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Identification of an Acyl-Enzyme Intermediate in a meta-Cleavage Product Hydrolase Reveals the Versatility of the Catalytic Triad

Author:
Ruzzini, Antonio C., Ghosh, Subhangi, Horsman, Geoff P., Foster, Leonard J., Bolin, Jeffrey T., Eltis, Lindsay D.
Source:
Journal of the American Chemical Society 2012 v.134 no.10 pp. 4615-4624
ISSN:
1520-5126
Subject:
acylation, biphenyl, crystal structure, histidine, hydrogen bonding, hydrolysis, mass spectrometry, oxyanions, oxygen, serine, serine proteinases, stable isotopes
Abstract:
Meta-cleavage product (MCP) hydrolases are members of the α/β-hydrolase superfamily that utilize a Ser-His-Asp triad to catalyze the hydrolysis of a C–C bond. BphD, the MCP hydrolase from the biphenyl degradation pathway, hydrolyzes 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to 2-hydroxypenta-2,4-dienoic acid (HPD) and benzoate. A 1.6 Å resolution crystal structure of BphD H265Q incubated with HOPDA revealed that the enzyme’s catalytic serine was benzoylated. The acyl-enzyme is stabilized by hydrogen bonding from the amide backbone of ‘oxyanion hole’ residues, consistent with formation of a tetrahedral oxyanion during nucleophilic attack by Ser112. Chemical quench and mass spectrometry studies substantiated the formation and decay of a Ser112-benzoyl species in wild-type BphD on a time scale consistent with turnover and incorporation of a single equivalent of ¹⁸O into the benzoate produced during hydrolysis in H₂¹⁸O. Rapid-scanning kinetic studies indicated that the catalytic histidine contributes to the rate of acylation by only an order of magnitude, but affects the rate of deacylation by over 5 orders of magnitude. The orange-colored catalytic intermediate, ESʳᵉᵈ, previously detected in the wild-type enzyme and proposed herein to be a carbanion, was not observed during hydrolysis by H265Q. In the newly proposed mechanism, the carbanion abstracts a proton from Ser112, thereby completing tautomerization and generating a serinate for nucleophilic attack on the C6-carbonyl. Finally, quantification of an observed pre-steady-state kinetic burst suggests that BphD is a half-site reactive enzyme. While the updated catalytic mechanism shares features with the serine proteases, MCP hydrolase-specific chemistry highlights the versatility of the Ser-His-Asp triad.
Agid:
5384797