Abstract
The homology based 3-Dimensional structure prediction of calcium dependent protein kinase Isoform 1 From Cicer arietinum (chick pea) was carried out using bioinformatics tools. The CPK1 sequence on Protein BLAST analysis for homology search revealed 100 hits and Out which a few had significant E score (E <0.005) and better sequence similarity. Multiple sequence alignment analysis of CPK1 using MultAlin and HHpred showed above 90% similarities with protein sequences of Thermotoga petriphila (Hypothetical protein), Geobacillus stereothermophilus (1w91; 99.5%; E score=1.2 E-11), Thermoanaerobacterium saccharolyticum (1uhv; 99.4%; E score=2.9 E-11) and Bacillus stereothermophilus (1qw9; 98.5%; E score=4.9 E-6) from the PDB database. The secondary structure of CPK1 using PSIPRED VIEW revealed many helices, strands and coils in the protein structure. The tertiary structure prediction of CPK1 by MODELLER 8v2 showed a (s/a) 8 fold. The program VERIFY 3D assessed the quality of the predicted structure of CPK1 with acceptable scores.
Highlights
Chickpea (Cicer arietinum) is one of the most important grain legume crops worldwide and a major source of protein for millions of families in developing countries.A protein kinase is a kinase enzyme that modifies other proteins by chemically adding phosphate groups to them
The structure of cpk1 reveals extensive interaction between autoinhibitory sequence and the kinase catalytic core, which partially blocks the active site in the inactive state of kinase
Ca2+ binding at the Cterm Cam-like domain release autoinhibitory part which opens up the active site
Summary
A protein kinase is a kinase enzyme that modifies other proteins by chemically adding phosphate groups to them (phosphorylation). This class of protein is further separated into subsets such as PKC alpha, PKC beta, and PKC gamma, each with specific functions. Phosphorylation usually results in a functional change of the target protein (substrate) by changing enzyme activity, cellular location, or association with other proteins. Up to 30% of all proteins may be modified by kinase activity, and kinases are known to regulate the majority of cellular pathways, especially those involved in signal transduction, the transmission of signals within the cell. Kinases are turned on or off by phosphorylation (sometimes by the kinase itself - cis-phosphorylation/ autophosphorylation), by binding of activator proteins or inhibitor proteins, or small molecules, or by controlling their location in the cell relative to their substrates
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