Download MendeleyA substrate-assisted mechanism of nucleophile activation in a ser-his-asp containing C-C bond hydrolase.
Ruzzini, A.C., Bhowmik, S., Ghosh, S., Yam, K.C., Bolin, J.T., Eltis, L.D.(2013) Biochemistry 52: 7428-7438
- PubMed: 24067021
- DOI: https://doi.org/10.1021/bi401156a
- Primary Citation of Related Structures:
4LXI, 4LYE - PubMed Abstract:
The meta-cleavage product (MCP) hydrolases utilize a Ser-His-Asp triad to hydrolyze a carbon-carbon bond. Hydrolysis of the MCP substrate has been proposed to proceed via an enol-to-keto tautomerization followed by a nucleophilic mechanism of catalysis. Ketonization involves an intermediate, ES(red), which possesses a remarkable bathochromically shifted absorption spectrum. We investigated the catalytic mechanism of the MCP hydrolases using DxnB2 from Sphingomonas wittichii RW1. Pre-steady-state kinetic and LC ESI/MS evaluation of the DxnB2-mediated hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid to 2-hydroxy-2,4-pentadienoic acid and benzoate support a nucleophilic mechanism catalysis. In DxnB2, the rate of ES(red) decay and product formation showed a solvent kinetic isotope effect of 2.5, indicating that a proton transfer reaction, assigned here to substrate ketonization, limits the rate of acylation. For a series of substituted MCPs, this rate was linearly dependent on MCP pKa2 (βnuc ∼ 1). Structural characterization of DxnB2 S105A:MCP complexes revealed that the catalytic histidine is displaced upon substrate-binding. The results provide evidence for enzyme-catalyzed ketonization in which the catalytic His-Asp pair does not play an essential role. The data further suggest that ES(red) represents a dianionic intermediate that acts as a general base to activate the serine nucleophile. This substrate-assisted mechanism of nucleophilic catalysis distinguishes MCP hydrolases from other serine hydrolases.
Organizational Affiliation:
Departments of †Biochemistry & Molecular Biology and ‡Microbiology & Immunology, The University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada.
