Homology Modeling of Nitrogenase Iron Protein of Nitrogen Fixing Actinomycete Arthrobacter sp

Abstract

Nitrogenase is an important enzyme associated with nitrogen fixation. Nitrogenase iron protein (Nif H) is one of the vital genes contributing to the nitrogen fixation. Arthrobacter sp. is one of the actinomycetes fixing atmospheric nitrogen. Nitrogenase iron protein of Arthrobacter sp. was retrieved from NCBI in FASTA format and a good template was selected by Basic Local Alignment Search tool and it was found to be Azotobacter vinelandii. The modeling of 3D structure of the protein was performed by Swiss model, GENO3D and ModWeb. The modeled 3D structure was evaluated by ProSA, VERIFY3D, PROCHECK, PROVE and ERRAT. The nitrogenase iron protein 3D structure modeled by ModWeb was found to be the best reliable model based on the above mentioned evaluation. The structural dynamics were performed by WEBnm@ and elNemo.3D structure of the nitrogenase iron protein was visualized by Rasmol.