Literature summary for 3.7.1.8 extracted from

Ruzzini, A.C.; Ghosh, S.; Horsman, G.P.; Foster, L.J.; Bolin, J.T.; Eltis, L.D.
Identification of an acyl-enzyme intermediate in a meta-cleavage product hydrolase reveals the versatility of the catalytic triad (2012), J. Am. Chem. Soc., 134, 4615-4624.

Cloned(Commentary)

Cloned (Comment)	Organism
gene bphD, expression of wild-type and mutant BphDs	Paraburkholderia xenovorans

Crystallization (Commentary)

Crystallization (Comment)	Organism
BphD H265Q and S112A/H265Q mutants in complex with substrate 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid, sitting drop vapour diffusion method, 0.001 ml of protein solution containing 4 mg/ml protein in 20 mM HEPES, pH 7.5, 20°C, 9 days, is mixed with 0.001 ml of reservoir solution containing 2.4 M malonate at pH 6.0-7.0, X-ray diffraction structure determination and analysis at 1.3 A and 1.9 A resolutions, respectively	Paraburkholderia xenovorans

Crystallization (Comment)

Organism

BphD H265Q and S112A/H265Q mutants in complex with substrate 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid, sitting drop vapour diffusion method, 0.001 ml of protein solution containing 4 mg/ml protein in 20 mM HEPES, pH 7.5, 20°C, 9 days, is mixed with 0.001 ml of reservoir solution containing 2.4 M malonate at pH 6.0-7.0, X-ray diffraction structure determination and analysis at 1.3 A and 1.9 A resolutions, respectively

Paraburkholderia xenovorans

Protein Variants

Protein Variants	Comment	Organism
H265Q	site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme and does not show formation of the carbanion catalytic intermediate in contrast to the wild-type enzyme	Paraburkholderia xenovorans
S112A/H265Q	site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme	Paraburkholderia xenovorans

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	pre-steady-state kinetic burst of BphD	Paraburkholderia xenovorans

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid + H2O	Paraburkholderia xenovorans	i.e. HOPDA	2-hydroxypenta-2,4-dienoic acid + benzoate	-	?

Organism

Organism	UniProt	Comment	Textmining
Paraburkholderia xenovorans	P47229	gene bphD	-

Reaction

Reaction	Comment	Organism	Reaction ID
2,6-dioxo-6-phenylhexa-3-enoate + H2O = benzoate + 2-oxopent-4-enoate	formation of a catalytic intermediate carbanion during hydrolysis, the carbanion abstracts a proton from Ser112, thereby completing tautomerization and generating a serinate for nucleophilic attack on the C6-carbonyl, catalytic mechanism, overview. BphD is a half-site reactive enzyme with versatility of the Ser-His-Asp triad, role of the catalytic His in acylation and deacylation	Paraburkholderia xenovorans	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid + H2O	i.e. HOPDA	Paraburkholderia xenovorans	2-hydroxypenta-2,4-dienoic acid + benzoate	-	?

Synonyms

Synonyms	Comment	Organism
BphD	-	Paraburkholderia xenovorans
MCP hydrolase	-	Paraburkholderia xenovorans
meta-cleavage product hydrolase	-	Paraburkholderia xenovorans

General Information

General Information	Comment	Organism
evolution	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	Paraburkholderia xenovorans
metabolism	BphD is the MCP hydrolase from the biphenyl degradation pathway and hydrolyzes 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to 2-hydroxypenta-2,4-dienoic acid (HPD) and benzoate	Paraburkholderia xenovorans