5AEW

Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans LB400 in complex with biphenyl

Summary for 5AEW

• Entry DOI: 10.2210/pdb5aew/pdb
• Related: 5AEU 5AEV
• Descriptor: BIPHENYL DIOXYGENASE SUBUNIT ALPHA, BIPHENYL DIOXYGENASE SUBUNIT BETA, FE2/S2 (INORGANIC) CLUSTER, ... (6 entities in total)
• Functional Keywords: oxidoreductase, biphenyl dioxygenase, bphae-ii9, biphenyl, polychlorinated biphenyls
• Biological source: BURKHOLDERIA XENOVORANS LB400; More
• Total number of polymer chains: 24
• Total formula weight: 887189.15

Authors

Dhindwal, S.,Gomez-Gil, L.,Sylvestre, M.,Eltis, L.D.,Bolin, J.T.,Kumar, P. (deposition date: 2015-01-10, release date: 2016-04-06, Last modification date: 2024-11-20)

Primary citation

Dhindwal, S.,Gomez-Gil, L.,Neau, D.B.,Pham, T.T.M.,Sylvestre, M.,Eltis, L.D.,Bolin, J.T.,Kumar, P.
Structural Basis of the Enhanced Pollutant-Degrading Capabilities of an Engineered Biphenyl Dioxygenase.
J.Bacteriol., 198:1499-, 2016

PubMed Abstract: Biphenyl dioxygenase, the first enzyme of the biphenyl catabolic pathway, is a major determinant of which polychlorinated biphenyl (PCB) congeners are metabolized by a given bacterial strain. Ongoing efforts aim to engineer BphAE, the oxygenase component of the enzyme, to efficiently transform a wider range of congeners. BphAEII9, a variant of BphAELB400 in which a seven-residue segment, (335)TFNNIRI(341), has been replaced by the corresponding segment of BphAEB356, (333)GINTIRT(339), transforms a broader range of PCB congeners than does either BphAELB400 or BphAEB356, including 2,6-dichlorobiphenyl, 3,3'-dichlorobiphenyl, 4,4'-dichlorobiphenyl, and 2,3,4'-trichlorobiphenyl. To understand the structural basis of the enhanced activity of BphAEII9, we have determined the three-dimensional structure of this variant in substrate-free and biphenyl-bound forms. Structural comparison with BphAELB400 reveals a flexible active-site mouth and a relaxed substrate binding pocket in BphAEII9 that allow it to bind different congeners and which could be responsible for the enzyme's altered specificity. Biochemical experiments revealed that BphAEII9 transformed 2,3,4'-trichlorobiphenyl and 2,2',5,5'-tetrachlorobiphenyl more efficiently than did BphAELB400 and BphAEB356 BphAEII9 also transformed the insecticide dichlorodiphenyltrichloroethane (DDT) more efficiently than did either parental enzyme (apparent kcat/Km of 2.2 ± 0.5 mM(-1) s(-1), versus 0.9 ± 0.5 mM(-1) s(-1) for BphAEB356). Studies of docking of the enzymes with these three substrates provide insight into the structural basis of the different substrate selectivities and regiospecificities of the enzymes.

PubMed: 26953337
DOI: 10.1128/JB.00952-15

Experimental method

X-RAY DIFFRACTION (1.88 Å)