Crystal structure of the ISC domain of VibB in complex with isochorismate

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.128 

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Structural insight into the ISC domain of VibB from Vibrio cholerae at atomic resolution: a snapshot just before the enzymatic reaction

Liu, S.Zhang, C.Li, N.Niu, B.Liu, M.Liu, X.Wei, T.Zhu, D.Huang, Y.Xu, S.Gu, L.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1329-1338

  • DOI: https://doi.org/10.1107/S090744491202848X
  • Primary Citation of Related Structures:  
    3TB4, 3TG2

  • PubMed Abstract: 

    The N-terminal isochorismatase (ISC) domain of VibB (VibB-ISC) catalyzes the vinyl ether hydrolysis of isochorismate to 2,3-dihydro-2,3-dihydroxybenzoate and pyruvate. Structures of the ISC domain and its complex with isochorismate have been determined at 1.35 and 1.10 Å resolution, respectively. Two catalytic waters which were absent from previously reported homologous structures were observed adjacent to isochorismate and the catalytic residues (Asp35 and Lys118) in the VibB-ISC complex. Molecular-dynamics (MD) simulations starting with the structure of the VibB-ISC complex suggest that the catalytic waters contribute to the hydrolysis of the vinyl ether by participating in two reactions. Firstly, they may function as a general acid to protonate the Asp35 carboxylate prior to isochorismate protonation; secondly, one of the catalytic waters may be activated by the ionizable side chain of Asp35 to perform a nucleophilic attack on the intermediate carbocation/oxocarbonium ion. The positions of the waters are both significantly affected by the mutation of Asp35 and Lys118. The structural, biochemical and MD results reveal the residues that are involved in substrate binding and provide clues towards defining a possible mechanism.

  • Organizational Affiliation

    State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan, Shandong 250100, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vibriobactin-specific isochorismatase223Vibrio choleraeMutation(s): 1 
Gene Names: VC_0771vibB
Find proteins for P0C6D3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P0C6D3 
Go to UniProtKB:  P0C6D3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6D3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ISC

Download Ideal Coordinates CCD File 
B [auth A](5S,6S)-5-[(1-carboxyethenyl)oxy]-6-hydroxycyclohexa-1,3-diene-1-carboxylic acid
C10 H10 O6
Query on PGE

Download Ideal Coordinates CCD File 
C6 H14 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.128 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.584α = 90
b = 55.584β = 90
c = 119.792γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2014-01-01
    Changes: Database references
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description