› 1q3v

X-ray diffraction
2.91Å resolution

Crystal structure of a wild-type Cre recombinase-loxP synapse: phosphotyrosine covalent intermediate

Released:
DOI: 10.2210/pdb1q3v/pdb
PDB entry 1q3v coloured by chain, front view.
PDB entry 1q3v coloured by chain, side view.
PDB entry 1q3v coloured by chain, top view.
Source organism: Punavirus P1
Primary publication:
Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation.
Ennifar E, Meyer JE, Buchholz F, Stewart AF, Suck D
Nucleic Acids Res 31 5449-60 (2003)
PMID: 12954782

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114422 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Recombinase cre Chains: A, B, E, F
Molecule details ›
Chains: A, B, E, F
Length: 347 amino acids
Theoretical weight: 39.07 KDa
Source organism: Escherichia virus P1
Expression system: Escherichia coli
UniProt:
  • Canonical: P06956 (Residues: 1-343; Coverage: 100%)
Gene name: cre
Sequence domains: Phage integrase family
Structure domains:
loxP DNA Chains: C, G
Molecule details ›
Chains: C, G
Length: 16 nucleotides
Theoretical weight: 4.96 KDa
Source organism: Punavirus P1
Expression system: Not provided
loxP DNA Chains: X, Y
Molecule details ›
Chains: X, Y
Length: 21 nucleotides
Theoretical weight: 6.45 KDa
Source organism: Punavirus P1
Expression system: Not provided
loxP DNA Chains: D, H
Molecule details ›
Chains: D, H
Length: 37 nucleotides
Theoretical weight: 11.39 KDa
Source organism: Punavirus P1
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand IOD 2 x IOD
Ligand MG 7 x MG
1 modified residue:
Ligand A3P 2 x A3P

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 108.938Å b: 164.16Å c: 194.759Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.247 0.247 0.276
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Mechanisms of site-specific recombination.
Grindley et al. (2006)
36 other articles

2 mentions without citation

Genetically encoded optical activation of DNA recombination in human cells.
Luo et al. (2016)
1 more