3v1l | pdb_00003v1l

Crystal Structure of the S112A/H265Q mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400

spinqualitylabelsall models 3v1l, resolution 2.11Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3v1l is a 1 chain structure with sequence from Burkholderia cepacia lb400. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: MLA Related: 2og1, 2ri6, 2pu7, 2puh, 2puj, 2rhw, 2rht, 3v1k, 3v1m, 3v1n Gene: bphD, Bxeno_C1120, Bxe_C1186 (Burkholderia cepacia LB400) Activity: 2,6-dioxo-6-phenylhexa-3-enoate hydrolase, with EC number 3.7.1.8 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [BPHD_BURXL] Catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to produce benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD). Publication Abstract from PubMed Meta-cleavage product (MCP) hydrolases are members of the alpha/beta-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 A 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 (18)O into the benzoate produced during hydrolysis in H(2)(18)O. 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, ES(red), 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. Identification of an Acyl-Enzyme Intermediate in a meta-Cleavage Product Hydrolase Reveals the Versatility of the Catalytic Triad.,Ruzzini AC, Ghosh S, Horsman GP, Foster LJ, Bolin JT, Eltis LD J Am Chem Soc. 2012 Mar 14;134(10):4615-24. Epub 2012 Mar 5. PMID:22339283 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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