› 5d49

X-ray diffraction
1.99Å resolution

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

Released:
DOI: 10.2210/pdb5d49/pdb
PDB entry 5d49 coloured by chain, front view.
PDB entry 5d49 coloured by chain, side view.
PDB entry 5d49 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 pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118530 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA nucleotidylexotransferase Chain: A
Molecule details ›
Chain: A
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') Chain: B
Molecule details ›
Chain: B
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*GP*C)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 8 nucleotides
Theoretical weight: 2.42 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*AP*AP*AP*A)-3') Chain: E
Molecule details ›
Chain: E
Length: 5 nucleotides
Theoretical weight: 1.52 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand MG 1 x MG
Ligand NA 1 x NA
Ligand SO4 2 x SO4
Ligand ACT 3 x ACT
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: C2
Unit cell:
a: 56.55Å b: 74.25Å c: 126.15Å
α: 90° β: 101.84° γ: 90°
R-values:
R R work R free
0.2 0.197 0.245
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

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

1 mention without citation

Eukaryotic Base Excision Repair: New Approaches Shine Light on Mechanism.
Beard et al. (2019)