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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.
    View publication on PubMedView publication on EuropePMC

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

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