› 4yp3

X-ray diffraction
1.89Å resolution

Mutant Human DNA Polymerase Eta Q38A/R61A Inserting dCTP Opposite an 8-Oxoguanine Lesion

Released:
DOI: 10.2210/pdb4yp3/pdb
PDB entry 4yp3 coloured by chain, front view.
PDB entry 4yp3 coloured by chain, side view.
PDB entry 4yp3 coloured by chain, top view.
Source organisms:
Primary publication:
Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase η in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2'-deoxyguanosine.
Su Y, Patra A, Harp JM, Egli M, Guengerich FP
J Biol Chem 290 15921-33 (2015)
PMID: 25947374

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-118334 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase eta Chain: A
Molecule details ›
Chain: A
Length: 435 amino acids
Theoretical weight: 48.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q9Y253 (Residues: 1-432; Coverage: 61%)
Gene names: POLH, RAD30, RAD30A, XPV
Sequence domains:
Structure domains:
DNA (5'-D(*TP*(8OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3') Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.68 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3') Chain: P
Molecule details ›
Chain: P
Length: 8 nucleotides
Theoretical weight: 2.43 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand DCP 1 x DCP
Ligand CA 2 x CA
Ligand GOL 2 x GOL
1 modified residue:
Ligand 8OG 1 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P61
Unit cell:
a: 98.769Å b: 98.769Å c: 81.966Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.171 0.168 0.216
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

Quick links

Citations

3 review citations

Translesion DNA polymerases in eukaryotes: what makes them tick?
Vaisman et al. (2017)
2 more

1 mention without citation

Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase η in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2'-deoxyguanosine.
Su et al. (2015)