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Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK.

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.

SUBMITTER: Wang N

PROVIDER: S-EPMC6821365 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK.

Wang Na N Bao Hongyu H Chen Liu L Liu Yanhong Y Li Yue Y Wu Baixing B Huang Hongda H

Nucleic acids research 20191101 19

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 impo ...[more]

PMID: 31504793

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