Impact of ions, pH and the nature of substrate on the structure and activity of a robust single-stranded DNA binding (SSB)-like protein from Phi11

The gene gp13 in bacteriophage Phi11 has been annotated as a Single-Stranded DNA binding protein (SSB protein, GenBank accession no. NC_004615.1). SSB proteins protect Single-stranded DNA intermediates generated during replication, recombination, and repair from nuclease degradation by binding to them. This highlights the importance of SSB proteins in the DNA metabolic processes. In this investigation, we have reported a systematic analysis of the structural and functional changes induced in rGp13 (the gene product of gp13) by several factors, such as metal ions and buffers of varying pH. The nature and length of the substrate required for the optimum function of rGp13 has also been investigated. Our results suggest that rGp13 is a robust protein which maintains its structure and function over a wide range of pH, with pH 4 being an exception. The monovalent cations used in this study seemed to have a stabilizing effect on the protein. Interestingly, among the divalent cations studied, only Zn²⁺ ions were found to completely destabilise rGp13, with a complete loss of the parallel β-sheet and α-helical content of the protein. This, in turn, totally abolished the DNA binding activity of rGp13. Another interesting observation from this study was that rGP13 could also bind to double-stranded DNA molecules. In summary, SSBs bind to dsDNA, ensuring genome integrity, protecting ssDNA, and impacting transcriptional processes. These crucial functions highlight their significance in maintaining cellular stability.