In Silico Phylogenetic Analysis and Molecular Modelling Study of 2-Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin | Zendy

Raghunath Satpathy | Zendy; V. Badireenath Konkimalla | Zendy; Jagnyeswar Ratha | Zendy

Open Access

In Silico Phylogenetic Analysis and Molecular Modelling Study of 2-Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin

Author(s) -

Raghunath Satpathy,

V. Badireenath Konkimalla,

Jagnyeswar Ratha

Publication year - 2016

Publication title -

advances in bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.33

H-Index - 20

eISSN - 1687-8035

pISSN - 1687-8027

DOI - 10.1155/2016/8701201

Subject(s) - dehalogenase , in silico , phylogenetic tree , biology , conserved sequence , sequence alignment , multiple sequence alignment , protein data bank (rcsb pdb) , amino acid , enzyme , biochemistry , computational biology , peptide sequence , bacteria , protein sequencing , genetics , gene

2-Haloalkanoic acid dehalogenase enzymes have broad range of applications, starting from bioremediation to chemical synthesis of useful compounds that are widely distributed in fungi and bacteria. In the present study, a total of 81 full-length protein sequences of 2-haloalkanoic acid dehalogenase from bacteria and fungi were retrieved from NCBI database. Sequence analysis such as multiple sequence alignment (MSA), conserved motif identification, computation of amino acid composition, and phylogenetic tree construction were performed on these primary sequences. From MSA analysis, it was observed that the sequences share conserved lysine (K) and aspartate (D) residues in them. Also, phylogenetic tree indicated a subcluster comprised of both fungal and bacterial species. Due to nonavailability of experimental 3D structure for fungal 2-haloalkanoic acid dehalogenase in the PDB, molecular modelling study was performed for both fungal and bacterial sources of enzymes present in the subcluster. Further structural analysis revealed a common evolutionary topology shared between both fungal and bacterial enzymes. Studies on the buried amino acids showed highly conserved Leu and Ser in the core, despite variation in their amino acid percentage. Additionally, a surface exposed tryptophan was conserved in all of these selected models.

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