Structures of LIG1 uncover the mechanism of sugar discrimination against a ribonucleotide at 3’- and 5’-end of the nick DNA

Abstract

Ribonucleotides can be incorporated by DNA polymerases and the subsequent joining of 3'-OH and 5'-P ends in the phosphodiester backbone at the nick by DNA ligase during DNA replication and repair is critical for maintaining genome stability. Although it has been extensively studied for DNA polymerases across families, the sugar discrimination mechanism of a human DNA ligase at atomic resolution is entirely missing. Here, for the first time, we determine X-ray structure of DNA ligase I (LIG1) in complex with nick DNA containing rG:C at the 3'-end and capture the ligase at the final phosphodiester bond formation step of the ligation reaction involving an adenylate (AMP) release. Moreover, we show mutagenic end joining of the nick DNA substrate with preinserted 3'-rG:C by LIG1 in vitro. Our findings reveal an important source of ribonucleotides embedded in genomic DNA, which could come from the failure of LIG1 to discriminate against a ribonucleotide at the 3'-end during nick sealing step of DNA replication and repair.