Single stranded binding protein: Difference between revisions

SSB proteins have been identified in many different organisms, but the most well understood SSB remains the SSB of E. coli.  E. coli SSB is a homotetramer consisting of four identical subunits which are each about 19 kDa in size <ref>PMID:2087220</ref>.  There are two different binding modes of the E. coli SSB when it complexes with ssDNA<ref>PMID:11993998</ref>.  Regulation of these modes has been found to be dependent on salt concentration, in addition to other unknown factors.  Under low salt conditions, the protein is less efficient as only two of the four identical subunits of E. coli SSB were found to bind to the ssDNA <ref>PMID:11993998</ref>.  Under high salt concentrations, however, all four subunits of the homotetramer bind to the ssDNA, increasing the number of nucleotides in contact with the SSB and thus favoring SSB-ssDNA interactions.  Depending on the salt concentration and other factors, estimates of the size of the site of interaction between SSB and ssDNA range anywhere from 30 to 73 nucleotides for each tetramer <ref>PMID:11993998</ref>.   

Active ''E. coli'' SSB is made of a homotetramer with extensive DNA binding domains that bind to a single strand of DNA <ref>PMID:2087220</ref>. The tetramers consist of α-helices, β-sheets, and random coils. Each subunit contains an α-helix and several β-sheets. The secondary structure also includes a NH2 terminus, which consists of multiple positively charged amino acids.  The DNA-binding domain lies within 115 amino acid residues from this terminus.  The COOH terminus includes many acidic amino acids <ref>PMID:2087220</ref>.

Though the SSB of ''E. coli'' is perhaps the best characterized, ssDNA binding proteins of many other organisms have also been identified.  Some proteins, such as the SSB of ''E. coli'' and human mitochondrial SSBs, bind as tetramers to ssDNA.  However, the SSB can have from one to as many as four OB-fold containing subunits in its structure.  For example, the structure of the SSB from ''Helicobacter pylori'' shown to the left is a homodimer composed of two identical subunits, each with the an OB-fold motif made of similar secondary structure elements such as an <scene name='56/566528/Alpha_helices/3'>α-helix</scene>and several <scene name='56/566528/Beta_sheets/1'>β-sheets</scene>.  Just like in the ''E. coli'' SSB, the OB-fold area in each subunit is used for single-stranded nucleic acid binding.  A phenylalanine residue (<scene name='56/566528/Phe_56/1'>Phe56</scene>) is again integral to ssDNA binding, as it is a site of cross-linking.  Tryptophan and lysine residues again play an important role in binding of ssDNA to the protein.