› 7sum

X-ray diffraction
2.9Å resolution

Crystal structure of human ligase I with nick duplexes containing cognate A:T

Released:
DOI: 10.2210/pdb7sum/pdb
PDB entry 7sum coloured by chain, front view.
PDB entry 7sum coloured by chain, side view.
PDB entry 7sum coloured by chain, top view.
Source organisms:
Primary publication:
Structures of LIG1 that engage with mutagenic mismatches inserted by polβ in base excision repair.
Tang Q, Gulkis M, McKenna R, Çağlayan M
Nat Commun 13 3860 (2022)
PMID: 35790757

Function and Biology Details

Reaction catalysed: 
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-122040 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA ligase 1 Chain: A
Molecule details ›
Chain: A
Length: 658 amino acids
Theoretical weight: 73.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P18858 (Residues: 261-918; Coverage: 72%)
Gene name: LIG1
Sequence domains:
DNA(5'-*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*A-3') Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.39 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA(5'-P*GP*TP*CP*GP*GP*AP*C-3') Chain: C
Molecule details ›
Chain: C
Length: 7 nucleotides
Theoretical weight: 2.14 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA(5'-*GP*TP*CP*CP*GP*AP*CP*TP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C-3') Chain: D
Molecule details ›
Chain: D
Length: 18 nucleotides
Theoretical weight: 5.46 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand AMP 1 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE 7B2
Spacegroup: P212121
Unit cell:
a: 65.255Å b: 116.589Å c: 124.156Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.18 0.227
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 mentions without citation

Structures of LIG1 that engage with mutagenic mismatches inserted by polβ in base excision repair.
Tang et al. (2022)
1 more