Single stranded binding protein: Difference between revisions
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Single-stranded DNA can interact with SSB through hydrogen bonds, stacking, or electronegative interactions. Though SSB proteins are found in a variety of different organisms, most interactions between SSB and ssDNA happen through the common structural motif of an oligosaccharide/oligonucleotide binding site, referred to as the OB fold <ref>Shamoo, Yousif. “Single Stranded DNA binding proteins.” ‘’Encyclopedia of Life Sciences.’’ MacMillan Publishers Ltd, Nature Publishing Group; 2002</ref>. The OB fold allows SSB to bind preferentially to ssDNA. Each subunit of a SSB has an OB fold (the SSB of E. coli thus has four OB folds, one per each of its four identical subunits). This fold consists of a 5-stranded β barrel that ends in an α-helix. | Single-stranded DNA can interact with SSB through hydrogen bonds, stacking, or electronegative interactions. Though SSB proteins are found in a variety of different organisms, most interactions between SSB and ssDNA happen through the common structural motif of an oligosaccharide/oligonucleotide binding site, referred to as the OB fold <ref>Shamoo, Yousif. “Single Stranded DNA binding proteins.” ‘’Encyclopedia of Life Sciences.’’ MacMillan Publishers Ltd, Nature Publishing Group; 2002</ref>. The OB fold allows SSB to bind preferentially to ssDNA. Each subunit of a SSB has an OB fold (the SSB of E. coli thus has four OB folds, one per each of its four identical subunits). This fold consists of a 5-stranded β barrel that ends in an α-helix. | ||
Several specific amino acid residues play essential roles in the binding of ssDNA to SSB. | Several specific amino acid residues play essential roles in the binding of ssDNA to SSB. <scene name='56/566528/Phe_60/1'>Phe60</scene> is a key residue involved in binding the ssDNA to the protein, as it has been shown to be the site for cross-linking. Tryptophan and Lysine residues are important in binding as well, as evidenced by modification treatments of lysine and tryptophan residues resulting a complete loss of binding activity for the protein. The two tryptophan residues involved in ssDNA binding are Trp40 and Trp54, which were determined by mutagenesis <ref>PMID:2087220</ref>. | ||
One more key residue in the binding site, His55, was determined by site-specific mutagenesis, as when His55 is substituted with Leu it decreases the overall binding affinity for ssDNA. All of these residues are found in a hydrophobic region, which is suitable for nucleotide base interactions. Treatments that modified arginine, cysteine, or tyrosine residues had no effect on binding of SSB to DNA, suggesting that these amino acids are not involved in significant interactions of the protein with the ssDNA. | One more key residue in the binding site, His55, was determined by site-specific mutagenesis, as when His55 is substituted with Leu it decreases the overall binding affinity for ssDNA. All of these residues are found in a hydrophobic region, which is suitable for nucleotide base interactions. Treatments that modified arginine, cysteine, or tyrosine residues had no effect on binding of SSB to DNA, suggesting that these amino acids are not involved in significant interactions of the protein with the ssDNA. | ||