5FQC | pdb_00005fqc

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 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

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 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.
School of Chemistry, University of Leeds, Leeds LS2 9JT, UK.
School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, 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 
• Modeled 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 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

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