The pivot point arginines identified in the β-pinwheel structure of C-terminal domain from Salmonella Typhi DNA Gyrase A subunit

• Published in: Scientific reports 2020-05, Vol.10 (1), p.7817, Article 7817
• Main Authors: Sachdeva, Ekta, Kaur, Gurpreet, Tiwari, Pragya, Gupta, Deepali, Singh, Tej P., Ethayathulla, Abdul S., Kaur, Punit
• Format: Article
• Language: English
• Subjects: 631/154; 631/45; 631/535; 631/57; 692/420; Amino Acid Sequence - genetics; Arginine; Arginine - genetics; Deoxyribonucleic acid; DNA; DNA Gyrase - genetics; DNA Gyrase - ultrastructure; DNA topoisomerase; Humanities and Social Sciences; Models, Molecular; multidisciplinary; Mutagenesis, Site-Directed; Mutation - genetics; Nucleotide sequence; Protein Binding - genetics; Protein Conformation, beta-Strand - genetics; Protein Domains - genetics; Salmonella; Salmonella typhi - enzymology; Salmonella typhi - genetics; Salmonella typhi - pathogenicity; Science; Science (multidisciplinary); Site-directed mutagenesis; Supercoiling; Therapeutic targets
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-64792-w

The essentiality of DNA Gyrase in basic cellular processes in bacterial pathogens makes it an ideal drug target. Though the Gyrase has a conserved mechanism of action, the complete DNA wrapping and binding process is still unknown. In this study, we have identified six arginine residues R556, R612, R667, R716, R766, and R817 in the DNA GyraseA – C-terminal domain from Salmonella enterica serovar Typhi (StGyrA-CTD) to be essential for DNA wrapping and sliding by a sequence and structure analysis. Through site-directed mutagenesis and EMSA studies, we observed that the substitution of R667 (blade 3) and R716 (blade 4) in StGyrA-CTD led to loss of DNA binding. Whereas, upon mutation of residue R612 (blade2), R766 (blade5) and R817 (blade6) along with supporting residue R712 (blade 4) a decrease in binding affinity was seen. Our results indicate that R667 and R716 act as a pivot point in DNA wrapping and sliding during gyrase catalytic activity. In this study, we propose that the DNA wrapping mechanism commences with DNA binding at blade3 and blade4 followed by other blades to facilitate the DNA sliding during supercoiling activity. This study provides a better understanding of the DNA binding and wrapping mechanism of GyrA-CTD in DNA Gyrase.