› 3tae

X-ray diffraction
2.71Å resolution

5-hydroxycytosine paired with dAMP in RB69 gp43

Released:
DOI: 10.2210/pdb3tae/pdb
PDB entry 3tae coloured by chain, front view.
PDB entry 3tae coloured by chain, side view.
PDB entry 3tae coloured by chain, top view.
Source organism: Escherichia phage RB69
Primary publication:
The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active site.
Zahn KE, Averill A, Wallace SS, Doublié S
Biochemistry 50 10350-8 (2011)
PMID: 22026756

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116922 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-directed DNA polymerase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 906 amino acids
Theoretical weight: 105.07 KDa
Source organism: Escherichia phage RB69
Expression system: Escherichia coli
UniProt:
  • Canonical: Q38087 (Residues: 1-903; Coverage: 100%)
Gene name: 43
Sequence domains:
Structure domains:
DNA (5'-D(*CP*CP*(5OC)P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3') Chains: E, G, I, K
Molecule details ›
Chains: E, G, I, K
Length: 18 nucleotides
Theoretical weight: 5.52 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided
DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*A)-3') Chains: F, H, J, L
Molecule details ›
Chains: F, H, J, L
Length: 15 nucleotides
Theoretical weight: 4.57 KDa
Source organism: Escherichia phage RB69
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P21
Unit cell:
a: 133.274Å b: 123.709Å c: 165.895Å
α: 90° β: 95.97° γ: 90°
R-values:
R R work R free
0.229 0.224 0.268
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

DNA Damage/Repair Management in Cancers.
Alhmoud et al. (2020)
1 more

2 mentions without citation

The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active site.
Zahn et al. (2011)
1 more