Circularly permuted proteins in the protein structure database
Circularly permuted proteins in the protein structure database
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DOI：
10.1110/ps.05801
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发表时间：
2001-09-01
期刊：
影响因子：
8
通讯作者：
Lee, B
中科院分区：
文献类型：
--
作者：
Jung, J;Lee, B
一些蛋白质在其序列被循环排列后与其他蛋白质同源。一些这样的蛋白质已经被识别，主要是通过序列比较，但也通过比较它们的三维结构。在这里，我们报告了对 SCOP 90% id 域数据库中所有蛋白质对进行系统搜索的结果，当其中一对的序列被循环排列时，这些蛋白质对在结构上是可重叠的。使用一组合理的标准，我们发现所有蛋白质结构域的 47% 在其序列被循环排列后可与数据库中的至少一个其他蛋白质结构域重叠。其中许多是对称蛋白质，它们叠加到另一种蛋白质上，无论有或没有序列的循环排列。然而，总共 3035 个结构域中有 412 个是不对称的，并且只有在序列进行循环排列后，这些结构域才能在结构上与另一种蛋白质重叠。其中包括大多数已知的和许多以前未检测到的具有远程同源性的循环排列蛋白质。
Some proteins are homologous to others after their sequence is circularly permuted. A few such proteins have been recognized, mainly by sequence comparison, but also by comparing their three-dimensional structures. Here we report the result of a systematic search for all protein pairs in the SCOP 90% id domain database that become structurally superimposable when the sequence of one of the pairs is circularly permuted. Using a reasonable set of criteria, we find that 47% of all protein domains are superimposable to at least one other protein domain in the database after their sequence is circularly permuted. Many of these are symmetric proteins, which superimpose to another protein both with and without a circular permutation of the sequence. However, 412 of the total 3035 domains are nonsymmetric, and these become structurally superimposable to another protein only after a circular permutation of the sequence. These include most known and many previously undetected circularly permuted proteins with remote homology.