2YFL

Crystal Structure of Biphenyl dioxygenase variant RR41 with 2-chloro dibenzofuran

Summary for 2YFL

• Entry DOI: 10.2210/pdb2yfl/pdb
• Related: 2XR8 2XRX 2XSH 2XSO 2YFI 2YFJ
• Descriptor: BIPHENYL DIOXYGENASE SUBUNIT ALPHA, BIPHENYL DIOXYGENASE SUBUNIT BETA, FE2/S2 (INORGANIC) CLUSTER, ... (6 entities in total)
• Functional Keywords: oxidoreductase, degradation, bpdo
• Biological source: BURKHOLDERIA XENOVORANS; More
• Total number of polymer chains: 12
• Total formula weight: 443852.73

Authors

Kumar, P.,Bolin, J.T. (deposition date: 2011-04-06, release date: 2012-05-16, Last modification date: 2023-12-20)

Primary citation

Kumar, P.,Mohammadi, M.,Dhindwal, S.,Pham, T.T.,Bolin, J.T.,Sylvestre, M.
Structural Insights Into the Metabolism of 2-Chlorodibenzofuran by an Evolved Biphenyl Dioxygenase.
Biochem.Biophys.Res.Commun., 421:757-, 2012

PubMed Abstract: The biphenyl dioxygenase of Burkholderia xenovorans LB400 (BphAE(LB400)) is a Rieske-type oxygenase that catalyzes the stereospecific oxygenation of many heterocyclic aromatics including dibenzofuran. In a previous work, we evolved BphAE(LB400) and obtained BphAE(RR41). This variant metabolizes dibenzofuran and 2-chlorodibenzofuran more efficiently than BphAE(LB400). However, the regiospecificity of BphAE(RR41) toward these substrates differs. Dibenzofuran is metabolized principally through a lateral dioxygenation whereas 2-chlorodibenzofuran is metabolized principally through an angular dioxygenation. In order to explain this difference, we examined the crystal structures of both substrate-bound forms of BphAE(RR41) obtained under anaerobic conditions. This structure analysis, in combination with biochemical data for a Ser283Gly mutant provided evidences that the substrate is compelled to move after oxygen-binding in BphAE(RR41):dibenzofuran. In BphAE(RR41):2-chlorodibenzofuran, the chlorine atom is close to the side chain of Ser283. This contact is missing in the BphAE(RR41):dibenzofuran, and strong enough in the BphAE(RR41):2-chlorodibenzofuran to help prevent substrate movement during the catalytic reaction.

PubMed: 22546558
DOI: 10.1016/J.BBRC.2012.04.078

Experimental method

X-RAY DIFFRACTION (2.6 Å)