› 8vzl

X-ray diffraction
2.41Å resolution

DNA Ligase 1 captured with pre-step 3 ligation at the rG:C nicksite

Released:
DOI: 10.2210/pdb8vzl/pdb
Model geometry
Fit model/data
PDB entry 8vzl coloured by chain, front view.
PDB entry 8vzl coloured by chain, side view.
PDB entry 8vzl coloured by chain, top view.
Source organisms:
Primary publication:
Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3'-end of nick DNA.
Balu KE, Gulkis M, Almohdar D, Çağlayan M
OpenAccess logo J Biol Chem 300 107216 (2024)
PMID: 38522520

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-270244 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
1 distinct DNA/RNA hybrid molecule
Macromolecules (4 distinct):
DNA ligase 1 Chain: A
Molecule details ›
Chain: A
Length: 669 amino acids
Theoretical weight: 74.33 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'-D(*GP*TP*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 18 nucleotides
Theoretical weight: 5.45 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*GP*TP*CP*GP*GP*AP*C)-3') Chain: C
DNA/RNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-R(P*G)-3') Chain: B

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 65.09Å b: 115.272Å c: 123.871Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.179 0.219
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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