2y99 | pdb_00002y99

Crystal Structure of cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB)from Pandoraea pnomenusa strain B-356 complex with co-enzyme NAD

spinqualitylabelsall models 2y99, resolution 2.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2y99 is a 2 chain structure with sequence from Atcc 11996. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: NAD Related: 3zv5, 3zv6, 2y93, 3zv4, 3zv3 Activity: Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase, with EC number 1.3.1.56 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Biphenyl dehydrogenase, a member of short-chain dehydrogenase/reductase enzymes, catalyzes the second step of the biphenyl/polychlorinated biphenyls catabolic pathway in bacteria. To understand the molecular basis for the broad substrate specificity of Pandoraea pnomenusa strain B-356 biphenyl dehydrogenase (BphB(B-356)), the crystal structures of the apo-enzyme, the binary complex with NAD(+), and the ternary complexes with NAD(+)-2,3-dihydroxybiphenyl and NAD(+)-4,4'-dihydroxybiphenyl were determined at 2.2-, 2.5-, 2.4-, and 2.1-A resolutions, respectively. A crystal structure representing an intermediate state of the enzyme was also obtained in which the substrate binding loop was ordered as compared with the apo and binary forms but it was displaced significantly with respect to the ternary structures. These five structures reveal that the substrate binding loop is highly mobile and that its conformation changes during ligand binding, starting from a disorganized loop in the apo state to a well organized loop structure in the ligand-bound form. Conformational changes are induced during ligand binding; forming a well defined cavity to accommodate a wide variety of substrates. This explains the biochemical data that shows BphB(B-356) converts the dihydrodiol metabolites of 3,3'-dichlorobiphenyl, 2,4,4'-trichlorobiphenyl, and 2,6-dichlorobiphenyl to their respective dihydroxy metabolites. For the first time, a combination of structural, biochemical, and molecular docking studies of BphB(B-356) elucidate the unique ability of the enzyme to transform the cis-dihydrodiols of double meta-, para-, and ortho-substituted chlorobiphenyls. Biochemical Studies and Ligand-bound Structures of Biphenyl Dehydrogenase from Pandoraea pnomenusa Strain B-356 Reveal a Basis for Broad Specificity of the Enzyme.,Dhindwal S, Patil DN, Mohammadi M, Sylvestre M, Tomar S, Kumar P J Biol Chem. 2011 Oct 21;286(42):37011-22. Epub 2011 Aug 31. PMID:21880718 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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