DB code: T00249

CATH domain 3.40.50.620 : Rossmann fold Catalytic domain
1.25.40.80 : Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat Catalytic domain
1.10.579.10 : DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 Catalytic domain
E.C. 4.1.99.3
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
1.10.579.10 : DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 T00085
1.25.40.80 : Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat T00085
3.40.50.620 : Rossmann fold S00314 S00549 S00316 S00317 S00318 S00315 T00085 D00300 M00177 M00178 T00106 T00114

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P05327 Deoxyribodipyrimidine photo-lyase
EC 4.1.99.3
DNA photolyase
Photoreactivating enzyme
YP_172102.1 (Protein)
NC_006576.1 (DNA/RNA sequence)
PF00875 (DNA_photolyase)
PF03441 (FAD_binding_7)
[Graphical View]
P61497 Deoxyribodipyrimidine photo-lyase
EC 4.1.99.3
DNA photolyase
Photoreactivating enzyme
YP_145341.1 (Protein)
NC_006462.1 (DNA/RNA sequence)
PF00875 (DNA_photolyase)
PF03441 (FAD_binding_7)
[Graphical View]

KEGG enzyme name
deoxyribodipyrimidine photo-lyase
photoreactivating enzyme
DNA photolyase
DNA-photoreactivating enzyme
DNA cyclobutane dipyrimidine photolyase
DNA photolyase
deoxyribonucleic photolyase
deoxyribodipyrimidine photolyase
photolyase
PRE
PhrB photolyase
deoxyribonucleic cyclobutane dipyrimidine photolyase
phr A photolyase
dipyrimidine photolyase (photosensitive)
deoxyribonucleate pyrimidine dimer lyase (photosensitive)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P05327 PHR_SYNP6 Cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA). Monomer. Binds 1 FAD per subunit. Binds 1 coenzyme F420 (8-HDF / 7,8-didemethyl-8-hydroxy- 5-deazaflavin) non-covalently per subunit.
P61497 PHR_THET8 Cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA). Monomer (By similarity). Binds 1 FAD per subunit.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00016 C00876 C03103 C08249
E.C.
Compound FAD Coenzyme F420 Cyclobutadipyrimidine Pyrimidine 5'-deoxynucleotide
Type amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,nucleotide amino acids,amide group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,carboxyl group,peptide/protein,phosphate group/phosphate ion nucleotide nucleotide
ChEBI 16238
 16238
 		16848
 16848
 		8676
 8676
PubChem 643975
 643975
 		46173772
 46173772
1owlA01 Unbound Unbound Unbound Unbound
1owmA01 Unbound Unbound Unbound Unbound
1ownA01 Unbound Unbound Unbound Unbound
1owoA01 Unbound Unbound Unbound Unbound
1owpA01 Unbound Unbound Unbound Unbound
1qnfA01 Unbound Analogue:HDF Unbound Unbound
1tezA01 Unbound Analogue:HDF Unbound Unbound
1tezB01 Unbound Analogue:HDF Unbound Unbound
1tezC01 Unbound Analogue:HDF Unbound Unbound
1tezD01 Unbound Analogue:HDF Unbound Unbound
1iqrA01 Unbound Unbound Unbound Unbound
1iquA01 Unbound Unbound Unbound Unbound
2j07A01 Unbound Analogue:HDF Unbound Unbound
2j08A01 Unbound Analogue:IRF Unbound Unbound
2j09A01 Unbound Analogue:FMN Unbound Unbound
1owlA02 Bound:FAD Unbound Unbound Unbound
1owmA02 Bound:FAD Unbound Unbound Unbound
1ownA02 Bound:FAD Unbound Unbound Unbound
1owoA02 Bound:FAD Unbound Unbound Unbound
1owpA02 Bound:FAD Unbound Unbound Unbound
1qnfA02 Bound:FAD Unbound Unbound Unbound
1tezA02 Bound:FAD Unbound Unbound Analogue:A-T-C-G-G-C-T-TCP-C-G-C (chain I)
1tezB02 Bound:FAD Unbound Unbound Analogue:A-T-C-G-G-C-T-TCP-C-G-C (chain K)
1tezC02 Bound:FAD Unbound Unbound Unbound
1tezD02 Bound:FAD Unbound Unbound Unbound
1iqrA02 Bound:FAD Unbound Unbound Unbound
1iquA02 Bound:FAD Unbound Unbound Analogue:TDR
2j07A02 Bound:FAD Unbound Unbound Unbound
2j08A02 Bound:FAD Unbound Unbound Unbound
2j09A02 Bound:FAD Unbound Unbound Unbound
1owlA03 Unbound Unbound Unbound Unbound
1owmA03 Unbound Unbound Unbound Unbound
1ownA03 Unbound Unbound Unbound Unbound
1owoA03 Unbound Unbound Unbound Unbound
1owpA03 Unbound Unbound Unbound Unbound
1qnfA03 Unbound Unbound Unbound Unbound
1tezA03 Unbound Unbound Unbound Unbound
1tezB03 Unbound Unbound Unbound Unbound
1tezC03 Unbound Unbound Unbound Unbound
1tezD03 Unbound Unbound Unbound Unbound
1iqrA03 Unbound Unbound Unbound Unbound
1iquA03 Unbound Unbound Unbound Unbound
2j07A03 Unbound Unbound Unbound Unbound
2j08A03 Unbound Unbound Unbound Unbound
2j09A03 Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [39] & Catalytic Site Atlas

