Single stranded binding protein: Difference between revisions
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====Binding Interactions in the Active Site==== | ====Binding Interactions in the Active Site==== | ||
<scene name='56/566528/Ssdna/1'>Single-stranded DNA</scene> 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 <scene name='56/566528/Ob_fold/1'>OB fold</scene> <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 <scene name='56/566528/Ob_fold/1'>OB fold</scene> (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. | <scene name='56/566528/Ssdna/1'>Single-stranded DNA</scene> 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 <scene name='56/566528/Ob_fold/1'>OB fold</scene> <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 <scene name='56/566528/Ob_fold/1'>OB fold</scene> (the SSB of E. coli thus has <scene name='56/566528/Ob_fold/2'>four OB folds</scene>, one per each of its <scene name='56/566528/Homotetramer/1'>four identical subunits</scene>). 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. <scene name='56/566528/Phe_60/2'>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 <scene name='56/566528/Trp_40_and_trp_54/1'>Trp40 and Trp54</scene>, which were determined by mutagenesis <ref>PMID:2087220</ref>. | Several specific amino acid residues play essential roles in the binding of ssDNA to SSB. <scene name='56/566528/Phe_60/2'>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 <scene name='56/566528/Trp_40_and_trp_54/1'>Trp40 and Trp54</scene>, which were determined by mutagenesis <ref>PMID:2087220</ref>. | ||