Summary information and primary citation

PDB-id
6kbx; DSSR-derived features in text and JSON formats
Class
DNA binding protein
Method
X-ray (1.221 Å)
Summary
Crystal structure of yedk in complex with ssDNA containing abasic site
Reference
Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang H (2019): "Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK." Nucleic Acids Res., 47, 10388-10399. doi: 10.1093/nar/gkz744.
Abstract
HMCES and yedK were recently identified as sensors of abasic sites in ssDNA. In this study, we present multiple crystal structures captured in the apo-, nonspecific-substrate-binding, specific-substrate-binding, and product-binding states of yedK. In combination with biochemical data, we unveil the molecular basis of AP site sensing in ssDNA by yedK. Our results indicate that yedK has a strong preference for AP site-containing ssDNA over native ssDNA and that the conserved Glu105 residue is important for identifying AP sites in ssDNA. Moreover, our results reveal that a thiazolidine linkage is formed between yedK and AP sites in ssDNA, with the residues that stabilize the thiazolidine linkage important for the formation of DNA-protein crosslinks between yedK and the AP sites. We propose that our findings offer a unique platform to develop yedK and other SRAP domain-containing proteins as tools for detecting abasic sites in vitro and in vivo.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js