SNAP output for PDB entry 7sx5 [SNAP web server]

PDB-id

7sx5; SNAP-derived features in text and JSON formats; DNAproDB

Class

ligase

Method

X-ray (2.8 Å)

Summary

Crystal structure of ligase i with nick duplexes containing mismatch a:c

Reference

Tang Q, Gulkis M, McKenna R, Caglayan M (2022): "Structures of LIG1 that engage with mutagenic mismatches inserted by pol beta in base excision repair." Nat Commun, 13, 3860. doi: 10.1038/s41467-022-31585-w.

Abstract

DNA ligase I (LIG1) catalyzes the ligation of the nick repair intermediate after gap filling by DNA polymerase (pol) β during downstream steps of the base excision repair (BER) pathway. However, how LIG1 discriminates against the mutagenic 3'-mismatches incorporated by polβ at atomic resolution remains undefined. Here, we determine the X-ray structures of LIG1/nick DNA complexes with G:T and A:C mismatches and uncover the ligase strategies that favor or deter the ligation of base substitution errors. Our structures reveal that the LIG1 active site can accommodate a G:T mismatch in the wobble conformation, where an adenylate (AMP) is transferred to the 5'-phosphate of a nick (DNA-AMP), while it stays in the LIG1-AMP intermediate during the initial step of the ligation reaction in the presence of an A:C mismatch at the 3'-strand. Moreover, we show mutagenic ligation and aberrant nick sealing of dG:T and dA:C mismatches, respectively. Finally, we demonstrate that AP-endonuclease 1 (APE1), as a compensatory proofreading enzyme, removes the mismatched bases and interacts with LIG1 at the final BER steps. Our overall findings provide the features of accurate versus mutagenic outcomes coordinated by a multiprotein complex including polβ, LIG1, and APE1 to maintain efficient repair.