5J8X

CRYSTAL STRUCTURE OF E. COLI PBP5 WITH 2C

• PDB DOI: https://doi.org/10.2210/pdb5J8X/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-08 Released: 2016-08-17 
• Deposition Author(s): Brem, J., Cain, R., McDonough, M.A., Clifton, I.J., Fishwick, C.W.G., Schofield, C.J.

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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 

Starting Model: experimental

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

• PubMed: 27499424 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.84 kDa 
• Atom Count: 2,598 
• Modelled Residue Count: 340 
• Deposited Residue Count: 387 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanyl-D-alanine carboxypeptidase DacA	A	387	Escherichia coli K-12	Mutation(s): 0  Gene Names: dacA, pfv, b0632, JW0627 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OK3	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 = 50.223	α = 90
b = 61.606	β = 90
c = 138.43	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): Brem, J., Cain, R., McDonough, M.A., Clifton, I.J., Fishwick, C.W.G., Schofield, C.J.

Revision History  

• 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
• Version 2.2: 2024-10-23
  Changes: Structure summary