› 4rzr

X-ray diffraction
2.2Å resolution

Bypass of a bulky adduct dG1,8 by DPO4

Released:
DOI: 10.2210/pdb4rzr/pdb
PDB entry 4rzr coloured by chain, front view.
PDB entry 4rzr coloured by chain, side view.
PDB entry 4rzr coloured by chain, top view.
Source organisms:
Primary publication:
Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase.
Vyas R, Efthimiopoulos G, Tokarsky EJ, Malik CK, Basu AK, Suo Z
J Am Chem Soc 137 12131-42 (2015)
PMID: 26327169

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-118155 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chains: A, D
Molecule details ›
Chains: A, D
Length: 352 amino acids
Theoretical weight: 40.26 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(*TP*TP*GP*C*(2JV)P*GP*AP*CP*TP*GP*GP*TP*AP*TP*TP*GP*GP*G)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 18 nucleotides
Theoretical weight: 5.84 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*CP*CP*CP*AP*AP*TP*AP*CP*CP*AP*GP*TP*C)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 13 nucleotides
Theoretical weight: 3.88 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand CA 4 x CA
Ligand NA 2 x NA
Ligand TRS 1 x TRS
Ligand DCP 1 x DCP
Ligand GOL 2 x GOL
1 modified residue:
Ligand 2JV 2 x 2JV

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P31
Unit cell:
a: 56.397Å b: 56.397Å c: 288.776Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.201 0.199 0.25
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 citation in other articles

Pre-steady-state kinetic investigation of bypass of a bulky guanine lesion by human Y-family DNA polymerases.
Tokarsky et al. (2016)
9 more

1 mention without citation

Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase.
Vyas et al. (2015)