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Pak. J. Bot., 44(2): 493-500, 2012.

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IN SILICO STUDIES ON STRUCTURE-FUNCTION OF DNA GCC- BOX BINDING DOMAIN OF BRASSICA NAPUS DREB1 PROTEIN

SYEDA QAMARUNNISA¹, MUSHTAQ HUSSAIN², NUSRAT JABEEN², SABOOHI RAZA³,  MUHAMMAD RAFIQ KHANANI², ABID AZHAR¹, JAVED A. QURESHI¹, SYED HASAN MUJTABA NAQVI^1*

Abstract: DREB1 is a transcriptional factor, which selectively binds with the promoters of the genes involved in stress response in the plants. Homology of DREB protein and its binding element have been detected in the genome of many plants. However, only a few reports exist that discusses the binding properties of this protein with the gene (s) promoter. In the present study, we have undertaken studies exploring the structure-function relationship of Brassica napus DREB1. Multiple sequence alignment, protein homology modeling and intermolecular docking of GCC-box binding domain (GBD) of the said protein was carried out using atomic coordinates of GBD from Arabdiopsis thaliana and GCC-box containing DNA respectively. Similarities and/or identities in multiple, sequence alignment, particularly at the functionally important amino acids, strongly suggested the binding specificity of B. napus DREB1 to GCC-box. Similarly, despite ~56% sequence homology, tertiary structures of both template and modeled protein were found to be extremely similar as indicated by root mean square deviation of 0.34Å. More similarities were established between GBD of both A. thaliana and B. napus DREB1 by conducting protein docking with the DNA containing GCC-box. It appears that both proteins interact through their β-sheet with the major DNA groove including both nitrogen bases and phosphate and sugar moieties. Additionally, in most cases the interacting residues were also found to be identical. Briefly, this study attempts to elucidate the molecular basis of DREB1 interaction with its target sequence in the promoter.
 

¹The Karachi Institute of Biotechnology and Genetic Engineering (KIBGE), University of Karachi.

²Department of Molecular Pathology-DDRRL, Dow University of Health Sciences,

³Nuclear Institute of Agriculture and Biology-PAEC- Tandojam, Pakistan.

^*Correspondence E-mail: mujtaba_n@yahoo.com; theonlyafshan@yahoo.com; Phone #: +9223002403922