title: An In Silico Approach for Characterization of an Aminoglycoside Antibiotic-Resistant Methyltransferase Protein from Pyrococcus furiosus (DSM 3638).
abstract: Pyrococcus furiosus is a hyperthermophilic archaea. A hypothetical protein of this archaea, PF0847, was selected for computational analysis. Basic local alignment search tool and multiple sequence alignment (MSA) tool were employed to search for related proteins. Both the secondary and tertiary structure prediction were obtained for further analysis. Three-dimensional model was assessed by PROCHECK and QMEAN6 programs. To get insights about the physical and functional associations of the protein, STRING network analysis was performed. Binding of the SAM (S-adenosyl-l-methionine) ligand with our protein, fetched from an antibiotic-related methyltransferase (PDB code: 3P2K: D), showed high docking energy and suggested the function of the protein as methyltransferase. Finally, we tried to look for a specific function of the proposed methyltransferase, and binding of the geneticin bound to the eubacterial 16S rRNA A-site (PDB code: 1MWL) in the active site of the PF0847 gave us the indication to predict the protein responsible for aminoglycoside antibiotic resistance.
authors.affiliation: Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, Bangladesh.
authors.forename: Arafat Rahman
authors.initials: AR
authors.lastname: Oany
authors.affiliation: Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh.
authors.forename: Tahmina Pervin
authors.initials: TP
authors.lastname: Jyoti
authors.affiliation: Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail, Bangladesh.
authors.forename: Shah Adil Ishtiyaq
authors.initials: SA
authors.lastname: Ahmad
keywords: 16S rRNA A-site; aminoglycoside antibiotic resistance; methyltransferase; molecular docking