Single-stranded DNA binding protein (SSB)  -  DNA

Biological function
The Escherichia coli single-stranded DNA (ssDNA)-binding protein (SSB) plays roles in DNA replication, recombination, and repair by stabilizing ssDNA intermediates that are generated during DNA processing. In addition, SSB interacts with a number of proteins involved in DNA metabolism using its C-terminal domain via four intrinsically disordered tails.

Structural evidence
The crystal structure of full-length homotetrameric single-stranded DNA (ssDNA)-binding protein from Escherichia coli (SSB) has been determined to 3.3 Å resolution and reveals that the entire C-terminal domain is disordered even in the presence of ssDNA. The N-terminal DNA-binding domain of the protein is well-ordered and is virtually indistinguishable from the previously determined structure of the chymotryptic fragment of SSB (SSBc) in complex with ssDNA. The absence of observable interactions with the core protein and the crystal packing of SSB together suggest that the disordered C-terminal domains likely extend laterally away from the DNA- binding domains.

Biochemical evidence
The binding of ssDNA to SSB is inhibited by the SSB C-terminal tails, specifically by the last 8 highly acidic amino acids that comprise the binding site for its multiple partner proteins. At moderate salt concentration, removal of the acidic C-terminal ends increases the intrinsic affinity for ssDNA and enhances the negative cooperativity between ssDNA binding sites, indicating that the C termini exert an inhibitory effect on ssDNA binding. This inhibitory effect decreases as the salt concentration increases. Binding of ssDNA to approximately half of the SSB subunits relieves the inhibitory effect for all of the subunits.

The inhibition by the C termini is due primarily to a less favorable entropy change upon ssDNA binding. These observations explain why ssDNA binding to SSB enhances the affinity of SSB for its partner proteins and suggest that the C termini of SSB may interact, at least transiently, with its ssDNA binding sites.

Mechanism category
flexibility modulation

Fuzzy tails enable a mechanism, when inhibition and its relief by ssDNA binding enhances the ability of SSB to selectively recruit its partner proteins to sites on DNA. Fuzziness may also facilitate interactions with components of the replication machinery in vivo.