› 4u6p

X-ray diffraction
2.59Å resolution

Structural mechanism of error-free bypass of major benzo[a]pyrene adduct by human polymerase kappa

Released:
DOI: 10.2210/pdb4u6p/pdb
PDB entry 4u6p coloured by chain, front view.
PDB entry 4u6p coloured by chain, side view.
PDB entry 4u6p coloured by chain, top view.
Source organisms:
Primary publication:
Structure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase κ.
Jha V, Bian C, Xing G, Ling H
Nucleic Acids Res 44 4957-67 (2016)
PMID: 27034468

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-118180 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase kappa Chains: A, B
Molecule details ›
Chains: A, B
Length: 526 amino acids
Theoretical weight: 60.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBT6 (Residues: 1-526; Coverage: 61%)
Gene names: DINB1, POLK
Sequence domains:
Structure domains:
DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*C)-3') Chains: C, P
Molecule details ›
Chains: C, P
Length: 9 nucleotides
Theoretical weight: 2.74 KDa
Source organism: unidentified
Expression system: Not provided
DNA (5'-D(*TP*AP*TP*GP*GP*TP*GP*AP*TP*CP*CP*GP*C)-3') Chains: D, T
Molecule details ›
Chains: D, T
Length: 13 nucleotides
Theoretical weight: 3.98 KDa
Source organism: unidentified
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 6 x MG
Ligand DCT 2 x DCT
Ligand PGE 1 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P212121
Unit cell:
a: 66.15Å b: 129.286Å c: 167.713Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.2 0.239
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Mechanisms of DNA damage, repair, and mutagenesis.
Chatterjee et al. (2017)
6 more

5 mentions without citation

Structure and function relationships in mammalian DNA polymerases.
Hoitsma et al. (2020)
4 more