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1owlA01
1owmA01
1ownA01
1owoA01
1owpA01
1qnfA01
1tezA01
1tezB01
1tezC01
1tezD01
1iqrA01
1iquA01
2j07A01
2j08A01
2j09A01
1owlA02
1owmA02
1ownA02
1owoA02
1owpA02
1qnfA02
1tezA02
1tezB02
1tezC02
1tezD02
1iqrA02
1iquA02
2j07A02
2j08A02
2j09A02
1owlA03 TRP 314;TRP 367;GLY 381;TRP 390
1owmA03 TRP 314;TRP 367;GLY 381;TRP 390
1ownA03 TRP 314;TRP 367;GLY 381;TRP 390
1owoA03 TRP 314;TRP 367;GLY 381;TRP 390
1owpA03 TRP 314;TRP 367;GLY 381;TRP 390
1qnfA03 TRP 314;TRP 367;GLY 381;TRP 390
1tezA03 TRP 314;TRP 367;GLY 381;TRP 390
1tezB03 TRP 314;TRP 367;GLY 381;TRP 390
1tezC03 TRP 314;TRP 367;GLY 381;TRP 390
1tezD03 TRP 314;TRP 367;GLY 381;TRP 390
1iqrA03 TRP 275;TRP 328;GLY 342;TRP 351
1iquA03 TRP 275;TRP 328;GLY 342;TRP 351
2j07A03 TRP 275;TRP 328;GLY 342;TRP 351
2j08A03 TRP 275;TRP 328;GLY 342;TRP 351
2j09A03 TRP 275;TRP 328;GLY 342;TRP 351

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.260-261
[2]
p.209-210
[5]
p.889-890
[6]
p.66-68
[8]
p.13563-13564
[10]
p.1211-1212
[11]
Fig.4, p.1792
[12]
p.1803-1804

