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 SSB protein (GenBank accession no. NC_004615.1). Single-stranded DNA intermediates are protected from nuclease degradation by SSB proteins which bind to them. The importance of SSB proteins in the DNA metabolic processes cannot be undermined. 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 α-helical and parallel β-sheet 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.