Uroporphyrinogen decarboxylation as a benchmark for the catalytic proficiency of enzymes
Uroporphyrinogen decarboxylation as a benchmark for the catalytic proficiency of enzymes
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DOI：
10.1073/pnas.0809838105
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发表时间：
2008-11-11
影响因子：
11.1
通讯作者：
Wolfenden, Richard
中科院分区：
文献类型：
--
作者：
Lewis, Charles A., Jr.;Wolfenden, Richard
酶在过渡状态下对改变的底物的亲和力的大小超过其对基态底物的亲和力，其因子与酶产生的速率增强相匹配。特别引人注目的是那些作为简单蛋白质催化剂的酶，不需要金属或其他辅助因子的帮助。为了确定人尿卟啉原脱羧酶在多大程度上提高了底物脱羧的速率，我们检测了吡咯酰-3-乙酸酯的自发脱羧速率。在高温下测量的一阶速率常数外推表明，在25℃无酶的情况下，该反应的半衰期为2.3 x 10(9)年。该酶与orotidine 5'-单磷酸脱羧酶（ODCase）没有明显的同源性，ODCase是另一种催化非常缓慢反应的无辅酶。有人提出，在这两种情况下，质子化的碱性残基（在人类UroD的情况下是Arg-37；在酵母ODCase的情况下是Lys-93）提供反离子，帮助底物的可剪切羧酸基团离开水进入相对非极性的环境，稳定CO2离开产生的初始碳离子，并提供取代其位置的质子。
The magnitude of an enzyme's affinity for the altered substrate in the transition state exceeds its affinity for the substrate in the ground state by a factor matching the rate enhancement that the enzyme produces. Particularly remarkable are those enzymes that act as simple protein catalysts, without the assistance of metals or other cofactors. To determine the extent to which one such enzyme, human uroporphyrinogen decarboxylase, enhances the rate of substrate decarboxylation, we examined the rate of spontaneous decarboxylation of pyrrolyl-3-acetate. Extrapolation of first-order rate constants measured at elevated temperatures indicates that this reaction proceeds with a half-life of 2.3 x 10(9) years at 25 degrees C in the absence of enzyme. This enzyme shows no significant homology with orotidine 5'-monophosphate decarboxylase (ODCase), another cofactorless enzyme that catalyzes a very slow reaction. It is proposed that, in both cases, a protonated basic residue (Arg-37 in the case of human UroD; Lys-93 in the case of yeast ODCase) furnishes a counterion that helps the scissile carboxylate group of the substrate leave water and enter a relatively nonpolar environment, stabilizes the incipient carbanion generated by the departure of CO2, and supplies the proton that takes its place.