1IWB

Crystal structure of diol dehydratase

Summary for 1IWB

• Entry DOI: 10.2210/pdb1iwb/pdb
• Related: 1DIO 1EEX 1EGM 1EGV
• Descriptor: DIOL DEHYDRATASE alpha chain, DIOL DEHYDRATASE beta chain, DIOL DEHYDRATASE gamma chain, ... (6 entities in total)
• Functional Keywords: beta-alpha-barrels, lyase
• Biological source: Klebsiella oxytoca; More
• Total number of polymer chains: 6
• Total formula weight: 210392.31

Authors

Shibata, N.,Masuda, J.,Morimoto, Y.,Yasuoka, N.,Toraya, T. (deposition date: 2002-05-01, release date: 2003-05-01, Last modification date: 2024-05-29)

Primary citation

Shibata, N.,Masuda, J.,Morimoto, Y.,Yasuoka, N.,Toraya, T.
Substrate-induced conformational change of a coenzyme B12-dependent enzyme: crystal structure of the substrate-free form of diol dehydratase
Biochemistry, 41:12607-12617, 2002

PubMed Abstract: 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.

PubMed: 12379103
DOI: 10.1021/bi026104z

Experimental method

X-RAY DIFFRACTION (1.85 Å)