1iwb
From Proteopedia
|
Crystal structure of diol dehydratase
Overview
Substrate binding triggers catalytic radical formation through the, cobalt-carbon bond homolysis in coenzyme B12-dependent enzymes. We have, determined the crystal structure of the substrate-free form of Klebsiella, oxytoca diol dehydratase*cyanocobalamin complex at 1.85 A resolution. The, structure contains two units of the heterotrimer consisting of alpha, beta, and gamma subunits. As compared with the structure of its, substrate-bound form, the beta subunits are tilted by approximately 3, degrees and cobalamin is also tilted so that pyrrole rings A and D are, significantly lifted up toward the substrate-binding site, whereas pyrrole, rings B and C are only slightly lifted up. The structure revealed that the, potassium ion in the substrate-binding site of the substrate-free enzyme, is also heptacoordinated; that is, two oxygen atoms of two water molecules, coordinate to it instead of the substrate hydroxyls. A modeling study in, which the structures of both the cobalamin moiety and the adenine ring of, the coenzyme were superimposed onto those of the enzyme-bound, cyanocobalamin and the adenine ring-binding pocket, respectively, demonstrated that the distortions of the Co-C bond in the substrate-free, form are already marked but slightly smaller than those in the, substrate-bound form. It was thus strongly suggested that the Co-C bond, becomes largely activated (labilized) when the coenzyme binds to the, apoenzyme even in the absence of substrate and undergoes homolysis through, the substrate-induced conformational changes of the enzyme. Kinetic, coupling of Co-C bond homolysis with hydrogen abstraction from the, substrate shifts the equilibrium to dissociation.
About this Structure
1IWB is a Protein complex structure of sequences from Klebsiella oxytoca with K and B12 as ligands. Active as Propanediol dehydratase, with EC number 4.2.1.28 Full crystallographic information is available from OCA.
Reference
Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase., Shibata N, Masuda J, Morimoto Y, Yasuoka N, Toraya T, Biochemistry. 2002 Oct 22;41(42):12607-17. PMID:12379103
Page seeded by OCA on Sat Nov 24 22:40:22 2007
