3GZX

Crystal Structure of the Biphenyl Dioxygenase in complex with Biphenyl from Comamonas testosteroni Sp. Strain B-356

Summary for 3GZX

• Entry DOI: 10.2210/pdb3gzx/pdb
• Related: 3GZY 3GZZ
• Descriptor: Biphenyl dioxygenase subunit alpha, Biphenyl dioxygenase subunit beta, FE (II) ION, ... (8 entities in total)
• Functional Keywords: dioxygenase, rieskie, non-heme iron, aromatic hydrocarbons catabolism, iron, iron-sulfur, metal-binding, nad, oxidoreductase
• Biological source: Comamonas testosteroni (Pseudomonas testosteroni); More
• Total number of polymer chains: 2
• Total formula weight: 74100.25

Authors

Kumar, P.,Colbert, C.L.,Bolin, J.T. (deposition date: 2009-04-08, release date: 2010-05-05, Last modification date: 2023-11-01)

Primary citation

Colbert, C.L.,Agar, N.Y.,Kumar, P.,Chakko, M.N.,Sinha, S.C.,Powlowski, J.B.,Eltis, L.D.,Bolin, J.T.
Structural Characterization of Pandoraea pnomenusa B-356 Biphenyl Dioxygenase Reveals Features of Potent Polychlorinated Biphenyl-Degrading Enzymes
Plos One, 8:e52550-e52550, 2013

PubMed Abstract: The oxidative degradation of biphenyl and polychlorinated biphenyls (PCBs) is initiated in Pandoraea pnomenusa B-356 by biphenyl dioxygenase (BPDO(B356)). BPDO(B356), a heterohexameric (αβ)(3) Rieske oxygenase (RO), catalyzes the insertion of dioxygen with stereo- and regioselectivity at the 2,3-carbons of biphenyl, and can transform a broad spectrum of PCB congeners. Here we present the X-ray crystal structures of BPDO(B356) with and without its substrate biphenyl 1.6-Å resolution for both structures. In both cases, the Fe(II) has five ligands in a square pyramidal configuration: H233 Nε2, H239 Nε2, D386 Oδ1 and Oδ2, and a single water molecule. Analysis of the active sites of BPDO(B356) and related ROs revealed structural features that likely contribute to the superior PCB-degrading ability of certain BPDOs. First, the active site cavity readily accommodates biphenyl with minimal conformational rearrangement. Second, M231 was predicted to sterically interfere with binding of some PCBs, and substitution of this residue yielded variants that transform 2,2'-dichlorobiphenyl more effectively. Third, in addition to the volume and shape of the active site, residues at the active site entrance also apparently influence substrate preference. Finally, comparison of the conformation of the active site entrance loop among ROs provides a basis for a structure-based classification consistent with a phylogeny derived from amino acid sequence alignments.

PubMed: 23308114
DOI: 10.1371/journal.pone.0052550

Experimental method

X-RAY DIFFRACTION (1.58 Å)