3TG2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.128 

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 D Biol Crystallogr 68: 1329-1338

  • DOI: 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vibriobactin-specific isochorismataseA223Vibrio choleraeMutation(s): 1 
Gene Names: VC_0771vibB
EC: 3.3.2.1
Find proteins for P0C6D3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore P0C6D3 
Go to UniProtKB:  P0C6D3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ISC
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
NTGWPRCCOQCMGE-YUMQZZPRSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
C [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



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