6KIJ

Crystal structure of yedK with ssDNA containing an abasic site

Summary for 6KIJ

• Entry DOI: 10.2210/pdb6kij/pdb
• Descriptor: SOS response-associated protein, DNA (5'-D(*GP*AP*TP*TP*CP*GP*TP*CP*G)-3'), PENTANE-3,4-DIOL-5-PHOSPHATE, ... (5 entities in total)
• Functional Keywords: dna repair, abasic site, dna binding protein
• Biological source: Escherichia coli; More
• Total number of polymer chains: 2
• Total formula weight: 28645.92

Authors

Wang, N.,Bao, H.,Huang, H. (deposition date: 2019-07-18, release date: 2019-08-07, Last modification date: 2024-10-23)

Primary citation

Wang, N.,Bao, H.,Chen, L.,Liu, Y.,Li, Y.,Wu, B.,Huang, H.
Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK.
Nucleic Acids Res., 47:10388-10399, 2019

PubMed 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.

PubMed: 31504793
DOI: 10.1093/nar/gkz744

Experimental method

X-RAY DIFFRACTION (1.58 Å)