6kij | pdb_00006kij

Crystal structure of yedK with ssDNA containing an abasic site

spinqualitylabelsall models 6kij, resolution 1.58Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6kij is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.58Å Ligands: GOL, PED Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function YEDK_ECOLI Publication Abstract from PubMed 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. Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK.,Wang N, Bao H, Chen L, Liu Y, Li Y, Wu B, Huang H Nucleic Acids Res. 2019 Nov 4;47(19):10388-10399. doi: 10.1093/nar/gkz744. PMID:31504793 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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