Lauren Ferris/Sandbox 2

A Brief Description

DdrB is a single-stranded DNA binding protein that is found in bacteria from the genus Deinococcus. DdrB is thought to mediate the repair of genomic DNA following extensive genomic fragmentation induced by radiation and other agents. In this role, DdrB’s function has been compared to that of a unique stress-inducible equivalent of a single-stranded DNA binding protein. However, its function is not limited to DNA binding, as the protein has also been implicated in suppressing Rec J exonuclease activity and promoting the annealing of complementary nucleotides.

VERY ROUGH DRAFT OF PROTEOPEDIA PAGE

Background

DNA Repair

Structure Description

DdrB is a multimeric protein composed of . Each of the units share a at the N-terminus. This is followed by a series of , in which some are solvent exposed and others pack against the N terminal motif.

Flexible regions with poor order include that link beta sheet 6 to sheet 7 and beta sheet 7 to 8. These sheets have such limited order that the crystal structure could not be solved for some of the residues as their was little to no density. This lack of order suggests that these regions may be intrinsically disordered.

The beta sheets of the N-terminal beta-beta-alpha motif form a 10 stranded anti-parallel B-barrel. The barrel gives rise to a pore in the middle of the structure with approximately a 10A diameter. This structure is stabilized by interactions with the alpha helices?. Also prevents about 30% of solvent accessible area of the monomer from being exposed to the surrounding environment.

Lack of electron density in the last 51 residues of the C terminus of DdrB --- so structural features can not be assigned.

PSIpred server predicts that the last 35 residues of the C-terminal end of DdrB are disordered.

- Domains, folds, and or motifs

Structural features that relate to function

Related Proteins

No proteins are classified as directly related

However, different regions of the DdrB protein share common features with other proteins.

The C-terminal end of the DdrB protein appears to be related to a sequence within the Deinococcus geothermalis. This sequence encodes a 83 amino acid protein with unknown function. There is a 72% similarity and a 63% identity.

The C-terminal region of single stranded DNA binding proteins also tend to be disordered (about 60 residues of the C-terminus). Negatively charged residues in this disordered region has been shown to enable protein-protein interactions. Interestingly, DdrB has some negatively charged residues in this disordered region as well. This similarity may suggest that DdrB mediates DNA repair through similar protein-protein interactions.