Torrance James W, Macarthur Malcolm W, Thornton Janet M
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SD, United Kingdom.
Proteins. 2008 May 1;71(2):813-30. doi: 10.1002/prot.21741.
The geometry of metal coordination by proteins is well understood, but the evolution of metal binding sites has been less studied. Here we present a study on a small number of well-documented structural calcium and zinc binding sites, concerning how the geometry diverges between relatives, how often nonrelatives converge towards the same structure, and how often these metal binding sites are lost in the course of evolution. Both calcium and zinc binding site structure is observed to be conserved; structural differences between those atoms directly involved in metal binding in related proteins are typically less than 0.5 A root mean square deviation, even in distant relatives. Structural templates representing these conserved calcium and zinc binding sites were used to search the Protein Data Bank for cases where unrelated proteins have converged upon the same residue selection and geometry for metal binding. This allowed us to identify six "archetypal" metal binding site structures: two archetypal zinc binding sites, both of which had independently evolved on a large number of occasions, and four diverse archetypal calcium binding sites, where each had evolved independently on only a handful of occasions. We found that it was common for distant relatives of metal-binding proteins to lack metal-binding capacity. This occurred for 13 of the 18 metal binding sites we studied, even though in some of these cases the original metal had been classified as "essential for protein folding." For most of the calcium binding sites studied (seven out of eleven cases), the lack of metal binding in relatives was due to point mutation of the metal-binding residues, whilst for zinc binding sites, lack of metal binding in relatives always involved more extensive changes, with loss of secondary structural elements or loops around the binding site.
蛋白质与金属配位的几何结构已得到充分理解，但金属结合位点的进化研究较少。在此，我们对少数有充分文献记载的结构钙和锌结合位点进行了一项研究，内容涉及亲属之间几何结构的差异程度、非亲属向相同结构趋同的频率，以及这些金属结合位点在进化过程中丢失的频率。观察到钙和锌结合位点的结构都是保守的；相关蛋白质中直接参与金属结合的那些原子之间的结构差异通常小于0.5埃均方根偏差，即使在远亲中也是如此。代表这些保守钙和锌结合位点的结构模板被用于在蛋白质数据库中搜索无关蛋白质在金属结合的残基选择和几何结构上趋同的情况。这使我们能够识别出六种“原型”金属结合位点结构：两种原型锌结合位点，它们都在大量情况下独立进化；以及四种不同的原型钙结合位点，每种仅在少数情况下独立进化。我们发现金属结合蛋白的远亲缺乏金属结合能力是很常见的。在我们研究的18个金属结合位点中有13个出现了这种情况，尽管在其中一些情况下，原来的金属被归类为“蛋白质折叠所必需”。对于大多数研究的钙结合位点（11个案例中的7个），亲属中缺乏金属结合是由于金属结合残基的点突变，而对于锌结合位点，亲属中缺乏金属结合总是涉及更广泛的变化，包括结合位点周围二级结构元件或环的丢失。