References
[1]
Resource
Comments REVIEW
Medline ID
PubMed ID
Journal Trends Biochem Sci
Year 1987
Volume 12
Pages 259-61
Authors Sancar GB, Sancar A
Title Structure and function of DNA photolyases.
Related PDB
Related UniProtKB P00914
[2]
Resource
Comments
Medline ID
PubMed ID 2282137
Journal Biofactors
Year 1990
Volume 2
Pages 207-11
Authors Jorns MS
Title DNA photorepair: chromophore composition and function in two classes of DNA photolyases.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 8377184
Journal J Mol Biol
Year 1993
Volume 233
Pages 167-9
Authors Miki K, Tamada T, Nishida H, Inaka K, Yasui A, de Ruiter PE, Eker AP
Title Crystallization and preliminary X-ray diffraction studies of photolyase (photoreactivating enzyme) from the cyanobacterium Anacystis nidulans.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8524158
Journal Methods Enzymol
Year 1995
Volume 258
Pages 319-43
Authors Kim ST, Heelis PF, Sancar A
Title Role of tryptophans in substrate binding and catalysis by DNA photolyase.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID 98025052
PubMed ID 9360600
Journal Nat Struct Biol
Year 1997
Volume 4
Pages 887-91
Authors Tamada T, Kitadokoro K, Higuchi Y, Inaka K, Yasui A, de Ruiter PE, Eker AP, Miki K
Title Crystal structure of DNA photolyase from Anacystis nidulans.
Related PDB 1qnf
Related UniProtKB P05327
[6]
Resource
Comments
Medline ID
PubMed ID 10747389
Journal Chemistry
Year 2000
Volume 6
Pages 62-72
Authors Butenandt J, Epple R, Wallenborn EU, Eker AP, Gramlich V, Carell T
Title A comparative repair study of thymine- and uracil-photodimers with model compounds and a photolyase repair enzyme.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 10946225
Journal Mutat Res
Year 2000
Volume 460
Pages 143-9
Authors Deisenhofer J
Title DNA photolyases and cryptochromes.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 11707580
Journal Proc Natl Acad Sci U S A
Year 2001
Volume 98
Pages 13560-5
Authors Komori H, Masui R, Kuramitsu S, Yokoyama S, Shibata T, Inoue Y, Miki K
Title Crystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism.
Related PDB 1iqr 1iqu
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 12169694
Journal J Biol Chem
Year 2002
Volume 277
Pages 38339-44
Authors Christine KS, MacFarlane AW 4th, Yang K, Stanley RJ
Title Cyclobutylpyrimidine dimer base flipping by DNA photolyase.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 15213381
Journal Acta Crystallogr D Biol Crystallogr
Year 2004
Volume 60
Pages 1205-13
Authors Kort R, Komori H, Adachi S, Miki K, Eker A
Title DNA apophotolyase from Anacystis nidulans: 1.8 A structure, 8-HDF reconstitution and X-ray-induced FAD reduction.
Related PDB 1owl 1owm 1own 1owo 1owp
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 15576622
Journal Science
Year 2004
Volume 306
Pages 1789-93
Authors Mees A, Klar T, Gnau P, Hennecke U, Eker AP, Carell T, Essen LO
Title Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair.
Related PDB 1tez
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 17051659
Journal Chembiochem
Year 2006
Volume 7
Pages 1798-806
Authors Klar T, Kaiser G, Hennecke U, Carell T, Batschauer A, Essen LO
Title Natural and non-natural antenna chromophores in the DNA photolyase from Thermus thermophilus.
Related PDB 2j07 2j08 2j09
Related UniProtKB

Comments
DNA photolyase catalyzes the repair of pyrimidine dimers in UV-damaged DNA in a reaction requiring visible light. These enzymes can be classified into two types, type-I and type-II.
Type-I photolyase contains FADH2 and a pterin derivative (5,10-methenyltetrahydrofolate; MTHF), whereas type-II enzyme contains FADHs and 8-hydroxy-5-deazariboflavin (8-HDF).
This enzyme belongs to the type-II enzyme group, whereas the type-I enzyme is annotated in T00085 in EzCatDB.
The reaction of this enzyme probably proceeds as follows:
(A) Excitation of 8-HDF by visible light, producing *MTHF
(B) Excitation energy transfer from *8-HDF to FADH-, giving *FADH-
(C) Electron transfer from *FADH- to Thy<>Thy, producing *FADH.
(D) The C5-C5 and C6-C6 sigma bonds of the cyclobutane ring are broken, producing .Thy- Thy
(E) Electron transfer from .Thy- Thy to *FADH., producing Thy Thy and FADH-

Created Updated
2004-07-09 2009-02-26