The cis-Pro touch-turn: a rare motif preferred at functional sites.
The cis-Pro touch-turn: a rare motif preferred at functional sites.
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cis-Pro touch-turn：功能位点首选的罕见基序。
DOI：
10.1002/prot.20101
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发表时间：
2004
期刊：
影响因子：
--
通讯作者：
Richardson,JaneS
中科院分区：
文献类型：
--
作者：
Videau,LizbethL;Arendall3rd,WBryan;Richardson,JaneS
摘要描述了一种新的蛋白质三维结构基序，称为顺式-Pro接触-转动。在这个四残基三肽基序中，中心肽是顺式的。在脯氨酸之前的残基2在Ramachandran图的“prePro区域”中具有接近130、75的值，或在L区域中具有接近60、60的值。C（1）-C（4）距离为4-5 π，两个侧翼肽彼此平行，形成货车范德华接触而不是氢键。显然，这种安排是局部不利的，因此很少见，通常只在生物功能需要时发生。在500个蛋白质数据库中的12个实例中，在果胶酸裂解酶、Ni-Fe氢化酶、葡糖淀粉酶、木聚糖酶和冠瘿碱脱氢酶的催化位点处以及在核糖核酸酶H、I型DNA聚合酶、核糖毒素和噬菌体基因3蛋白的主要结合位点处发现顺式-Pro接触-转角。在这些蛋白质家族的每一个中，触摸轮流担任不同的角色，其功能的重要性是由保守和诱变数据支持。在分析这些3D图案的保护模式，新的方法进行深入的质量评价的结构生物信息学数据，以区分显着的例外和错误。蛋白质2004; 56：298-309.
ABSTRACT A new motif of three-dimensional (3D) protein structure is described, called the cis-Pro touch-turn. In this four-residue, three-peptide motif, the central peptide is cis. Residue 2, which precedes the proline, has, values either in the “prePro region” of the Ramachandran plot near 130, 75 or in the L region near 60, 60. The C (1)–C (4) distance is 4–5 Å and the two flanking peptides lie parallel to one another, making van der Waals contact rather than a hydrogen bond. Apparently, this arrangement is locally unfavorable and therefore rare, usually occurring only if needed for biological function. Of the 12 examples in a 500-protein database, cis-Pro touch-turns are found at the catalytic sites of pectate lyase, Ni-Fe hydrogenase, glucoamylase, xylanase, and opine dehydrogenase and at the primary binding sites of ribonuclease H, type I DNA polymerase, ribotoxin, and phage gene 3 protein. In each of these protein families, the touch-turns serve different roles; their functional importance is supported by conservation and mutagenesis data. In analyzing the conservation patterns of these 3D motifs, new methods for in-depth quality evaluation of the structural bioinformatic data are employed to distinguish between significant exceptions and errors. Proteins 2004; 56: 298–309.