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Year : 2011  |  Volume : 2  |  Issue : 3  |  Page : 47  

In silico structural analysis of a Brassica juncea sequence containing kinase specific domain


1 Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
2 Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture & Technology, Pantnagar, India

Date of Web Publication26-May-2012

Correspondence Address:
Gohar Taj
Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture & Technology, Pantnagar
India
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Source of Support: None, Conflict of Interest: None


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How to cite this article:
Ahmad J, Baig MS, Qureshi I, Taj G. In silico structural analysis of a Brassica juncea sequence containing kinase specific domain. J Nat Sc Biol Med 2011;2, Suppl S1:47

How to cite this URL:
Ahmad J, Baig MS, Qureshi I, Taj G. In silico structural analysis of a Brassica juncea sequence containing kinase specific domain. J Nat Sc Biol Med [serial online] 2011 [cited 2020 Feb 24];2, Suppl S1:47. Available from: http://www.jnsbm.org/text.asp?2011/2/3/47/95788

Protein kinase is a enzyme that modifies other proteins by adding phosphate groups from ATP to amino acid side chains of proteins. An estimated 1 to 3% of functional eukaryotic genes encode protein kinases, suggesting that they are involved in many aspects of cellular regulation and metabolism. The present work describes the amplification of a sequence coding for serine/threonine kinase specific domain from B. juncea by PCR amplification. A pair of gene specific primers was successfully used to amplify a 744 bp fragment that codes for a partial length (171 amino acids) of protein kinase gene. The protein sequence showed 100% similarity with high temperature kinase 1(HT1) of Arabidopsis thaliana and zea mays respectively using BLAST. Multiple sequence alignment indicated maximum homology from amino acid residues 8-171with its homologues. Phylogenetic tree was also constructed by studying evolutionary relationship of kinase containing domain sequence showed maximum relatedness with HT1 Zea mays. Furthermore, the modeled structure of sequence analyzed by modbase (Modeller 9v8), identified 4 homology structure. Out of 4 showed maximum sequence homology (43%) with TAK1 is a member of the MAPKKK family of protein kinases, which is involved in intracellular signaling pathways. Modeled structure composed of 36% helical (13 helices; 111 residues) and 15% beta sheet (15 strands; 48 residues). Ramachanden plot showed residues in most favored regions are 84.3% less than 90% due to the more presence of proline and glycine residues. Analysis by Netphos 2.0 software indicates the 11 phosphorylation sites. These observations have been resulted that our sequence showing similarities with kinase specific domain containing protein.




 

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