Homology modeling and molecular docking studies of ArnA protein from Erwinia amylovora: role in polymyxin antibiotic resistance

• Published in: Journal of plant biochemistry and biotechnology 2015-10, Vol.24 (4), p.425-432
• Main Authors: Sonawane, Kailas D., Parulekar, Rishikesh S., Malkar, Radhika S., Nimbalkar, Pranhita R., Barage, Sagar H., Jadhav, Deepak B.
• Format: Article
• Language: English
• Subjects: Biomedical and Life Sciences; Cell Biology; Life Sciences; Original Article; Plant Biochemistry; Protein Science; Receptors
• ISSN: 0971-7811; 0974-1275
• DOI: 10.1007/s13562-014-0293-3

The resistivity of plant pathogen Erwinia amylovora against the polymyxin group of antibiotics is enhanced by modification of lipid A from lipopolysaccharide with 4-amino-4-deoxy L-arabinose (Ara4N) catalyzed by a bifunctional protein ArnA. ArnA is the first enzyme in the lipid A modification pathway with distinct dehydrogenase and transformylase domains which has been known in development of resistivity to polymyxin group of antibiotics. Thus, three dimensional structure of ArnA protein from Erwinia amylovora was constructed using homology modeling technique. The quality and reliability of the generated 3-D model was then assessed by different online available programs such as What if, PROCHECK, QMEAN, ProSA along with superimposition by UCSF Chimera. Sequence analysis study of ArnA protein from E. coli , Erwinia amylovora , Yersinia pestis , Ps. aeruginosa and Salmonella showed conserved domains with exact active site residues. Molecular docking study of ArnA protein with substrate UDP-GlcA and different inhibitors such as 5-formyl-5,6,7,8 tetrahydrofolate, leucovorin and 5-methyl tetrahydrofolate revealed similar binding pocket. The residues ASN492, ARG510, SER433 and ARG619 of ArnA protein are involved in interactions with inhibitors. Thus, this study could be useful to understand the proper binding mode of inhibitors to inhibit the lipid A modification pathway of ArnA protein from plant pathogen Erwinia amylovora .