1dhy
From Proteopedia
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KKS102 BPHC ENZYME
Overview
The crystal structure of an enzyme having polychlorinated-biphenyl, degrading activity, the BphC enzyme from Pseudomonas sp. strain KKS102, has been solved as a free form at 1.8 A resolution. This is the first, three-dimensional structure among the extradiol-type dioxygenases. Based, on 34,387 reflections (10.0 to 1.8 A, completeness 87.8%), a current, R-factor of 20.4% (with a free R-factor of 24.3%) was obtained with a, model obeying standard geometry within 0.011 A in bond lengths and 1.91, degrees in bond angles. The BphC enzyme is a homo-octamer and each subunit, is composed of two domains: Domain 1 (N-terminal part) and Domain 2, (C-terminal part). Each domain contains two repetitions of a novel folding, motif (the "beta alpha beta beta beta" motif) each consisting of ca 55, amino acid residues. A single Fe ion in the active site coordinates the, side-chains of three amino acid residues (His145, His209 and Glu260) and, two solvent molecules. The coordination geometry is that of a square, pyramid. In addition to the free form of the BphC enzyme, we have solved, two three-dimensional structures of the BphC enzyme complexed with its, substrates, 2,3-dihydroxybiphenyl (2,3-DHBP) or 3-methylcatechol (3-MCT)., These substrates were found intact in the active site probably because of, the oxidation of the Fe ion into ferric form (as judged by EPR spectra) in, the present crystals. In both of the two substrate complexes, the two, hydroxyl groups of the substrate, together with the three enzymatic, side-chain ligands, were found to form a penta-coordinated system around, the Fe ion roughly arranged in a trigonal bipyramidal configuration. The, active site structures appear to be essentially consistent with the, reaction mechanism proposed so far.
About this Structure
1DHY is a Single protein structure of sequence from Pseudomonas sp. with FE as ligand. Active as Biphenyl-2,3-diol 1,2-dioxygenase, with EC number 1.13.11.39 Full crystallographic information is available from OCA.
Reference
Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102., Senda T, Sugiyama K, Narita H, Yamamoto T, Kimbara K, Fukuda M, Sato M, Yano K, Mitsui Y, J Mol Biol. 1996 Feb 9;255(5):735-52. PMID:8636975
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