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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Anatomy of a proficient enzyme: The structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog
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Anatomy of a proficient enzyme: The structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog

机译：精通酶的解剖：存在和不存在潜在过渡态类似物时，牛尿苷5'-单磷酸脱羧酶的结构

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摘要

Orotidine 5'-phosphate decarboxylase produces the largest rate enhancement that has been reported for any enzyme. The crystal structure of the recombinant Saccharomyces cerevisiae enzyme has been determined in the absence and presence of the proposed transition state analog 6-hydroxyuridine 5'-phosphate, at a reso- lution of 2.1 A and 2.4 A, respectively. Orotidine 5'-phosphate decarboxylase folds as a TIM-barrel with the ligand binding site near the open end of the barrel. The binding of 6-hydroxyuridine 5'-phosphate is accompanied by protein loop movements that envelop the ligand almost completely, forming numerous favor- able interactions with the phosphoryl group, the ribofuranosyl group. and the pyrimidine ring. Lysine-93 appears to be anchored in such a way as to optimize electrostatic interactions with devel- oping negative charge at C-6 of the pyrimidine ring, and to donate the proton that replaces the carboxylate group at C-6 of the product. In addition. H-bonds from the active site to O-2 and O-4 help to delocalize negative charge in the transition state. Interac- tions between the enzyme and the phosphoribosyl group anchor the pyrimidine within the active site, helping to explain the phosphoribosyl group's remarkably large contribution to catalysis despite its distance from the site of decarboxylation.
机译：卵磷脂5'-磷酸脱羧酶产生最大的速率增加，这是任何酶所报道的。在不存在和存在拟议的过渡态类似物6-羟基尿苷5'-磷酸的条件下，分别测定了重组酿酒酵母酶的晶体结构，其分辨率分别为2.1 A和2.4A。卵磷脂5'-磷酸脱羧酶折叠成TIM桶，配体结合位点靠近桶的开口端。 6-羟基尿苷5'-磷酸的结合伴随着蛋白质环的运动，该环几乎完全包裹了配体，与磷酰基，呋喃核糖基形成了许多有利的相互作用。和嘧啶环。赖氨酸93的锚固方式可以优化静电相互作用，并在嘧啶环C-6处带有负电荷，并提供质子取代产物C-6上的羧酸根。此外。从活性位点到O-2和O-4的H键有助于在过渡态中使负电荷离域。酶和磷酸核糖基之间的相互作用将嘧啶锚定在活性位点内，这有助于解释尽管磷酸核糖基距脱羧位点很远，但对催化的贡献很大。

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