Title:In silico Protein Structure Modeling and Conservation Analysis of ChrR, a Class-I Chromate Reducing Flavoenzyme from Pseudomonas putida
Volume: 20
Issue: 9
Author(s): Shivani H Viradia and Anjana K Vala
Affiliation:
Keywords:
Binding sites, chromium reductase, conservation analysis, protein modeling, Pseudomonas putida, structural bioinformatics.
Abstract: Hexavalent chromium [Cr(VI)] is a widespread environmental pollutant, arising as a by-product of numerous
industrial processes. Bacteria can reduce toxic and carcinogenic Cr(VI) to insoluble and less toxic Cr(III), offering promise
for an environmental friendly and affordable solution to chromate pollution. ChrR, a class I chromate-reducing flavoenzyme
from Pseudomonas putida is an efficient chromate reducer. The crystal structure of ChrR is yet unknown to the
scientific community, hence a three-dimensional (3D) structure is very essential for structural studies, protein – ligand interaction
simulations and designing novel bioremediation strategies. The 3D model of the P. putida ChrR protein was predicted
using in silico approach. Due to low percentage of sequence identity for homology modeling, I-TASSER was used
for structure prediction which combines the methods of threading, ab initio modeling and structural refinement. The stereo
chemical quality of the best model was validated with 90.6% residues under favored region from Ramachandran plot. The
modeled protein was submitted to Protein Model Database and can be downloaded with the ID PM0077375. The degree
of conservation was mapped onto the predicted model and ligand binding sites were found. The results of conservation
analysis and binding site prediction were combined to show several highly conserved binding sites. Altogether, the structure
for ChrR has been predicted. The work reveals novel universally conserved residues. These residues could be candidates
for binding interactions and provide the basis for designing advanced chromium bioremediation strategies.
