Evolution of prokaryotic subtilases: Genome-wide analysis reveals novel subfamilies with different catalytic residues
Evolution of prokaryotic subtilases: Genome-wide analysis reveals novel subfamilies with different catalytic residues
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DOI：
10.1002/prot.21290
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发表时间：
2007-05-15
影响因子：
2.9
通讯作者：
Boekhorst, Jos
中科院分区：
文献类型：
--
作者：
Siezen, Roland J.;Renckens, Bernadet;Boekhorst, Jos
枯草杆菌样丝氨酸蛋白酶（subtilases）是一个非常多样化的丝氨酸蛋白酶家族，具有低序列同源性，通常局限于三个催化残基周围的区域。从不同的隐马尔可夫模型（HMM）开始，基于S8家族（枯草菌素）和S53家族（sedolisins）催化残基周围的序列校准，我们迭代搜索了313种真细菌和古细菌的全基因组中的所有orf。在164个基因组中，共鉴定出567个orf具有一个或多个具有催化残基的保守区域。其中绝大多数包含S8家族“经典”催化残基（Asp-His-Ser）周围的所有三个区域，而！63个蛋白被鉴定为S53 （sedolisin）家族成员（Glu-Asp-Ser）。超过30个蛋白质被发现属于两个新的亚群，在催化残基上有其他的进化变化，并且产生了新的hmm来搜索它们。在一个子集中，催化Asp被等效的Glu（即Glu- his - ser家族）所取代。另一个亚群类似于sedolisins，但保守的催化Asp并不位于与亲核试剂Glu相同的螺旋上，而是位于拓扑相似位置的P-sheet链上，这是同源性建模的结果。原核生物枯草酶数据库（www.cmbi.ru.nI/subtilases）提供了对已识别的枯草酶、保守序列区域、建议的家族细分和适当的hmm进行搜索的所有信息的访问。通过改进的搜索方法，我们首次预测了超过100种蛋白质是枯草酶，从而提高了基因组注释。
Subtilisin-like serine proteases (subtilases) are a very diverse family of serine proteases with low sequence homology, often limited to regions surrounding the three catalytic residues. Starting with different Hidden Markov Models (HMM), based on sequence alignments around the catalytic residues of the S8 family (subtilisins) and S53 family (sedolisins), we iteratively searched all ORFs in the complete genomes of 313 eubacteria and archaea. In 164 genomes we identified a total of 567 ORFs with one or more of the conserved regions with a catalytic residue. The large majority of these contained all three regions around the "classical" catalytic residues of the S8 family (Asp-His-Ser), while! 63 proteins were identified as S53 (sedolisin) family members (Glu-Asp-Ser). More than 30 proteins were found to belong to two novel subsets with other evolutionary variations in catalytic residues, and new HMMs were generated to search for them. In one subset the catalytic Asp is replaced by an equivalent, Glu (i.e. Glu-His-Ser family). The other subset resembles sedolisins, but the conserved catalytic Asp is not located on the same helix as the nucleophile Glu, but rather on a P-sheet strand in a topologically similar position, as suggested by homology modeling. The Prokaryotic Subtilase Database (www.cmbi.ru.nI/subtilases) provides access to all information on the identified subtilases, the conserved sequence regions, the proposed family subdivision, and the appropriate HMMs to search for them. Over 100 proteins were predicted to be subtilases for the first time by our improved searching methods, thereby improving genome annotation.