3TB4

Crystal structure of the ISC domain of VibB

Summary for 3TB4

• Entry DOI: 10.2210/pdb3tb4/pdb
• Descriptor: Vibriobactin-specific isochorismatase, octyl beta-D-glucopyranoside, TRIETHYLENE GLYCOL, ... (7 entities in total)
• Functional Keywords: isc domain, isochorismatase, hydrolase
• Biological source: Vibrio cholerae
• Total number of polymer chains: 1
• Total formula weight: 25490.08

Authors

Liu, S.,Zhang, C.,Niu, B.,Li, N.,Liu, M.,Wei, T.,Zhu, D.,Xu, S.,Gu, L. (deposition date: 2011-08-05, release date: 2012-08-29, Last modification date: 2023-11-01)

Primary citation

Liu, S.,Zhang, C.,Li, N.,Niu, B.,Liu, M.,Liu, X.,Wei, T.,Zhu, D.,Huang, Y.,Xu, S.,Gu, L.
Structural insight into the ISC domain of VibB from Vibrio cholerae at atomic resolution: a snapshot just before the enzymatic reaction
Acta Crystallogr.,Sect.D, 68:1329-1338, 2012

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.

PubMed: 22993087
DOI: 10.1107/S090744491202848X

Experimental method

X-RAY DIFFRACTION (1.35 Å)