5J8X

CRYSTAL STRUCTURE OF E. COLI PBP5 WITH 2C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural basis of metallo-beta-lactamase, serine-beta-lactamase and penicillin-binding protein inhibition by cyclic boronates.

Brem, J.Cain, R.Cahill, S.McDonough, M.A.Clifton, I.J.Jimenez-Castellanos, J.C.Avison, M.B.Spencer, J.Fishwick, C.W.Schofield, C.J.

(2016) Nat Commun 7: 12406-12406

  • DOI: https://doi.org/10.1038/ncomms12406
  • Primary Citation of Related Structures:  
    5FQ9, 5FQB, 5FQC, 5J8X

  • PubMed Abstract: 

    β-Lactamases enable resistance to almost all β-lactam antibiotics. Pioneering work revealed that acyclic boronic acids can act as 'transition state analogue' inhibitors of nucleophilic serine enzymes, including serine-β-lactamases. Here we report biochemical and biophysical analyses revealing that cyclic boronates potently inhibit both nucleophilic serine and zinc-dependent β-lactamases by a mechanism involving mimicking of the common tetrahedral intermediate. Cyclic boronates also potently inhibit the non-essential penicillin-binding protein PBP 5 by the same mechanism of action. The results open the way for development of dual action inhibitors effective against both serine- and metallo-β-lactamases, and which could also have antimicrobial activity through inhibition of PBPs.


  • Organizational Affiliation

    Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-alanyl-D-alanine carboxypeptidase DacA387Escherichia coli K-12Mutation(s): 0 
Gene Names: dacApfvb0632JW0627
EC: 3.4.16.4 (PDB Primary Data), 3.5.2.6 (PDB Primary Data)
UniProt
Find proteins for P0AEB2 (Escherichia coli (strain K12))
Explore P0AEB2 
Go to UniProtKB:  P0AEB2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEB2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OK3
Query on OK3

Download Ideal Coordinates CCD File 
B [auth A](4~{R})-4-[[4-(aminomethyl)phenyl]carbonylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid
C17 H18 B N2 O6
QLXKUYDHLJOWQG-AWEZNQCLSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.223α = 90
b = 61.606β = 90
c = 138.43γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 2.0: 2019-10-30
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description