6JV4

Crystal structure of metallo-beta-lactamase VMB-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Genetic and Biochemical Characterization of VMB-1, a Novel Metallo-beta-Lactamase Encoded by a Conjugative, Broad-Host Range IncC Plasmid from Vibrio spp.

Zheng, Z.Cheng, Q.Chan, E.W.Chen, S.

(2020) Adv Biosyst 4: e1900221-e1900221

  • DOI: https://doi.org/10.1002/adbi.201900221
  • Primary Citation of Related Structures:  
    6JV4

  • PubMed Abstract: 

    The increasing incidence of phenotypic resistance to carbapenems in recent years is mainly attributed to acquisition of mobile carbapenemase-encoding genetic elements by major bacterial pathogens. Here, a novel carbapenemase known as Vibrio metallo-β-lactamase 1 (VMB-1), which is encoded by a gene (bla VMB-1 ) located in an integron-bearing, highly transmissible IncC type plasmid, namely pVB1796, is identified and characterized, both genetically and functionally. Recovered from a foodborne Vibrio alginolyticus strain that exhibits resistance to all known β-lactam antibiotics, pVB1796 is found to possess a hybrid backbone that exhibits unique features of both type 1 and type 2 IncC elements. VMB-1 exhibits 94% sequence homology with several recently reported but poorly characterized metallo-β-lactamases (MBLs) produced by the marine organisms Alteromonadaceae, Glaciecola, and Thalassomonas actiniarum. Sequence alignment analysis shows that VMB-1 shares a structurally identical active site with subclass B1 MBLs. Importantly, pVB1796 is found to be efficiently transferred from Vibrio to other Gram-negative bacterial pathogens, including Salmonella typhimurium, Klebsiella pneumoniae, and Acinetobacter baumanni, via conjugation. These findings suggest that bla VMB-1 -bearing plasmids have the potential to be disseminated to other Gram-negative bacterial pathogens in the near future and render carbapenems useless in treatment of multidrug resistant infections.


  • Organizational Affiliation

    Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen, 518052, P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VMB-1
A, B, C, D
234Vibrio alginolyticusMutation(s): 0 
Gene Names: vmb-1
EC: 3.5.2.6
UniProt
Find proteins for A0A5Q5ADH9 (Vibrio alginolyticus)
Explore A0A5Q5ADH9 
Go to UniProtKB:  A0A5Q5ADH9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5Q5ADH9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT (Subject of Investigation/LOI)
Query on CIT

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
K [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
N [auth D],
O [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.957α = 90
b = 94.981β = 90
c = 145.503γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2020-06-10
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references, Derived calculations