Two-tiered enforcement of high-fidelity DNA ligation

Patrick J O’Brien,Amanda A Riccio,Thomas J Jurkiw,Percy P Tumbale,R Scott Williams,Matthew J Schellenberg

doi:10.1038/s41467-019-13478-7

Abstract

DNA ligases catalyze the joining of DNA strands to complete DNA replication, recombination and repair transactions. To protect the integrity of the genome, DNA ligase 1 (LIG1) discriminates against DNA junctions harboring mutagenic 3′-DNA mismatches or oxidative DNA damage, but how such high-fidelity ligation is enforced is unknown. Here, X-ray structures and kinetic analyses of LIG1 complexes with undamaged and oxidatively damaged DNA unveil that LIG1 employs Mg2+-reinforced DNA binding to validate DNA base pairing during the adenylyl transfer and nick-sealing ligation reaction steps. Our results support a model whereby LIG1 fidelity is governed by a high-fidelity (HiFi) interface between LIG1, Mg2+, and the DNA substrate that tunes the enzyme to release pro-mutagenic DNA nicks. In a second tier of protection, LIG1 activity is surveilled by Aprataxin (APTX), which suppresses mutagenic and abortive ligation at sites of oxidative DNA damage.

Highlights

DNA ligases catalyze the joining of DNA strands to complete DNA replication, recombination and repair transactions
Consistent with previous ligase 1 (LIG1) structures determined at moderate resolution (3.0 Å)[7], the enzyme completely envelopes the DNA with the DNA-binding domain (DBD), adenylylation domain (AdD), and oligonucleotide-binding domain (OBD) encircling the nicked DNA (Fig. 1c)
We used structural and quantitative biochemical approaches to elucidate the mechanisms by which the replicative human DNA ligase, LIG1, discriminates against improper 3′ termini (Fig. 7a)

Summary

Introduction

DNA ligases catalyze the joining of DNA strands to complete DNA replication, recombination and repair transactions. X-ray crystal structures of the three human DNA ligases (LIG1, LIG3, and LIG4) in complex with DNA have revealed a conserved ligase three-domain core architecture that encircles the DNA nick[6,7,8,9], induces partial unwinding and alignment of the 3′- and 5′-DNA ends, and distorts the 3′-OH strand into a C3′-endo sugar conformation to adopt an A-form like geometry[7,8,9] Despite these similarities, DNA ligases display different fidelity profiles and are either tuned for high-fidelity ligation (e.g., human DNA ligase 1 homologs) or have relaxed stringency for correct DNA base pairing during DNA nick sealing (e.g., DNA ligase 4)[5,10,11,12]. Inhibitors that increase concentrations of oxidatively damaged nucleotide pools is hypothesized to act in part by promoting

Methods

Results

Conclusion