Natural history of S-adenosylmethionine-binding proteins.
Natural history of S-adenosylmethionine-binding proteins.
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DOI：
10.1186/1472-6807-5-19
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发表时间：
2005-10-14
影响因子：
--
通讯作者：
Mushegian AR
中科院分区：
文献类型：
--
作者：
Kozbial PZ;Mushegian AR
S-腺苷甲硫氨酸是多种化学基团的来源，用于几乎每一类生物分子的生物合成和修饰。需要 S-腺苷甲硫氨酸的最显着的反应（甲基转移）是由一大类酶（S-腺苷甲硫氨酸依赖性甲基转移酶）进行的，这些酶一直是大量结构功能研究的焦点。然而，这些酶的进化轨迹，尤其是其他类别的 S-腺苷甲硫氨酸结合蛋白的进化轨迹仍然知之甚少。我们通过计算比较各种 S-腺苷甲硫氨酸结合蛋白的序列和结构来解决这个问题。罗斯曼折叠和 TIM 桶这两种广泛的折叠在进化过程中被反复用于不同类型的 S-腺苷甲硫氨酸转化。也有招募其他相对常见的折叠来进行 S-腺苷甲硫氨酸结合的情况。几类蛋白质具有独特的不相关折叠，专门用于一种化学类型，并通过内部结构域重复的主题统一。在一些情况下，当进化相关的酶改变了 S-腺苷甲硫氨酸的结合模式和化学转化类型时，功能分歧是显而易见的。当完全不同类别的 S-腺苷甲硫氨酸结合蛋白执行生化相似的过程时，也存在功能趋同的情况。远程序列相似性的比较和系统发育模式的分析表明，细胞生命的最后一个普遍共同祖先具有来自至少 5 个类别的 10 至 20 个 S-腺苷甲硫氨酸结合蛋白，提供了 S-腺苷甲硫氨酸的形成、多胺生物合成以及包括核酸和肽链释放因子在内的几种底物的甲基化。我们观察到了一些以前不知道相关的家族之间的新关系，并定义了 15 个 SAM 结合蛋白的大超家族，其中至少有 5 个可能代表了最后的共同祖先。
S-adenosylmethionine is a source of diverse chemical groups used in biosynthesis and modification of virtually every class of biomolecules. The most notable reaction requiring S-adenosylmethionine, transfer of methyl group, is performed by a large class of enzymes, S-adenosylmethionine-dependent methyltransferases, which have been the focus of considerable structure-function studies. Evolutionary trajectories of these enzymes, and especially of other classes of S-adenosylmethionine-binding proteins, nevertheless, remain poorly understood. We addressed this issue by computational comparison of sequences and structures of various S-adenosylmethionine-binding proteins. Two widespread folds, Rossmann fold and TIM barrel, have been repeatedly used in evolution for diverse types of S-adenosylmethionine conversion. There were also cases of recruitment of other relatively common folds for S-adenosylmethionine binding. Several classes of proteins have unique unrelated folds, specialized for just one type of chemistry and unified by the theme of internal domain duplications. In several cases, functional divergence is evident, when evolutionarily related enzymes have changed the mode of binding and the type of chemical transformation of S-adenosylmethionine. There are also instances of functional convergence, when biochemically similar processes are performed by drastically different classes of S-adenosylmethionine-binding proteins. Comparison of remote sequence similarities and analysis of phyletic patterns suggests that the last universal common ancestor of cellular life had between 10 and 20 S-adenosylmethionine-binding proteins from at least 5 fold classes, providing for S-adenosylmethionine formation, polyamine biosynthesis, and methylation of several substrates, including nucleic acids and peptide chain release factor. We have observed several novel relationships between families that were not known to be related before, and defined 15 large superfamilies of SAM-binding proteins, at least 5 of which may have been represented in the last common ancestor.
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