactamase classes.


  • Organizational Affiliation
    • Department of Molecular Medicine, University of South Florida, Tampa, Florida, USA.

Macromolecule Content 

  • Total Structure Weight: 75.98 kDa 
  • Atom Count: 5,435 
  • Modeled Residue Count: 684 
  • Deposited Residue Count: 692 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
D-ala-D-ala-carboxypeptidase
A, B
346Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 0 
Gene Names: dacCPA14_12100
EC: 3.4.16.4
UniProt
Find proteins for A0A0H2ZFH3 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore A0A0H2ZFH3 
Go to UniProtKB:  A0A0H2ZFH3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2ZFH3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.263 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 232.143α = 90
b = 39.909β = 111.03
c = 85.461γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations