Department of Bioengineering, McGill University, Montreal, QC, Canada.
Mol Biol Evol. 2018 Nov 1;35(11):2597-2606. doi: 10.1093/molbev/msy177.
Enzymes are known to fine-tune their sequences to optimize catalytic function, yet quantitative evolutionary design principles of enzymes remain elusive on the proteomic scale. Recently, it was found that the catalytic site in enzymes induces long-range evolutionary constraint, where even sites distant to the catalytic site are more conserved than expected. Given that protein-fold usage is generally different between enzymes and nonenzymes, it remains an open question to what extent this long-range evolutionary constraint in enzymes is dictated, either directly or indirectly, by the special three-dimensional structure of the enzyme. To investigate this question, we have compared evolutionary properties of enzymes with those of counterpart pseudoenzymes that share the same protein fold but are catalytically inactive. We found that the long-range evolutionary constraint observed in enzymes is significantly reduced in pseudoenzyme counterparts, despite very high structural similarity (∼1.5 Å RMSD on average). Furthermore, this significant reduction in long-range evolutionary constraint is observed even in pseudoenzyme counterparts which retain the ligand-binding ability of enzymes. Finally, the distance between the site that induces the highest gradient of sequence conservation and the pseudocatalytic site in pseudoenzymes is significantly larger than the corresponding distance in enzymes. Taken together, our results suggest that the long-range evolutionary constraint in enzymes is induced mainly by the presence of the catalytic site rather than by the special three-dimensional structure of the enzyme, and that such long-range evolutionary constraint in enzymes depends mainly on the catalytic function of the active site rather than on the ligand-binding ability of the enzyme.
酶的序列已知可以微调以优化催化功能，但酶的蛋白质组学规模的定量进化设计原则仍然难以捉摸。最近发现，酶中的催化位点诱导长程进化约束，即使远离催化位点的位点也比预期更保守。鉴于酶和非酶之间的蛋白质折叠使用通常不同，酶中的这种长程进化约束在多大程度上直接或间接地由酶的特殊三维结构决定，这仍然是一个悬而未决的问题。为了研究这个问题，我们比较了酶和具有相同蛋白质折叠但无催化活性的对应伪酶的进化特性。我们发现，尽管具有非常高的结构相似性（平均约为 1.5Å RMSD），但在伪酶对应物中观察到的酶中的长程进化约束显着降低。此外，即使在保留酶的配体结合能力的伪酶对应物中，也观察到这种长程进化约束的显着降低。最后，在伪酶中，诱导序列保守性最高梯度的位点与伪催化位点之间的距离明显大于酶中的对应距离。总之，我们的结果表明，酶中的长程进化约束主要是由催化位点的存在引起的，而不是由酶的特殊三维结构引起的，并且酶中的这种长程进化约束主要取决于活性位点的催化功能，而不是酶的配体结合能力。
