› 4gc6

X-ray diffraction
2.9Å resolution

Crystal structure of Dpo4 in complex with N-MC-dAMP opposite dT

Released:
DOI: 10.2210/pdb4gc6/pdb
PDB entry 4gc6 coloured by chain, front view.
PDB entry 4gc6 coloured by chain, side view.
PDB entry 4gc6 coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Differential furanose selection in the active sites of archaeal DNA polymerases probed by fixed-conformation nucleotide analogues.
Ketkar A, Zafar MK, Banerjee S, Marquez VE, Egli M, Eoff RL
Biochemistry 51 9234-44 (2012)
PMID: 23050956

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-117537 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 358 amino acids
Theoretical weight: 41.09 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli BL21(DE3)
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*TP*CP*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 14 nucleotides
Theoretical weight: 4.39 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
DNA (5'-D(*TP*CP*AP*TP*GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.39 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand 0OH 1 x 0OH
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21212
Unit cell:
a: 93.641Å b: 103.357Å c: 52.491Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.202 0.276
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Ribonucleotide discrimination by translesion synthesis DNA polymerases.
Vaisman et al. (2018)
1 more

2 mentions without citation

Expanding the repertoire of methanocarba nucleosides from purinergic signaling to diverse targets.
Jacobson et al. (2021)
1 more