› 2q2t

X-ray diffraction
2.3Å resolution

Structure of Chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick

Released:
DOI: 10.2210/pdb2q2t/pdb
PDB entry 2q2t coloured by chain, front view.
PDB entry 2q2t coloured by chain, side view.
PDB entry 2q2t 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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113107 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
1 distinct DNA/RNA hybrid molecule
Macromolecules (4 distinct):
DNA ligase Chain: A
Molecule details ›
Chain: A
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' Chain: B
Molecule details ›
Chain: B
Length: 21 nucleotides
Theoretical weight: 6.49 KDa
Source organism: Paramecium bursaria Chlorella virus 1
Expression system: Not provided
5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3' Chain: D
Molecule details ›
Chain: D
Length: 11 nucleotides
Theoretical weight: 3.34 KDa
Source organism: Paramecium bursaria Chlorella virus 1
Expression system: Not provided
5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
Source organism: Paramecium bursaria Chlorella virus 1
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand AMP 1 x AMP
1 modified residue:
Ligand OMC 1 x OMC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 66.301Å b: 81.29Å c: 96.418Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.214 0.261
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

Oligonucleotide/oligosaccharide-binding fold proteins: a growing family of genome guardians.
Flynn et al. (2010)
3 more

16 mentions without citation

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