2fcc

X-ray diffraction
2.3Å resolution

Crystal Structure of T4 Pyrimidine Dimer Glycosylase (T4-Pdg) Covalently Complexed with a DNA Substrate Containing Abasic Site

Released:

Function and Biology Details

Reactions catalysed:
Cleaves the N-glycosidic bond between the 5'-pyrimidine residue in cyclobutadipyrimidine (in DNA) and the corresponding deoxy-D-ribose residue
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:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Endonuclease V Chains: A, B
Molecule details ›
Chains: A, B
Length: 137 amino acids
Theoretical weight: 15.97 KDa
Source organism: Escherichia virus T4
Expression system: Escherichia coli
UniProt:
  • Canonical: P04418 (Residues: 2-138; Coverage: 99%)
Structure domains: T4 endonuclease V
DNA (5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 13 nucleotides
Theoretical weight: 3.86 KDa
Source organism: Escherichia virus T4
Expression system: Not provided
DNA (5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU)P*GP*G)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 13 nucleotides
Theoretical weight: 4.22 KDa
Source organism: Escherichia virus T4
Expression system: Not provided

Ligands and Environments

2 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X26C
Spacegroup: P6422
Unit cell:
a: 184.059Å b: 184.059Å c: 100.855Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.249 0.249 0.274
Expression systems:
  • Escherichia coli
  • Not provided