› 4rua

X-ray diffraction
3.07Å resolution

Crystal structure of Y-family DNA polymerase Dpo4 bypassing a MeFapy-dG adduct

Released:
DOI: 10.2210/pdb4rua/pdb
PDB entry 4rua coloured by chain, front view.
PDB entry 4rua coloured by chain, side view.
PDB entry 4rua coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase η and Sulfolobus solfataricus P2 Polymerase IV.
Patra A, Banerjee S, Johnson Salyard TL, Malik CK, Christov PP, Rizzo CJ, Stone MP, Egli M
J Am Chem Soc 137 7011-4 (2015)
PMID: 25988947

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118151 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 341 amino acids
Theoretical weight: 39.02 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-341; Coverage: 97%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
Nucleic acids Template: TCAT(MF7)GAATCCTTCCCCC Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.42 KDa
Source organism: synthetic construct
Expression system: Not provided
Nucleic acids Primar: GGGGGAAGGATTC Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 4.1 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DTP 1 x DTP
Ligand CA 3 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P21212
Unit cell:
a: 95.451Å b: 102.716Å c: 53.432Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.163 0.258
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 citation in other articles

Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η.
Genna et al. (2016)
9 more

1 mention without citation

Structural Basis for Error-Free Bypass of the 5-N-Methylformamidopyrimidine-dG Lesion by Human DNA Polymerase η and Sulfolobus solfataricus P2 Polymerase IV.
Patra et al. (2015)