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STRUCTURAL ANALYSIS AND 3D-MODELLING OF FUR PROTEIN FROM BRADYRHIZOBIUM JAPONICUM

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Author(s): RAGHVENDRA PRATAP SINGH | RAM NAGEENA SINGH | ALOK KUMAR SRIVASTAVA | SUDHEER KUMAR | R.C. DUBEY | DILIP K. ARORA

Journal: Journal of Applied Sciences in Environmental Sanitation
ISSN 0126-2807

Volume: 6;
Issue: 3;
Start page: 357;
Date: 2011;
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Keywords: Fur | modelling | Ramachandran plot | conservation homology

ABSTRACT
The expression of iron-regulated genes in bacteria is typically controlled by the ferric uptake regulator (Fur) protein, a global transcriptional repressor that regulates functions as diverse as iron acquisition, oxidative stress, virulence and acid tolerance. To understand the operational mechanism of transcriptional regulation, it is imperative to understand the structural model of fur protein. In the present study a complete structural analysis and 3-D modelling of fur protein of Bradyrhizobium japonicum, was carried out. The 151 amino acid sequence of the fur protein was retrieved from NCBI database. For structural and functional characterization, molecular formula, pI, EC, AI, GRAVY, instability index, half-life time, disulfide bridges and secondary structure were predicted. Based on the PDB Blast report, pdb file of Vibrio cholerae was used as template for three dimensional structure of the fur protein, was predicted by using the software MODELLER. Predicted model was further assessed by VERIFY-3D and PROCHECK graph, which show with acceptable scores and the reliability of final refined model. Ramachandran plot shown that, fur protein have 86.3% fully allowed region, 11.5% additionally allowed region, 1.4% generously allowed region and 0.7%disallowed region. The conservation homology was evaluated by multiple sequence alignment and phylogenetic tree using CONSURF server, showing above 72% identities with Rhizobium leguminosarum. The overall result provides the evidence of good quality of model and furnish a adequate foundation for functional analysis of experimentally derived crystal structures.
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