Single stranded binding protein: Difference between revisions
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'''Single-stranded DNA-binding protein''' '''(SSB)''' binds to single-stranded regions of DNA. This binding serves a variety of functions - it prevents the strands from hardening too early during replication, it protects the single-stranded DNA from being broken down by nucleases during repair, and it removes the secondary structure of the strands so that other enzymes are able to access them and act effectively upon the strands<ref>PMID:2087220</ref>. | '''Single-stranded DNA-binding protein''' '''(SSB)''' binds to single-stranded regions of DNA. This binding serves a variety of functions - it prevents the strands from hardening too early during replication, it protects the single-stranded DNA from being broken down by nucleases during repair, and it removes the secondary structure of the strands so that other enzymes are able to access them and act effectively upon the strands<ref>PMID:2087220</ref>. | ||
Single-stranded DNA (ssDNA) is utilized primarily during the course of major aspects of DNA metabolism such as replication, recombination and repair <ref>PMID: 2087220</ref>. In addition to stabilizing ssDNA, SSB proteins also bind to and control the function of many other proteins that are involved in all | Single-stranded DNA (ssDNA) is utilized primarily during the course of major aspects of DNA metabolism such as replication, recombination and repair <ref>PMID: 2087220</ref>. In addition to stabilizing ssDNA, SSB proteins also bind to and control the function of many other proteins that are involved in all three of these major DNA metabolic processes. During DNA replication, SSB molecules bind to the newly separated individual DNA strands, keeping the strands separated by holding them in place so that each strand can serve as a template for new DNA synthesis<ref>Berg JM, Tymoczko JL, Stryer L. ''Biochemistry''. 6th edition. New York: W H Freeman; 2006.</ref>. | ||
==Structure of ''E. coli'' SSB== | ==Structure of ''E. coli'' SSB== | ||
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<scene name='56/566528/Ssdna/1'>Single-stranded DNA</scene> can interact with SSB through hydrogen bonds, stacking, or electrostatic 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/4'>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 <scene name='56/566528/Beta_barrel/1'>5 stranded β barrel</scene> that ends in an <scene name='56/566528/Beta_barrel/2'>α-helix</scene>. | <scene name='56/566528/Ssdna/1'>Single-stranded DNA</scene> can interact with SSB through hydrogen bonds, stacking, or electrostatic 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/4'>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 <scene name='56/566528/Beta_barrel/1'>5 stranded β barrel</scene> that ends in an <scene name='56/566528/Beta_barrel/2'>α-helix</scene>. | ||
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 in 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>. | ||
One more key residue in the binding site, <scene name='56/566528/His_55/2'>His55</scene>, was determined by site-specific mutagenesis, as when <scene name='56/566528/His_55/2'>His55</scene> is substituted with Leu it decreases the overall binding affinity for ssDNA. All of these residues are found in a <scene name='56/566528/Hydrophobic_region/2'>hydrophobic region</scene>, 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, <scene name='56/566528/His_55/2'>His55</scene>, was determined by site-specific mutagenesis, as when <scene name='56/566528/His_55/2'>His55</scene> is substituted with Leu it decreases the overall binding affinity for ssDNA. All of these residues are found in a <scene name='56/566528/Hydrophobic_region/2'>hydrophobic region</scene>, 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. | ||
