Substrate-Induced Conformational Change of a Coenzyme B12-Dependent Enzyme:  Crystal Structure of the Substrate-Free Form of Diol Dehydratase

• Published in: Biochemistry (Easton) 2002-10, Vol.41 (42), p.12607-12617
• Main Authors: Shibata, Naoki, Masuda, Jun, Morimoto, Yukio, Yasuoka, Noritake, Toraya, Tetsuo
• Format: Article
• Language: English
• Subjects: Binding Sites; Carbon - chemistry; Cations, Monovalent; Cobalt - chemistry; Cobamides - chemistry; Crystallization; Crystallography, X-Ray; Klebsiella - enzymology; Models, Molecular; Potassium - chemistry; Propanediol Dehydratase - chemistry; Protein Conformation; Substrate Specificity; Vitamin B 12 - chemistry
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi026104z

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 Å resolution. The structure contains two units of the heterotrimer consisting of α, β, and γ subunits. As compared with the structure of its substrate-bound form, the β subunits are tilted by ∼3° 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.