Varfolomeev S D, Uporov I V, Fedorov E V
School of Chemistry, Lomonosov Moscow State University, Moscow, Russia.
Biochemistry (Mosc). 2002 Oct;67(10):1099-108. doi: 10.1023/a:1020907122341.
Comparison and multiple alignments of amino acid sequences of a representative number of related enzymes demonstrate the existence of certain positions of amino acid residues which are permanently reproducible in all members of the whole family. The use of the bioinformatic approach revealed conservative residues in each of the related enzymes and ranked amino acid conservatism for the overall enzymatic catalysis. Glycine and aspartic acid residues were shown to be the most essential for structure and catalytic activity of enzymes. Amino acid residues forming catalytic subsite of the active site of enzymes are always highly conservative. Analysis revealed that aspartic acid carboxyl group is the most frequently employed nucleophilic (in deprotonated form) and electrophilic (in protonated form) agent involved in activation of molecules by the mechanism of general base and acidic catalyses in the catalytic sites of enzymes. Glycine is a unique amino acid possessing the highest possibilities for rotation along C-C and C-N bonds of the polypeptide chain. The conservative fixation of the glycine residue in polypeptide chains of related enzymes provides a possibility for directed assembly of amino acid residues into the catalytic subsite structure. It is possible that the conservative glycines provide known conformational mobility of the protein and the active site. Methods of molecular modeling were used for analysis of structural substitutions of conservative and non-conservative glycines and their effects on geometry of catalytic site of typical hydrolases. The substitution of glycine(s) for alanine significantly altered the catalytic site structures.
对大量相关酶的代表性氨基酸序列进行比较和多重比对，结果表明，在整个酶家族的所有成员中，某些氨基酸残基位置是可永久重现的。生物信息学方法的应用揭示了每种相关酶中的保守残基，并对整体酶催化的氨基酸保守性进行了排序。甘氨酸和天冬氨酸残基被证明对酶的结构和催化活性最为关键。构成酶活性位点催化亚位点的氨基酸残基总是高度保守的。分析表明，天冬氨酸羧基是在酶催化位点通过一般碱催化和酸催化机制激活分子时最常用的亲核试剂（以去质子化形式）和亲电试剂（以质子化形式）。甘氨酸是一种独特的氨基酸，在多肽链的C-C键和C-N键上具有最高的旋转可能性。相关酶多肽链中甘氨酸残基的保守固定为将氨基酸残基定向组装到催化亚位点结构中提供了可能。保守的甘氨酸可能提供了已知的蛋白质构象灵活性和活性位点。分子建模方法用于分析保守和非保守甘氨酸的结构取代及其对典型水解酶催化位点几何形状的影响。用丙氨酸取代甘氨酸会显著改变催化位点结构。
