LIG1 syndrome mutations remodel a cooperative network of ligand binding interactions to compromise ligation efficiency

Abstract

Human DNA ligase I (LIG1) is the main replicative ligase and it also seals DNA breaks to complete DNA repair and recombination pathways. Immune compromised patients harbor hypomorphic LIG1 alleles encoding substitutions of conserved arginine residues, R771W and R641L, that compromise LIG1 activity through poorly defined mechanisms. To understand the molecular basis of LIG1 syndrome mutations, we determined high resolution X-ray structures and performed systematic biochemical characterization of LIG1 mutants using steady-state and pre-steady state kinetic approaches. Our results unveil a cooperative network of plastic DNA-LIG1 interactions that connect DNA substrate engagement with productive binding of Mg2+ cofactors for catalysis. LIG1 syndrome mutations destabilize this network, compromising Mg2+ binding affinity, decreasing ligation efficiency, and leading to elevated abortive ligation that may underlie the disease pathology. These findings provide novel insights into the fundamental mechanism by which DNA ligases engage with a nicked DNA substrate, and they suggest that disease pathology of LIG1 syndrome could be modulated by Mg2+ levels.

Structures of LIG1 that engage with mutagenic mismatches inserted by polβ in base excision repair

“…1 ). In addition, similar to the previously reported LIG1 structures 29 – 32 , LIG1 containing the DNA binding (DBD), adenylation (AdD), and oligonucleotide binding (OBD) domains completely encircles the nick DNA containing the cognate or mismatched ends (Supplementary Figs. 2 and 3 ).…”

“…4b ). As reported in the previously solved LIG1 structures 29 – 32 , F635 and F872, which are located on the AdD and OBD domains of LIG1, respectively, are forced into the minor groove and play important roles in the catalysis 33 . However, in the LIG1/A:T and G:T structures, we did not observe a difference in the position of F635, which was located near the upstream end, where it was positioned near the sugar moiety of the 3′-end (Supplementary Fig.…”

Structures of LIG1 engaging with mutagenic mismatches inserted by polβ in base excision repair

“…Similar to the previously reported LIG1 structures (54–57), we observed that LIG1 completely envelopes the DNA with DNA binding (DBD), adenylylation (AdD), and oligonucleotide binding (OBD) domains encircling the nick DNA with correct or mismatched ends (Supplementary Figure 2). Moreover, we observed that the structures of LIG1/A:T nick DNA harbors a Watson-Crick conformation with two hydrogen bonds, while G:T and A:C 3′-terminal pairs show the Wobble hydrogen bonding, which is similar to DNA polymerase/mismatch structures for G:T and A:C (Figure 2 and Supplementary Figure 3).…”

“…All mammalian and bacterial ATP-dependent DNA ligases contain a highly conserved the catalytic core consisting of the oligonucleotide binding domain (OBD) and the adenylation (AdD) or nucleotidyl transferase (NTase) domain (3–5). Despite of this C-terminal core architecture, they display different fidelity profiles depending on the type (human ligase I, IIIα, or IV) and source of DNA ligase (54–57,73–95). Metal ions play important roles in steps 1 and 3 of the ligation reaction (1–13).…”

MEFV, IRF8, ADA, PEPD, and NBAS gene variants and elevated serum cytokines in a patient with unilateral sporadic Meniere's disease and vascular congestion over the endolymphatic sac

“…The IL-17 signaling axis has been implicated in the development of rheumatoid arthritis and the impairment of IL-17 signaling in the disease progression of psoriasis ( Ho et al., 2010 ). LIG1 encodes DNA ligase 1, which is the primary replicative ligase and interacts with proliferating cell nuclear antigen (PCNA) via an N-terminal PCNA-interacting protein box, and mutations in this gene have been implicated in several immunological diseases ( Jurkiw et al., 2021 ). RAG1 encodes the RAG1 protein, which modulates V(D)J recombination, which assembles and diversifies immunoglobulin and T-cell receptor genes in developing B and T lymphocytes ( Brecht et al., 2020 ).…”