Comparative analysis of amino acid composition in the active site of nirk gene encoding copper-containing nitrite reductase (CuNiR) in bacterial spp. (April 2017)

• Record Type: Journal Article
• Authors: Adhikari, Utpal Kumar; Rahman, M. Mizanur
• Is Part Of: Computational biology and chemistry. Volume 67(2017)
• Page Start: 102
• Page End: 113
• Publication Date: 2017-04
• Subjects: Nirk gene -- Denitrification -- Phylogenetic tree -- Comparative model -- Function prediction -- Active site; Chemistry -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; Biochemistry -- Data processing; Biology -- Data processing; Molecular biology -- Data processing; Periodicals; Electronic journals; 542.85
• DOI: 10.1016/j.compbiolchem.2016.12.011
• Languages: English
• ISSNs: 1476-9271

Abstract

Graphical abstract: Highlights: In this study, we analyzed CuNiR enzyme of bacterial spp. which are responsible for denitrification process. All the selected species contain disordered regions in their primary structure. Phylogenetic tree revealed that the selected sequences come from a common ancestor. Domain analysis showed two important domains (multicopper-oxidase type-I and type-II). Active site analysis exposed clear difference among the amino acid compositions. Abstract: The nir k gene encoding the copper-containing nitrite reductase (CuNiR), a key catalytic enzyme in the environmental denitrification process that helps to produce nitric oxide from nitrite. The molecular mechanism of denitrification process is definitely complex and in this case a theoretical investigation has been conducted to know the sequence information and amino acid composition of the active site of CuNiR enzyme using various Bioinformatics tools. 10 Fasta formatted sequences were retrieved from the NCBI database and the domain and disordered regions identification and phylogenetic analyses were done on these sequences. The comparative modeling of protein was performed through Modeller 9v14 program and visualized by PyMOL tools. Validated protein models were deposited in the Protein Model Database (PMDB) (PMDB id: PM0080150 to PM0080159). Active sites of nir k encoding CuNiR enzyme were identified by Castp server. The PROCHECK showed significant scores for four protein models in the most favored regions of the Ramachandran plot. Active sites and cavities prediction exhibited that the amino acid, namely Glycine, Alanine, Histidine, Aspartic acid, Glutamic acid, Threonine, and Glutamine were common in four predicted protein models. The present in silico study anticipates that active site analyses result will pave the way for further research on the complex denitrification mechanism of the selected species in the experimental laboratory.