5FQC

Crystal structure of the metallo-beta-lactamase VIM-2 with 2C

• PDB DOI: https://doi.org/10.2210/pdb5FQC/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-08 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: 1.45 Å
• R-Value Free: 0.184 
• R-Value Work: 0.155 
• R-Value Observed: 0.155 

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.76 kDa 
• Atom Count: 4,090 
• Modelled Residue Count: 464 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-LACTAMASE	A, B	242	Pseudomonas aeruginosa	Mutation(s): 0  EC: 3.5.2.6
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa) Explore Q9K2N0  Go to UniProtKB:  Q9K2N0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OK3	H [auth A], O [auth B]	(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
DMS	I [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	C [auth A], D [auth A], J [auth B], K [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.184 
• R-Value Work: 0.155 
• R-Value Observed: 0.155 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.931	α = 90
b = 79.152	β = 130.16
c = 67.135	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALEPACK	data scaling
PHASER	phasing

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 1.1: 2018-02-21
  Changes: Database references
• Version 2.0: 2019-10-30
  Changes: Data collection, Derived calculations, Experimental preparation, Non-polymer description, Other, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description