6P09 image
Deposition Date 2019-05-16
Release Date 2019-12-11
Last Version Date 2023-10-11
Entry Detail
PDB ID:
6P09
Keywords:
LIGASE/DNA
Title:
Human DNA Ligase 1 Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.05 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
6P09 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA ligase 1
Gene (Uniprot):LIG1
Chain IDs:A
Chain Length:645
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P18858 Pfam ID:PF04675, PF01068, PF04679 EC:6.5.1.1
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*C)-3')
Chain IDs:B
Chain Length:11
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3')
Chain IDs:C
Chain Length:7
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Chain IDs:D
Chain Length:18
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
AMP
MG
PEG
Primary Citation
Two-tiered enforcement of high-fidelity DNA ligation.
Nat Commun 10 5431 5431 (2019)
PMID: 31780661 DOI: 10.1038/s41467-019-13478-7

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
6P09