Structure Study of Vitamin B12 enzyme, Diol Dehydratase

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Two crystal forms of Klebsiella oxytoca diol dehydratase complexed with cyanocobalamin have been obtained and crystallographic structure analysis have been performed. The crystals belong to two different space groups, according to the corresponding crystallization condition. One crystal (form I) belongs to the space group P2_12_12_1 with unit cell dimensions of a=76.2, b=122.3, c=209.6 Å, and diffracts up to 2.2Å resolution using an X-ray beam from a synchrotron radiation source. The other crystal (form II) belongs to the space group P2_1 with unit cell dimensions of a=75.4, b=132.7, c=298.8Å, β=91.9° and diffracts up to 3.0Å resolution. The three-dimensional structure of form I was determined at 2.2Å resolution. Diol dehydratase exists in a dimeric form of hetero-trimer, (αβγ)_2. The B_<12> molecule is bound between the α and β subunits in the "base-on" mode, that is, 5,6-dimethylbenzimidazole of the nucleotide moiety is coordinated to the cobalt atom in the lower axial position. The α subunit includes a (β/α)_8 barrel. The substrate and an essential potassium ion exist deeply buried inside the barrel. Based on unique direct interactions between potassium ion and two hydroxyl groups of the substrate, propanediol, direct participation of a potassium ion in enzyme catalysis is proposed.