› 2q2u

X-ray diffraction
3Å resolution

Structure of Chlorella virus DNA ligase-product DNA complex

Released:
DOI: 10.2210/pdb2q2u/pdb
PDB entry 2q2u coloured by chain, front view.
PDB entry 2q2u coloured by chain, side view.
PDB entry 2q2u coloured by chain, top view.
Source organism: Paramecium bursaria Chlorella virus 1
Primary publication:
Structural basis for nick recognition by a minimal pluripotent DNA ligase.
Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S
Nat Struct Mol Biol 14 770-8 (2007)
PMID: 17618295

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113108 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (3 distinct):
DNA ligase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 319 amino acids
Theoretical weight: 36.83 KDa
Source organism: Paramecium bursaria Chlorella virus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O41026 (Residues: 1-298; Coverage: 100%)
Gene name: A544R
Sequence domains:
Structure domains:
5'-D(*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*T)-3' Chains: E, G, I, K
Molecule details ›
Chains: E, G, I, K
Length: 21 nucleotides
Theoretical weight: 6.49 KDa
Source organism: Paramecium bursaria Chlorella virus 1
Expression system: Not provided
5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3' Chains: F, H, J, L
Molecule details ›
Chains: F, H, J, L
Length: 21 nucleotides
Theoretical weight: 6.42 KDa
Source organism: Paramecium bursaria Chlorella virus 1
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand OMC 4 x OMC

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X9A
Spacegroup: P1
Unit cell:
a: 66.475Å b: 92.895Å c: 89.633Å
α: 70.32° β: 78.45° γ: 89.87°
R-values:
R R work R free
0.249 0.249 0.283
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

7 review citations

Eukaryotic DNA ligases: structural and functional insights.
Ellenberger et al. (2008)
6 more

3 mentions without citation

Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds.
Williamson et al. (2020)
2 more