Literature summary for 4.1.99.3 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)

Cloned (Comment)	Organism
recombinant expression of GST-tagged enzyme	Oryza sativa Japonica Group

Crystallization (Commentary)

Crystallization (Comment)	Organism
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

Crystallization (Comment)

Organism

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

Organism	UniProt	Comment	Textmining
Oryza sativa Japonica Group	Q6F6A2	cultivar Sasanishiki	-

Purification (Commentary)

Purification (Comment)	Organism
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

Reaction	Comment	Organism	Reaction ID
cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)	substrate/cofactor binding and reaction mechanism, catalytic active site Met397, overview	Oryza sativa Japonica Group	a

Synonyms

Synonyms	Comment	Organism
CPD2PHR	-	Oryza sativa Japonica Group
eukaryotic Class II CPD PHR	-	Oryza sativa Japonica Group
eukaryotic class II cyclobutane pyrimidine dimer photolyase	-	Oryza sativa Japonica Group
PHR	-	Oryza sativa Japonica Group

Cofactor

Cofactor	Comment	Organism	Structure
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

General Information	Comment	Organism
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
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