1eex

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spinqualitylabelsall models 1eex, resolution 1.7Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

Overview

BACKGROUND: Adenosylcobalamin (coenzyme B(12)) serves as a cofactor for, enzymatic radical reactions. The adenosyl radical, a catalytic radical in, these reactions, is formed by homolysis of the cobalt-carbon bond of the, coenzyme, although the mechanism of cleavage of its organometallic bond, remains unsolved. RESULTS: We determined the three-dimensional structures, of diol dehydratase complexed with adeninylpentylcobalamin and with, cyanocobalamin at 1.7 A and 1.9 A resolution, respectively, at cryogenic, temperatures. In the adeninylpentylcobalamin complex, the adenine ring is, bound parallel to the corrin ring as in the free form and, methylmalonyl-CoA-mutase-bound coenzyme, but with the other side facing, pyrrole ring C. All of its nitrogen atoms except for N(9) are, hydrogen-bonded to mainchain amide oxygen and amide nitrogen atoms, a, sidechain hydroxyl group, and a water molecule. As compared with the, cyanocobalamin complex, the sidechain of Seralpha224 rotates by 120, degrees to hydrogen bond with N(3) of the adenine ring. CONCLUSIONS: The, structure of the adenine-ring-binding site provides a molecular basis for, the strict specificity of diol dehydratase for the coenzyme adenosyl, group. The superimposition of the structure of the free coenzyme on that, of enzyme-bound adeninylpentylcobalamin demonstrated that the tight, enzyme-coenzyme interactions at both the cobalamin moiety and adenine ring, of the adenosyl group would inevitably lead to cleavage of the, cobalt-carbon bond. Rotation of the ribose moiety around the glycosidic, linkage makes the 5'-carbon radical accessible to the hydrogen atom of the, substrate to be abstracted.

About this Structure

1EEX is a Protein complex structure of sequences from Klebsiella oxytoca with K, COY and PGO as ligands. Active as Propanediol dehydratase, with EC number 4.2.1.28 Full crystallographic information is available from OCA.

Reference

How a protein generates a catalytic radical from coenzyme B(12): X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex., Masuda J, Shibata N, Morimoto Y, Toraya T, Yasuoka N, Structure. 2000 Jul 15;8(7):775-88. PMID:10903944

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