An Enzyme with High Catalytic Proficiency Utilizes Distal Site Substrate Binding Energy to Stabilize the Closed State but at the Expense of Substrate Inhibition.
An Enzyme with High Catalytic Proficiency Utilizes Distal Site Substrate Binding Energy to Stabilize the Closed State but at the Expense of Substrate Inhibition.
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DOI：
10.1021/acscatal.1c05524
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发表时间：
2022-03-04
期刊：
影响因子：
12.9
通讯作者：
Waltho, Jonathan P.
中科院分区：
文献类型：
--
作者：
Robertson, Angus J.;Cruz-Navarrete, F. Aaron;Wood, Henry P.;Vekaria, Nikita;Hounslow, Andrea M.;Bisson, Claudine;Cliff, Matthew J.;Baxter, Nicola J.;Waltho, Jonathan P.
关键词：
理解酶的巨大催化潜能的基础因素是催化和酶设计的基础。酶能够部分地通过利用来自底物的非反应部分的结合能来实现高催化效率。特别是，酶与底物含有一个nonreactioning磷酸二阴离子基团协调在一个远端网站已被建议利用这种结合能主要是为了促进构象变化从一个开放的非活性形式到一个封闭的活性形式，而不是诱导基态不稳定或稳定的过渡态。然而，该模型的详细结构证据有限。在这里，我们使用β-磷酸葡萄糖变位酶（βPGM）来研究在远端位点结合磷酸二阴离子基团、采用封闭的酶形式和催化能力之间的关系。βPGM通过近端位点的磷酰基转移反应催化β-葡萄糖1-磷酸异构化为葡萄糖6-磷酸，同时在远端位点配位底物的磷酸双阴离子基团。β-PGM具有最大的催化活性之一，并且在其催化循环期间经历显著的结构域闭合。我们发现，在远端位点的侧链取代导致底物结合减少，使封闭的活性形式不稳定，但不足以排除通过一个完全封闭的，近过渡态构象。此外，我们发现，在远端网站的磷酸双阴离子基团的结合刺激结构域关闭，即使在近端网站的转移磷酰基基团的情况下，解释了先前报道的β-葡萄糖1-磷酸抑制。最后，我们的研究结果支持一种趋势，即涉及磷酸化底物的具有高催化活性的酶表现出更大的稳定封闭活性形式的需求。
Understanding the factors that underpin the enormous catalytic proficiencies of enzymes is fundamental to catalysis and enzyme design. Enzymes are, in part, able to achieve high catalytic proficiencies by utilizing the binding energy derived from nonreacting portions of the substrate. In particular, enzymes with substrates containing a nonreacting phosphodianion group coordinated in a distal site have been suggested to exploit this binding energy primarily to facilitate a conformational change from an open inactive form to a closed active form, rather than to either induce ground state destabilization or stabilize the transition state. However, detailed structural evidence for the model is limited. Here, we use β-phosphoglucomutase (βPGM) to investigate the relationship between binding a phosphodianion group in a distal site, the adoption of a closed enzyme form, and catalytic proficiency. βPGM catalyzes the isomerization of β-glucose 1-phosphate to glucose 6-phosphate via phosphoryl transfer reactions in the proximal site, while coordinating a phosphodianion group of the substrate(s) in a distal site. βPGM has one of the largest catalytic proficiencies measured and undergoes significant domain closure during its catalytic cycle. We find that side chain substitution at the distal site results in decreased substrate binding that destabilizes the closed active form but is not sufficient to preclude the adoption of a fully closed, near-transition state conformation. Furthermore, we reveal that binding of a phosphodianion group in the distal site stimulates domain closure even in the absence of a transferring phosphoryl group in the proximal site, explaining the previously reported β-glucose 1-phosphate inhibition. Finally, our results support a trend whereby enzymes with high catalytic proficiencies involving phosphorylated substrates exhibit a greater requirement to stabilize the closed active form.
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影响因子：
2.9
作者：
Dai, Jianying;Finci, Lorenzo;Zhang, Chunchun;Lahiri, Sushmita;Zhang, Guofeng;Peisach, Ezra;Allen, Karen N.;Dunaway-Mariano, Debra
通讯作者：
Dunaway-Mariano, Debra
DOI：
10.1073/pnas.1534873100
发表时间：
2003-10-14
影响因子：
11.1
作者：
Hur, S;Bruice, TC
通讯作者：
Bruice, TC
影响因子：
5.7
作者：
Baxter, Nicola J.;Zacharchenko, Thomas;Williamson, Mike P.
通讯作者：
Williamson, Mike P.
DOI：
10.1107/s0907444909042073
发表时间：
2010-01
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Chen VB;Arendall WB 3rd;Headd JJ;Keedy DA;Immormino RM;Kapral GJ;Murray LW;Richardson JS;Richardson DC
通讯作者：
Richardson DC
影响因子：
2.9
作者：
Go, Maybelle K.;Koudelka, Astrid;Richard, John P.
通讯作者：
Richard, John P.