› 6u6b

X-ray diffraction
3.11Å resolution

Structure of human DNA polymerase beta misinserting dAMPNPP opposite the 5'G of the cisplatin Pt-GG intrastrand crosslink with Manganese in the active site

Released:
DOI: 10.2210/pdb6u6b/pdb
PDB entry 6u6b coloured by chain, front view.
PDB entry 6u6b coloured by chain, side view.
PDB entry 6u6b coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into the promutagenic bypass of the major cisplatin-induced DNA lesion.
Ouzon-Shubeita H, Vilas CK, Lee S
Biochem J 477 937-951 (2020)
PMID: 32039434

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-120672 (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 BL21(DE3)
UniProt:
  • Canonical: P06746 (Residues: 1-335; Coverage: 100%)
Gene name: POLB
Sequence domains:
DNA (5'-D(*CP*CP*CP*AP*CP*GP*GP*CP*CP*CP*AP*TP*CP*AP*CP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 16 nucleotides
Theoretical weight: 4.75 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(P*GP*GP*TP*GP*AP*TP*GP*GP*GP*C)-3') Chain: P
Molecule details ›
Chain: P
Length: 10 nucleotides
Theoretical weight: 3.14 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(P*GP*TP*GP*GP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 5 nucleotides
Theoretical weight: 1.58 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MN 2 x MN
Ligand NA 2 x NA
Ligand DZ4 1 x DZ4
Ligand CPT 1 x CPT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P21
Unit cell:
a: 53.43Å b: 78.216Å c: 53.965Å
α: 90° β: 110.57° γ: 90°
R-values:
R R work R free
0.224 0.222 0.268
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 citations in other articles

Functionalized Lineage Tracing Can Enable the Development of Homogenization-Based Therapeutic Strategies in Cancer.
Gutierrez et al. (2022)

1 mention without citation

Structural insights into the promutagenic bypass of the major cisplatin-induced DNA lesion.
Ouzon-Shubeita et al. (2020)