› 5d4b

X-ray diffraction
2.66Å resolution

Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination

Released:
DOI: 10.2210/pdb5d4b/pdb
PDB entry 5d4b coloured by chain, front view.
PDB entry 5d4b coloured by chain, side view.
PDB entry 5d4b coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination.
Loc'h J, Rosario S, Delarue M
Structure 24 1452-63 (2016)
PMID: 27499438

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
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-118531 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA nucleotidylexotransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 400 amino acids
Theoretical weight: 45.7 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P09838 (Residues: 132-510; Coverage: 74%)
Gene names: Dntt, Tdt
Sequence domains:
Structure domains:
DNA (5'-D(*AP*AP*AP*AP*AP*C)-3') Chains: C, D, E
Molecule details ›
Chains: C, D, E
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*TP*TP*TP*TP*GP*G)-3') Chain: F
Molecule details ›
Chain: F
Length: 7 nucleotides
Theoretical weight: 2.13 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand NA 2 x NA
Ligand SO4 8 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P212121
Unit cell:
a: 56.73Å b: 71.45Å c: 198.17Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.207 0.247
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

The molecular basis and disease relevance of non-homologous DNA end joining.
Zhao et al. (2020)
5 more

2 mentions without citation

3dDNA: A Computational Method of Building DNA 3D Structures.
Zhang et al. (2022)
1 more