› 6cti

X-ray diffraction
2Å resolution

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CCL2, beta, gamma dTTP analogue

Released:
DOI: 10.2210/pdb6cti/pdb
PDB entry 6cti coloured by chain, front view.
PDB entry 6cti coloured by chain, side view.
PDB entry 6cti coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mapping Functional Substrate-Enzyme Interactions in the pol β Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.
Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH
Biochemistry 57 3934-3944 (2018)
PMID: 29874056

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-119694 (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: 38.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06746 (Residues: 1-335; Coverage: 100%)
Gene name: POLB
Sequence domains:
Structure domains:
DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 16 nucleotides
Theoretical weight: 4.85 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3') Chain: P
Molecule details ›
Chain: P
Length: 10 nucleotides
Theoretical weight: 3.05 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(P*GP*TP*CP*GP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 5 nucleotides
Theoretical weight: 1.54 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand NA 3 x NA
Ligand MG 1 x MG
Ligand CL 2 x CL
Ligand VT8 1 x VT8
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21
Unit cell:
a: 50.618Å b: 79.117Å c: 55.407Å
α: 90° β: 107° γ: 90°
R-values:
R R work R free
0.18 0.177 0.227
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 citation in other articles

A Transition-State Perspective on Y-Family DNA Polymerase η Fidelity in Comparison with X-Family DNA Polymerases λ and β.
Oertell et al. (2019)
4 more

1 mention without citation

An N-capping asparagine-lysine-proline (NKP) motif contributes to a hybrid flexible/stable multifunctional peptide scaffold.
Cardoso et al. (2022)