› 6nkv

X-ray diffraction
1.85Å resolution

Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CHF analogue of dGTP

Released:
DOI: 10.2210/pdb6nkv/pdb
PDB entry 6nkv coloured by chain, front view.
PDB entry 6nkv coloured by chain, side view.
PDB entry 6nkv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Revealing an Internal Stabilization Deficiency in the DNA Polymerase β K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH
Biochemistry 59 955-963 (2020)
PMID: 31999437

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120343 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase beta Chain: A
Molecule details ›
Chain: A
Length: 335 amino acids
Theoretical weight: 38.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06746 (Residues: 1-335; Coverage: 100%)
Gene name: POLB
Sequence domains:
DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 16 nucleotides
Theoretical weight: 4.86 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*TP*(2DT))-3') Chain: P
Molecule details ›
Chain: P
Length: 10 nucleotides
Theoretical weight: 3.04 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(P*TP*TP*CP*GP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 5 nucleotides
Theoretical weight: 1.51 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MG 2 x MG
Ligand NA 3 x NA
Ligand CL 3 x CL
Ligand GFH 1 x GFH
1 modified residue:
Ligand 2DT 1 x 2DT

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21
Unit cell:
a: 50.636Å b: 79.707Å c: 55.412Å
α: 90° β: 107.63° γ: 90°
R-values:
R R work R free
0.167 0.164 0.203
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 mention without citation

Revealing an Internal Stabilization Deficiency in the DNA Polymerase β K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Batra et al. (2020)