6MK6

Carbapenemase VCC-1 from Vibrio cholerae N14-02106


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular Basis for the Potent Inhibition of the Emerging Carbapenemase VCC-1 by Avibactam.

Mangat, C.S.Vadlamani, G.Holicek, V.Chu, M.Larmour, V.L.C.Vocadlo, D.J.Mulvey, M.R.Mark, B.L.

(2019) Antimicrob Agents Chemother 63

  • DOI: 10.1128/AAC.02112-18
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In 2016, we identified a new class A carbapenemase, VCC-1, in a nontoxigenic Vibrio cholerae strain that had been isolated from retail shrimp imported into Canada for human consumption. Shortly thereafter, seven additional VCC-1-producing < ...

    In 2016, we identified a new class A carbapenemase, VCC-1, in a nontoxigenic Vibrio cholerae strain that had been isolated from retail shrimp imported into Canada for human consumption. Shortly thereafter, seven additional VCC-1-producing V. cholerae isolates were recovered along the German coastline. These isolates appear to have acquired the VCC-1 gene ( bla VCC-1 ) independently from the Canadian isolate, suggesting that bla VCC-1 is mobile and widely distributed. VCC-1 hydrolyzes penicillins, cephalothin, aztreonam, and carbapenems and, like the broadly disseminated class A carbapenemase KPC-2, is only weakly inhibited by clavulanic acid or tazobactam. Although VCC-1 has yet to be observed in the clinic, its encroachment into aquaculture and other areas with human activity suggests that the enzyme may be emerging as a public health threat. To preemptively address this threat, we examined the structural and functional biology of VCC-1 against the FDA-approved non-β-lactam-based inhibitor avibactam. We found that avibactam restored the in vitro sensitivity of V. cholerae to meropenem, imipenem, and ertapenem. The acylation efficiency was lower for VCC-1 than for KPC-2 and akin to that of Pseudomonas aeruginosa PAO1 AmpC ( k 2 / K i  = 3.0 × 10 3 M -1  s -1 ). The tertiary structure of VCC-1 is similar to that of KPC-2, and they bind avibactam similarly; however, our analyses suggest that VCC-1 may be unable to degrade avibactam, as has been found for KPC-2. Based on our prior genomics-based surveillance, we were able to target VCC-1 for detailed molecular studies to gain early insights that could be used to combat this carbapenemase in the future.


    Organizational Affiliation

    Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada brian.mark@umanitoba.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B, C, D
265Vibrio choleraeMutation(s): 0 
Gene Names: BC353_18910
EC: 3.5.2.6
Find proteins for A0A0U3IB62 (Vibrio cholerae)
Go to UniProtKB:  A0A0U3IB62
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.93α = 90
b = 46.65β = 99.28
c = 113.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada148496

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence