PIN域类超家族的全面分类,Nucleic Acids Research

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PIN域类超家族的全面分类
Nucleic Acids Research ( IF 16.6 ) Pub Date : 2017-05-31 , DOI: 10.1093/nar/gkx494
Dorota Matelska , Kamil Steczkiewicz , Krzysztof Ginalski

PIN样结构域构成了广泛的核酸酶超家族，其反应机理，底物特异性，生物学功能和分类学分布各不相同。具有PIN样结构域的蛋白质参与中央细胞过程，例如DNA复制和修复，mRNA降解，转录调控和ncRNA成熟。在这项工作中，我们将识别和分类最完整的PIN类域，以对整个PIN域类超家族中的序列-结构-功能关系进行首次全面分析。使用用于远程同源性检测的高度敏感方法的传递序列搜索导致鉴定了几个新家族，包括Pfam（DUF1308，DUF4935）和CDD（COG2454）的代表，以及未归入公共领域数据库的其他23个家族。进一步的序列聚类揭示了单个序列聚类之间的关系，并且在某些家族中显示出异质性，表明可能存在功能差异。PIN结构域样超家族具有五个结构组，70个确定的簇，超过100,000种蛋白质和广泛的生物学功能，是最大，最多样化的核酸酶超家族之一。对序列和结构，域结构以及基因组环境的详细分析使我们能够预测几个新家族的生物学功能，包括新的毒素-抗毒素成分，参与tRNA / rRNA成熟和转录/翻译调控的蛋白质。PIN结构域样超家族具有五个结构组，70个确定的簇，超过100,000种蛋白质和广泛的生物学功能，是最大，最多样化的核酸酶超家族之一。对序列和结构，域结构以及基因组环境的详细分析使我们能够预测几个新家族的生物学功能，包括新的毒素-抗毒素成分，参与tRNA / rRNA成熟和转录/翻译调控的蛋白质。PIN结构域样超家族具有五个结构组，70个确定的簇，超过100,000种蛋白质和广泛的生物学功能，是最大，最多样化的核酸酶超家族之一。对序列和结构，域结构以及基因组环境的详细分析使我们能够预测几个新家族的生物学功能，包括新的毒素-抗毒素成分，参与tRNA / rRNA成熟和转录/翻译调控的蛋白质。

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Comprehensive classification of the PIN domain-like superfamily

PIN-like domains constitute a widespread superfamily of nucleases, diverse in terms of the reaction mechanism, substrate specificity, biological function and taxonomic distribution. Proteins with PIN-like domains are involved in central cellular processes, such as DNA replication and repair, mRNA degradation, transcription regulation and ncRNA maturation. In this work, we identify and classify the most complete set of PIN-like domains to provide the first comprehensive analysis of sequence–structure–function relationships within the whole PIN domain-like superfamily. Transitive sequence searches using highly sensitive methods for remote homology detection led to the identification of several new families, including representatives of Pfam (DUF1308, DUF4935) and CDD (COG2454), and 23 other families not classified in the public domain databases. Further sequence clustering revealed relationships between individual sequence clusters and showed heterogeneity within some families, suggesting a possible functional divergence. With five structural groups, 70 defined clusters, over 100,000 proteins, and broad biological functions, the PIN domain-like superfamily constitutes one of the largest and most diverse nuclease superfamilies. Detailed analyses of sequences and structures, domain architectures, and genomic contexts allowed us to predict biological function of several new families, including new toxin-antitoxin components, proteins involved in tRNA/rRNA maturation and transcription/translation regulation.

更新日期：2017-05-31

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