› 2hvq

X-ray diffraction
2.4Å resolution

Structure of Adenylated full-length T4 RNA Ligase 2

Released:
DOI: 10.2210/pdb2hvq/pdb
PDB entry 2hvq coloured by chain, front view.
PDB entry 2hvq coloured by chain, side view.
PDB entry 2hvq coloured by chain, top view.
Source organism: Escherichia virus T4
Primary publication:
RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward.
Nandakumar J, Shuman S, Lima CD
Cell 127 71-84 (2006)
PMID: 17018278

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152250 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA ligase 2 Chain: A
Molecule details ›
Chain: A
Length: 335 amino acids
Theoretical weight: 38.03 KDa
Source organism: Escherichia virus T4
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P32277 (Residues: 1-334; Coverage: 100%)
Gene names: 24.1, Y10A
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
1 modified residue:
Ligand APK 1 x APK

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 48.02Å b: 57.85Å c: 119.49Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.211 0.274
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

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

4 mentions without citation

The structure of an archaeal homodimeric ligase which has RNA circularization activity.
Brooks et al. (2008)
3 more