8V1U

Human DNA Ligase I F872A bound to adenylated nicked DNA with a 5' terminal ribonucleotide

Summary for 8V1U

• Entry DOI: 10.2210/pdb8v1u/pdb
• Descriptor: DNA ligase 1, ADENOSINE MONOPHOSPHATE, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3'), ... (11 entities in total)
• Functional Keywords: adenylation domain, metalloenzyme, ligase, ligase-dna complex, dna binding protein, ligase/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 83979.72

Authors

Tumbale, P.P.,Williams, R.S. (deposition date: 2023-11-21, release date: 2025-07-02, Last modification date: 2026-01-14)

Primary citation

Tumbale, P.P.,Jurkiw, T.J.,Krahn, J.M.,Bokil, N.V.,Admiraal, S.J.,Pedersen, L.C.,Williams, J.S.,Kunkel, T.A.,O'Brien, P.J.,Williams, R.S.
Molecular basis for RNA discrimination by human DNA ligase 1.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: DNA ligase 1 (LIG1) finalizes DNA replication and repair by catalyzing the joining of DNA nicks. LIG1 is highly specific for DNA-DNA junctions over DNA-RNA junctions, discriminating strongly against a single ribonucleotide at the 5' side of the nick. This selectivity of LIG1 prevents futile and potentially mutagenic DNA-RNA cleavage and re-ligation cycles during Okazaki fragment maturation or ribonucleotide excision repair of genome-embedded ribonucleotide monophosphates (rNMPs), but the determinants of LIG1 rNMP discrimination are ill-defined. We report structural and kinetic analysis of LIG1 DNA-RNA complexes showing that LIG1 employs an aromatic steric gate to stabilize the enzyme-substrate complex and directly exclude rNMP-containing polynucleotides. Mutation of this RNA gate compromises the adenylyl-transfer and nick-sealing reactions but decreases the discrimination against an rNMP-containing substrate by ∼3600-fold. Our results establish the role of the conserved steric gate in ribonucleotide discrimination by high-fidelity (HiFi) DNA ligases at each step of the ligation reaction, which has parallels to the ribonucleotide discrimination by HiFi DNA polymerases.

PubMed: 40239996
DOI: 10.1093/nar/gkaf299

Experimental method

X-RAY DIFFRACTION (2 Å)