PDF(Pubmed)
Abstract：
Currently, the main α-amylase family GH13 has been divided into 47 subfamilies in CAZy, with new subfamilies regularly emerging. The present in silico study was performed to highlight the groups, represented by the maltogenic amylase from Thermotoga neapolitana and the α-amylase from Haloarcula japonica, which are worth of creating their own new GH13 subfamilies. This enlarges functional annotation and thus allows more precise prediction of the function of putative proteins. Interestingly, those two share certain sequence features, e.g. the highly conserved cysteine in the second conserved sequence region (CSR-II) directly preceding the catalytic nucleophile, or the well-preserved GQ character of the end of CSR-VII. On the other hand, the two groups bear also specific and highly conserved positions that distinguish them not only from each other but also from representatives of remaining GH13 subfamilies established so far. For the T. neapolitana maltogenic amylase group, it is the stretch of residues at the end of CSR-V highly conserved as L-[DN]. The H. japonica α-amylase group can be characterized by a highly conserved [WY]-[GA] sequence at the end of CSR-II. Other specific sequence features include an almost fully conserved aspartic acid located directly preceding the general acid/base in CSR-III or well-preserved glutamic acid in CSR-IV. The assumption that these two groups represent two mutually related, but simultaneously independent GH13 subfamilies has been supported by phylogenetic analysis as well as by comparison of tertiary structures. The main α-amylase family GH13 has thus been expanded by two novel subfamilies GH13_48 and GH13_49. KEY POINTS: • In silico analysis of two groups of family GH13 members with characterized representatives • Identification of certain common, but also some specific sequence features in seven CSRs • Creation of two novel subfamilies-GH13_48 and GH13_49 within the CAZy database.
摘要：
目前,在CAZy中，主要的α-淀粉酶家族GH13已分为47个亚家族，新的亚家族定期出现。目前的计算机模拟研究是为了突出这些群体，由来自Thermotoganeapolitana的麦芽糖淀粉酶和来自Haloarculajaponica的α-淀粉酶代表，这是值得创建自己的新GH13亚家族。这扩大了功能注释，因此可以更精确地预测推定蛋白质的功能。有趣的是,这两个共享某些序列特征，例如，在催化亲核试剂正前方的第二个保守序列区（CSR-II）中的高度保守的半胱氨酸，或CSR-VII结尾保存完好的GQ特征。另一方面,这两个群体还具有特定和高度保守的立场，这些立场不仅将它们彼此区分开来，而且将它们与迄今建立的其余GH13亚家族的代表区分开来。对于产麦芽淀粉酶组，它是CSR-V末端高度保守为L-[DN]的一段残基。H.japonicaα-淀粉酶组的特征在于CSR-II末端的高度保守的[WY]-[GA]序列。其他特定序列特征包括位于CSR-III中的一般酸/碱正前方的几乎完全保守的天冬氨酸或CSR-IV中保存良好的谷氨酸。假设这两组代表两个相互关联的，但是同时，系统发育分析以及三级结构的比较支持了独立的GH13亚家族。因此,主要的α-淀粉酶家族GH13被两个新的亚家族GH13_48和GH13_49扩展。关键要点：•对具有表征代表的两组GH13家族成员进行计算机模拟分析•确定某些共同的，还有七个CSR中的一些特定序列特征•在CAZy数据库中创建两个新的亚家族-GH13_48和GH13_49。
