Literature summary for 1.14.12.18 extracted from

Kumar, P.; Gomez-Gil, L.; Mohammadi, M.; Sylvestre, M.; Eltis, L.D.; Bolin, J.T.
Anaerobic crystallization and initial X-ray diffraction data of biphenyl 2,3-dioxygenase from Burkholderia xenovorans LB400: addition of agarose improved the quality of the crystals (2011), Acta Crystallogr. Sect. F, 67, 59-62.

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Cloned(Commentary)

Cloned (Comment)	Organism
expressed in Escherichia coli C41 (DE3) cells	Paraburkholderia xenovorans
expression of His-tagged subunits alpha and beta and mutant variants in Escherichia coli strain C41 (DE3)	Paraburkholderia xenovorans
expression of His-tagged subunits alpha and beta and mutant variants in Escherichia coli strain C41(DE3)	Paraburkholderia xenovorans

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant BPDOLB400, sitting drop vapour diffusion method, anaerobic conditions, method optimization, 0.002 ml of 8 mg/ml protein in 25 mM HEPES, pH 7.3, containing 0.25 mM ferrous ammonium sulfate, and 2 mM dithiothreitol, is mixed with 0.002 ml of reservoir solution containing 20-25% w/v PEG 8000 or PEG 5000 MME, 50 mM PIPES, pH 6.5, 100 mM ammonium acetate, 5% v/v glycerol, and 0.2% w/v agarose, successful crystallization only occurs at pH 6.5, X-ray diffraction structure determination and analysis at 2.4-2.8 A resolution	Paraburkholderia xenovorans
sitting drop vapor diffusion method, using 20-25% (w/v) PEG 8000 or PEG 5000 MME, 50 mM PIPES pH 6.5, 100 mM ammonium acetate, 5% (v/v) glycerol and 0.2% (w/v) agarose	Paraburkholderia xenovorans

Crystallization (Comment)

Organism

purified recombinant BPDOLB400, sitting drop vapour diffusion method, anaerobic conditions, method optimization, 0.002 ml of 8 mg/ml protein in 25 mM HEPES, pH 7.3, containing 0.25 mM ferrous ammonium sulfate, and 2 mM dithiothreitol, is mixed with 0.002 ml of reservoir solution containing 20-25% w/v PEG 8000 or PEG 5000 MME, 50 mM PIPES, pH 6.5, 100 mM ammonium acetate, 5% v/v glycerol, and 0.2% w/v agarose, successful crystallization only occurs at pH 6.5, X-ray diffraction structure determination and analysis at 2.4-2.8 A resolution

Paraburkholderia xenovorans

sitting drop vapor diffusion method, using 20-25% (w/v) PEG 8000 or PEG 5000 MME, 50 mM PIPES pH 6.5, 100 mM ammonium acetate, 5% (v/v) glycerol and 0.2% (w/v) agarose

Paraburkholderia xenovorans

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
biphenyl + NADH + H+ + O2	Paraburkholderia xenovorans	-	2,3-dihydro-dihydroxybiphenyl + NAD+	-	?
biphenyl + NADH + H+ + O2	Paraburkholderia xenovorans	-	(1S,2R)-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+	-	?

Organism

Organism	UniProt	Comment	Textmining
Paraburkholderia xenovorans	-	-	-
Paraburkholderia xenovorans	P37333	subunit alpha	-
Paraburkholderia xenovorans	P37334	subunit beta	-

Purification (Commentary)

Purification (Comment)	Organism
-	Paraburkholderia xenovorans
recombinant His-tagged subunits alpha and beta and mutant variants from Escherichia coli strain C41 (DE3) by affinity chromatography, the tag is cleaved off by thrombin	Paraburkholderia xenovorans
recombinant His-tagged subunits alpha and beta and mutant variants from Escherichia coli strain C41(DE3) by affinity chromatography, the tag is cleaved off by thrombin	Paraburkholderia xenovorans

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
biphenyl + NADH + H+ + O2	-	Paraburkholderia xenovorans	2,3-dihydro-dihydroxybiphenyl + NAD+	-	?
biphenyl + NADH + H+ + O2	-	Paraburkholderia xenovorans	(1S,2R)-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+	-	?

Synonyms

Synonyms	Comment	Organism
BPDO	-	Paraburkholderia xenovorans
BPDOLB400	-	Paraburkholderia xenovorans

Cofactor

Cofactor	Comment	Organism	Structure
NADH	-	Paraburkholderia xenovorans

General Information

General Information	Comment	Organism
metabolism	biphenyl 2,3-dioxygenase catalyzes the initial step in the degradation of biphenyl and some polychlorinated biphenyls	Paraburkholderia xenovorans