4lye | pdb_00004lye

Crystal structure of the S105A mutant of a C-C hydrolase, DxnB2 from Sphingomonas wittichii RW1, in complex with substrate HOPDA

spinqualitylabelsall models 4lye, resolution 2.33Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4lye is a 1 chain structure with sequence from Sphww. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: HPK Related: 4lxg, 4lyd, 4lxh, 4lxi Gene: dxnB2, Swit_3055 (SPHWW) Activity: 2,6-dioxo-6-phenylhexa-3-enoate hydrolase, with EC number 3.7.1.8 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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, ESred, possessing 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 (HOPDA) to 2-hydroxy-2,4-pentadienoic acid (HPD) and benzoate support a nucleophilic mechanism catalysis. In DxnB2, the rate of ESred 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 (betanuc ~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 ESred 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. A substrate-assisted mechanism of nucleophile activation in a Ser-His-Asp containing C-C bond hydrolase.,Ruzzini AC, Bhowmik S, Ghosh S, Yam KC, Bolin JT, Eltis LD Biochemistry. 2013 Sep 25. PMID:24067021 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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