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Review
. 2004 Aug;186(16):5189-96.
doi: 10.1128/JB.186.16.5189-5196.2004.

Biphenyl dioxygenases: functional versatilities and directed evolution

Kensuke Furukawa  1 , Hikaru Suenaga, Masatoshi Goto
Affiliations
Review

Biphenyl dioxygenases: functional versatilities and directed evolution

Kensuke Furukawa et al. J Bacteriol. 2004 Aug.
No abstract available

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Figures

FIG. 1.
FIG. 1.
Catabolic pathway for degradation of biphenyl and organization of the bph gene cluster in P. pseudoalcaligenes KF707. Compounds: I, biphenyl; II, 2,3-dihydroxy-4-phenylhexa-4,6-diene (dihydrodiol compound); III, 2,3-dihydroxybiphenyl; IV, HOPD (biphenyl meta-cleavage compound); V, benzoic acid; VI, 2-hydroxypenta-2,4-dienoic acid; VII, 4-hydroxy-2-oxovaleric acid; VIII, pyruvic acid; IX, acetaldehyde; X, acetyl-coenzyme A. The BphR1 protein, belonging to the GntR family, is a transcriptional regulator involved in the expression of bphR1 and bphX0X1X2X3D. The function of orf3 remains unclear (83, 84). ISP, iron-sulfur protein.
FIG. 2.
FIG. 2.
Organization of bph gene clusters in various strains. KF707-bph, P. pseudoalcaligenes KF707 bph gene cluster (20, 79, 83, 84); LB400-bph, Burkholderia sp. strain LB400 (15, 28, 54, 68); KF715-bph, P. putida KF715 (26, 59); KKS102-bph, Pseudomonas sp. strain KKS102 (36, 37, 39); Tn4371-bph, Ralstonia eutropha A5 (57); B-356-bph, C. testosteroni B-356 (10, 78); P6-bph, R. globerulus P6 (5, 6, 61); M5-bpd, Rhodococcus sp. strain M5 (44, 45, 82); RHA1-bph, Rhodococcus sp. strain RHA1 (48, 71, 85). Homologous genes with the same function are depicted in the same colors.
FIG. 3.
FIG. 3.
Proposed transcriptional regulation of bph genes in P. pseudoalcaligenes KF707. Two regulatory systems are involved in this regulation. The BphR2 protein positively regulates the bphA1A2A3A4BC genes and allow biphenyl to convert to HOPD. The BphR1 protein binds with HOPD and activates transcription of the bphR1 gene itself. The BphR1 protein is also involved in the expression of the bphX region and bphD. See the text for a detailed explanation. The data for the figure are from reference .
FIG. 4.
FIG. 4.
Binding model of evolved biphenyl dioxygenase with diphenylamine. The three-dimensional structure of the biphenyl dioxygenase (pSHF1072) was constructed based on that of naphthalene dioxygenase (34). The binding model of dioxygenase with diphenylamine was constructed with MOE software (CGI Co. Ltd.). Phe-277 (depicted in magenta) in the original enzyme was changed to Tyr (in green) in the evolved enzyme along with three other amino acids. The configuration of the substrate (diphenylamine) is depicted in red in the original enzyme and in lime in the evolved enzyme. Note that the 2,3 position of diphenylamine faces the catalytic mononuclear iron center in the evolved enzyme (depicted as a large red ball).
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