› 2wq6

X-ray diffraction
2.3Å resolution

Structure of the 6-4 photolyase of D. melanogaster in complex with the non-natural N4-methyl T(Dewar)C lesion

Released:
DOI: 10.2210/pdb2wq6/pdb
PDB entry 2wq6 coloured by chain, front view.
PDB entry 2wq6 coloured by chain, side view.
PDB entry 2wq6 coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
DNA (6-4) photolyases reduce Dewar isomers for isomerization into (6-4) lesions.
Glas AF, Kaya E, Schneider S, Heil K, Fazio D, Maul MJ, Carell T
J Am Chem Soc 132 3254-5 (2010)
PMID: 20166732

Function and Biology Details

Reaction catalysed: 
Cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115912 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Photolyase/cryptochrome alpha/beta domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 543 amino acids
Theoretical weight: 62.91 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8SXK5 (Residues: 1-520; Coverage: 96%)
Gene names: CG2488, phr6-4
Sequence domains:
Structure domains:
5'-D(*AP*CP*AP*GP*CP*GP*GP*TDYP*CDWP*GP* CP*AP*AP*GP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.65 KDa
Source organism: Drosophila melanogaster
Expression system: Not provided
5'-D(*TP*AP*CP*CP*TP*GP*CP*GP*AP*CP* CP*GP*CP*TP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 15 nucleotides
Theoretical weight: 4.55 KDa
Source organism: Drosophila melanogaster
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand FAD 1 x FAD
No bound ligands
2 modified residues:
Ligand TDY 1 x TDY
Ligand CDW 1 x CDW

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 89.169Å b: 87.486Å c: 91.856Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.201 0.228
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Reaction mechanisms of DNA photolyase.
Brettel et al. (2010)
5 more

1 mention without citation

The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature.
Cellini et al. (2021)