Related Experiment Video
Updated: Apr 27, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Analysis of P-Loop and its Flanking Region Subsequence of Diverse NTPases Reveals Evolutionary Selected Residues
Ekta Pathak1, Neelam Atri2, Rajeev Mishra1
1Bioinformatics, MMV, Banaras Hindu University, India.
Abstract:
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.
Related Concept Videos
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Bacterial RNA Polymerase
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
Allosteric Proteins-ATCase
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
Mitochondrial Precursor Proteins
Most of the mitochondrial...

