6P0B image
Entry Detail
PDB ID:
6P0B
Keywords:
LIGASE
Title:
Human DNA Ligase 1 (E346A/E592A) Bound to an Adenylated, dideoxy Terminated DNA nick with 200 mM Mg2+
Biological Source:
Source Organism:
Homo sapiens, synthetic construct
Host Organism:
Escherichia coli
PDB Version:
Deposition Date:
2019-05-16
Release Date:
2019-12-11
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.20 Å
R-Value Free:
0.20
R-Value Work:
0.16
R-Value Observed:
0.17
Space Group:
P 21 21 21
6P0B validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA ligase 1
Mutations:E346A, E592A
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
Description: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
Description: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
Description: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.

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Protein

Chemical

Disease

Primary Citation of related structures
6P0B