Literature summary extracted from
Hitomi, K.; Arvai, A.S.; Yamamoto, J.; Hitomi, C.; Teranishi, M.; Hirouchi, T.; Yamamoto, K.; Iwai, S.; Tainer, J.A.; Hidema, J.; Getzoff, E.D.
Eukaryotic class II cyclobutane pyrimidine dimer photolyase structure reveals basis for improved ultraviolet tolerance in plants (2012), J. Biol. Chem., 287, 12060-12069.
Cloned(Commentary)
EC Number |
Cloned (Comment) |
Organism |
---|
4.1.99.3 |
recombinant expression of GST-tagged enzyme |
Oryza sativa Japonica Group |
Crystallization (Commentary)
EC Number |
Crystallization (Comment) |
Organism |
---|
4.1.99.3 |
purified recombinant detagged enzyme, hanging drop vapor diffusion method, protein in 50 mM Tris-HCl (pH 8.0), 50 mM NaCl, 1 mM DTT, and 5% glycerol is mixed with 100 mM sodium cacodylate, pH 6.5, 200 mM ammonium sulfate, and 30% w/v PEG 8000 for crystal form I, and with 32% w/v PEG 4000, 5% urea, 100 mM imidazole/malate, pH 7.4 for crystal form II, 4°C, X-ray diffraction structure determination and analysis at 1.7 A resolution |
Oryza sativa Japonica Group |
Organism
EC Number |
Organism |
UniProt |
Comment |
Textmining |
---|
4.1.99.3 |
Oryza sativa Japonica Group |
Q6F6A2 |
cultivar Sasanishiki |
- |
Purification (Commentary)
EC Number |
Purification (Comment) |
Organism |
---|
4.1.99.3 |
recombinant GST-tagged enzyme, the GST is cleaved by treatment with thrombin at 25°C for 2 h and removed by using a heparin column |
Oryza sativa Japonica Group |
Reaction
EC Number |
Reaction |
Comment |
Organism |
Reaction ID |
---|
4.1.99.3 |
cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA) |
substrate/cofactor binding and reaction mechanism, catalytic active site Met397, overview |
Oryza sativa Japonica Group |
|
Synonyms
EC Number |
Synonyms |
Comment |
Organism |
---|
4.1.99.3 |
CPD2PHR |
- |
Oryza sativa Japonica Group |
4.1.99.3 |
eukaryotic Class II CPD PHR |
- |
Oryza sativa Japonica Group |
4.1.99.3 |
eukaryotic class II cyclobutane pyrimidine dimer photolyase |
- |
Oryza sativa Japonica Group |
4.1.99.3 |
PHR |
- |
Oryza sativa Japonica Group |
Cofactor
EC Number |
Cofactor |
Comment |
Organism |
Structure |
---|
4.1.99.3 |
FAD |
the C-terminal domain frames a concave pocket that holds the FAD cofactor in the U-shaped conformation. The U-shaped FAD is positioned with the isoalloxazine ring buried and the adenine ring solvent-exposed beneath the substrate binding pocket. A salt bridge (Arg396 to Asp427) across the isoalloxazine ring orients the guanidinium to stabilize a semiquinone radical at the C4a position. Cofactor binding and interactions with the enzyme, overview |
Oryza sativa Japonica Group |
|
General Information
EC Number |
General Information |
Comment |
Organism |
---|
4.1.99.3 |
evolution |
the PHR/CRY family consists of two major classes, class I and class II, the enzyme from rice belongs to class II |
Oryza sativa Japonica Group |
4.1.99.3 |
additional information |
structure-activity relationships in class II PHRs, overview. Structural comparisons with prokaryotic class I CPD PHRs identify differences in the binding site for UV-damaged DNA substrate |
Oryza sativa Japonica Group |