Pathak Ekta, Atri Neelam, Mishra Rajeev
Bioinformatics, MMV, Banaras Hindu University, India.
Department of Botany, MMV, Banaras Hindu University, India.
Bioinformation. 2014 Apr 23;10(4):216-20. doi: 10.6026/97320630010216. eCollection 2014.
The P-loop NTPases are involved in diverse cellular functions. Members of the P-loop NTPase superfamily are characterized by presence of a highly conserved sequence pattern GxxxxGKS/T, known as Walker A motif. This motif adopts an archetypal P-loop conformation which allows accommodation of the triphosphate moiety of a bound nucleotide. Despite the presence of Walker A as a common sequence motif, P-loop NTPases exhibit extreme sequence divergence which hampers their phylogenetic or evolutionary classification. Here, we show that P-loop and its flanking region subsequence (termed as "extended-WalkerA motif") contain distinct signatures that can be utilized to classify NTPase domain of functionally diverse proteins. We find a clearly classified group of diverse NTPases of Conserved Domain Database such as G-proteins, Ylqf, RecA like, DExDc, AAA, CPT, NK, ABC transporter and NifH proteins.
P 环 NTP 酶参与多种细胞功能。P 环 NTP 酶超家族的成员具有一个高度保守的序列模式 GxxxxGKS/T，即沃克 A 基序。该基序采用典型的 P 环构象，可容纳结合核苷酸的三磷酸部分。尽管存在沃克 A 作为共同序列基序，但 P 环 NTP 酶表现出极大的序列差异，这阻碍了它们的系统发育或进化分类。在此，我们表明 P 环及其侧翼区域子序列（称为“扩展沃克 A 基序”）包含不同的特征，可用于对功能多样的蛋白质的 NTP 酶结构域进行分类。我们在保守结构域数据库中发现了一组分类明确的不同 NTP 酶，如 G 蛋白、Ylqf、RecA 样、DExDc、AAA、CPT、NK、ABC 转运蛋白和 NifH 蛋白。
