Ruzheinikov S N, Burke J, Sedelnikova S, Baker P J, Taylor R, Bullough P A, Muir N M, Gore M G, Rice D W
Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom.
Structure. 2001 Sep;9(9):789-802. doi: 10.1016/s0969-2126(01)00645-1.
Bacillus stearothermophilus glycerol dehydrogenase (GlyDH) (glycerol:NAD(+) 2-oxidoreductase, EC 1.1.1.6) catalyzes the oxidation of glycerol to dihydroxyacetone (1,3-dihydroxypropanone) with concomitant reduction of NAD(+) to NADH. Analysis of the sequence of this enzyme indicates that it is a member of the so-called iron-containing alcohol dehydrogenase family. Despite this sequence similarity, GlyDH shows a strict dependence on zinc for activity. On the basis of this, we propose to rename this group the family III metal-dependent polyol dehydrogenases. To date, no structural data have been reported for any enzyme in this group.
The crystal structure of B. stearothermophilus glycerol dehydrogenase has been determined at 1.7 A resolution to provide structural insights into the mechanistic features of this family. The enzyme has 370 amino acid residues, has a molecular mass of 39.5 kDa, and is a homooctamer in solution.
Analysis of the crystal structures of the free enzyme and of the binary complexes with NAD(+) and glycerol show that the active site of GlyDH lies in the cleft between the enzyme's two domains, with the catalytic zinc ion playing a role in stabilizing an alkoxide intermediate. In addition, the specificity of this enzyme for a range of diols can be understood, as both hydroxyls of the glycerol form ligands to the enzyme-bound Zn(2+) ion at the active site. The structure further reveals a previously unsuspected similarity to dehydroquinate synthase, an enzyme whose more complex chemistry shares a common chemical step with that catalyzed by glycerol dehydrogenase, providing a striking example of divergent evolution. Finally, the structure suggests that the NAD(+) binding domain of GlyDH may be related to that of the classical Rossmann fold by switching the sequence order of the two mononucleotide binding folds that make up this domain.
嗜热栖热放线菌甘油脱氢酶（GlyDH）（甘油：NAD(+) 2 -氧化还原酶，EC 1.1.1.6）催化甘油氧化为二羟基丙酮（1,3 -二羟基丙酮），同时将NAD(+)还原为NADH。对该酶序列的分析表明它是所谓含铁醇脱氢酶家族的一员。尽管有这种序列相似性，但GlyDH的活性严格依赖于锌。基于此，我们提议将这个家族重新命名为III族金属依赖性多元醇脱氢酶。迄今为止，该家族中任何一种酶的结构数据都尚未报道。
已确定嗜热栖热放线菌甘油脱氢酶的晶体结构，分辨率为1.7 Å，以提供对该家族机制特征的结构见解。该酶有370个氨基酸残基，分子量为39.5 kDa，在溶液中是同源八聚体。
对游离酶以及与NAD(+)和甘油形成的二元复合物的晶体结构分析表明，GlyDH的活性位点位于酶的两个结构域之间的裂隙中，催化锌离子在稳定醇盐中间体方面发挥作用。此外，该酶对一系列二醇的特异性是可以理解的，因为甘油的两个羟基都与活性位点处与酶结合的Zn(2+)离子形成配体。该结构进一步揭示了与脱氢奎尼酸合酶此前未被怀疑的相似性，脱氢奎尼酸合酶更复杂的化学反应与甘油脱氢酶催化的反应有一个共同的化学步骤，这是趋异进化的一个显著例子。最后，该结构表明，通过改变构成该结构域的两个单核苷酸结合折叠的序列顺序，GlyDH的NAD(+)结合结构域可能与经典的罗斯曼折叠结构域相关。
