催化三联体
参考

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蛋白酶中常见的催化三联体电荷中继系统。酸残基（通常为谷氨酸或天冬氨酸）对齐并极化碱（通常为组氨酸），以激活亲核体（通常为丝氨酸或半胱氨酸，偶见苏氨酸）。三联体降低了亲核残基的pKa，然后进攻底物。氧阴离子穴一般会为酰胺骨架充上正电荷（偶尔为侧链），使电荷在过渡态的底物上稳定聚集
不同的氨基酸残基组合构成了各个酶中用于水解的催化三联体。左边是三联体中的亲核体、碱和酸成分。右边是不同的底物，以剪刀指示将断裂的键。β-内酰胺中可以断开两个不同的键（1：青霉素酰化酶，2：β-内酰胺酶）
半胱氨酸蛋白酶（上）与丝氨酸蛋白酶（下）催化机理之差异。其中酶分子用黑色标识，蛋白质底物用红色标识。两种机理之差异在于：（a）巯基电离 （b）酸性基团可以没有 （c）羟基脱质子与进攻协同 （d）酸、碱性基团间形成氢键 （e）离去部分与碱性基团必须精确配合 （f）丝氨酸离去基团需质子化
趋异演化导致同一超家族各酶三联体运用的亲核试剂不同。图为胰凝乳蛋白酶（PA超家族，S1家族）的丝氨酸三联体和烟草花叶病毒蛋白酶（PA超家族，C3家族）的半胱氨酸三联体。
趋同进化使得不同的酶中出现了相同排列、相同空间结构的催化三联体：酸性基团-碱性基团-亲核基团。图示为枯草杆菌蛋白酶(SB超家族, S8家族)，prolyl oligopeptidase (SC超家族, S9家族), 烟草花叶病毒蛋白酶（PA超家族，C3家族）和木瓜蛋白酶 (CA超家族, C1家族)的催化三联体。
苏氨酸蛋白酶向着以N端作为活性位点的方向趋同进化。图示为蛋白酶体和鸟氨酸乙酰基转移酶中起催化作用的N端丝氨酸。