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

Comput Biol Chem. 2017 Apr;67:102-113. doi: 10.1016/j.compbiolchem.2016.12.011. Epub 2016 Dec 31.

Abstract

The nirk 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 nirk 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.

Keywords: Active site; Comparative model; Denitrification; Function prediction; Nirk gene; Phylogenetic tree.

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / chemistry*
  • Amino Acids / genetics
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Catalytic Domain / genetics
  • Computational Biology
  • Computer Simulation
  • Evolution, Molecular
  • Models, Chemical
  • Models, Molecular
  • Nitrite Reductases / chemistry*
  • Nitrite Reductases / genetics
  • Protein Domains / genetics
  • Sequence Alignment

Substances

  • Amino Acids
  • Bacterial Proteins
  • Nitrite Reductases