3TG2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.101 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.,Sect.D 68: 1329-1338

  • DOI: 10.1107/S090744491202848X
  • Primary Citation of Related Structures:  

  • 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 determin ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vibriobactin-specific isochorismatase
A
223Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 1 
Gene Names: vibB
EC: 3.3.2.1
Find proteins for P0C6D3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  P0C6D3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
ISC
Query on ISC

Download SDF File 
Download CCD File 
A
(5S,6S)-5-[(1-carboxyethenyl)oxy]-6-hydroxycyclohexa-1,3-diene-1-carboxylic acid
ISOCHORISMIC ACID
C10 H10 O6
NTGWPRCCOQCMGE-YUMQZZPRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.101 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.127 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.584α = 90.00
b = 55.584β = 90.00
c = 119.792γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data collection
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2014-01-01
    Type: Database references