Single stranded binding protein: Difference between revisions

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Refayat Ahsen, Rachel Craig, Alexander Berchansky, Michal Harel

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 Single-stranded DNA (ssDNA) is utilized primarily during the course of major aspects of DNA metabolism such as replication, recombination and repair (PMID: 2087220). In addition to stabilizing ssDNA, SSB proteins also bind to and control the function of many other proteins that are involved in all of 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>.
-==Overview==
+==Structure of E. coli SSB==
 <StructureSection load='1eyg' size='400' side='right' frame='true' caption='Structure of Single Stranded DNA-Binding Protein bound to ssDNA (PDB entry [[1eyg]])' scene=''>
+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 (Lohman).  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>.
-The single stranded DNA binding protein (SSB) of E. coli plays an important role in three aspects of DNA metabolism – namely in replication, repair and recombination.  During DNA replication, SSB molecules bind to the newly separated <scene name='56/566528/Dna/1'>DNA strands</scene>, keeping the strands separated by holding them in place so that each strand can serve as a template <ref>Berg JM, Tymoczko JL, Stryer L. ''Biochemistry''. 6th edition. New York: W H Freeman; 2006.</ref>.
+Active E. coli SSB is made of a homotetramer with extensive DNA binding domains that bind to a single strand of DNA (PMID: 2087220). 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 (PMID: 2087220).
-SSB proteins have been identified in organisms from viruses to humans. The only organisms known to lack them are Thermoproteales, a group of extremophile archaea, where they have been displaced by the protein ThermoDBP. While many phage and viral SSBs function as monomers and eukaryotes encode heterotrimeric RPA (Replication Protein A), the best characterized SSB is that from the bacteria ''E. coli'' which, like most bacterial SSBs exists as a tetramer.  Active ''E. coli'' SSB is composed of four identical 19 kDa subunits. Binding of single-stranded DNA to the tetramer can occur in different "modes", with SSB occupying different numbers of DNA bases depending on a number of factors, including salt concentration. For example, the (SSB)<sub>65</sub> binding mode, in which approximately 65 nucleotides of DNA wrap around the SSB tetramer and contact all four of its subunits, is favoured at high salt concentrations ''in vitro''. At lower salt concentrations, the (SSB)<sub>35</sub> binding mode, in which about 35 nucleotides bind to only two of the SSB subunits, tends to form. Further work is required to elucidate the functions of the various binding modes ''in vivo''.
 </StructureSection>