› 4tqs

X-ray diffraction
2.06Å resolution

Ternary complex of Y-family DNA polymerase Dpo4 with (5'S)-8,5'-Cyclo-2'-deoxyguanosine and dCTP

Released:
DOI: 10.2210/pdb4tqs/pdb
PDB entry 4tqs coloured by chain, front view.
PDB entry 4tqs coloured by chain, side view.
PDB entry 4tqs coloured by chain, top view.
Source organisms:
Primary publication:
Kinetic and structural mechanisms of (5'S)-8,5'-cyclo-2'-deoxyguanosine-induced dna replication stalling.
Xu W, Ouellette AM, Wawrzak Z, Shriver SJ, Anderson SM, Zhao L
Biochemistry 54 639-51 (2015)
PMID: 25569151

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-118163 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chains: A, B
Molecule details ›
Chains: A, B
Length: 358 amino acids
Theoretical weight: 41.09 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-352; Coverage: 100%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3') Chains: C, P
Molecule details ›
Chains: C, P
Length: 12 nucleotides
Theoretical weight: 3.81 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*TP*CP*AP*CP*(2LF)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') Chains: D, T
Molecule details ›
Chains: D, T
Length: 18 nucleotides
Theoretical weight: 5.37 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand DCP 2 x DCP
Ligand MG 4 x MG
Ligand DOC 2 x DOC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P21
Unit cell:
a: 52.12Å b: 184.242Å c: 52.124Å
α: 90° β: 110.09° γ: 90°
R-values:
R R work R free
0.231 0.228 0.29
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

5',8-Cyclopurine Lesions in DNA Damage: Chemical, Analytical, Biological, and Diagnostic Significance.
Chatgilialoglu et al. (2019)
2 more

1 mention without citation

Haemolytic actinoporins interact with carbohydrates using their lipid-binding module.
Tanaka et al. (2017)