› 2hvr

X-ray diffraction
2.45Å resolution

Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 3'-deoxyribonucleotide at the nick

Released:
DOI: 10.2210/pdb2hvr/pdb
PDB entry 2hvr coloured by chain, front view.
PDB entry 2hvr coloured by chain, side view.
PDB entry 2hvr coloured by chain, top view.
Source organism: Tequatrovirus 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:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113100 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
2 distinct DNA/RNA hybrid molecules
Macromolecules (4 distinct):
RNA ligase 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 335 amino acids
Theoretical weight: 37.71 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:
5'-D(*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP*CP*AP*AP*TP*TP*G)-3' Chains: C, F
Molecule details ›
Chains: C, F
Length: 24 nucleotides
Theoretical weight: 7.44 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided
5'-D(*CP*AP*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC)P*C)-3' Chains: D, G
Molecule details ›
Chains: D, G
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided
5'-R(P*A)-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*T)-3' Chains: E, H
Molecule details ›
Chains: E, H
Length: 13 nucleotides
Theoretical weight: 3.98 KDa
Source organism: Tequatrovirus T4
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand BTB 3 x BTB
1 modified residue:
Ligand OMC 2 x OMC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 83.569Å b: 106.16Å c: 125.329Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.236 0.236 0.295
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

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

4 mentions without citation

DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues.
Yan et al. (2017)
3 more