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
16848
8676
PubChem 643975
46173772
1owlA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1owmA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1ownA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1owoA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1owpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1qnfA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:HDF Unbound Unbound
1tezA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:HDF Unbound Unbound
1tezB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:HDF Unbound Unbound
1tezC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:HDF Unbound Unbound
1tezD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:HDF Unbound Unbound
1iqrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1iquA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2j07A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:HDF Unbound Unbound
2j08A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:IRF Unbound Unbound
2j09A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:FMN Unbound Unbound
1owlA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
1owmA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
1ownA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
1owoA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
1owpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
1qnfA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
1tezA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Analogue:A-T-C-G-G-C-T-TCP-C-G-C (chain I)
1tezB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Analogue:A-T-C-G-G-C-T-TCP-C-G-C (chain K)
1tezC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
1tezD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
1iqrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
1iquA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Analogue:TDR
2j07A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
2j08A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
2j09A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
1owlA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1owmA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1ownA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1owoA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1owpA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1qnfA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1tezA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1tezB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1tezC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1tezD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1iqrA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1iquA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2j07A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2j08A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2j09A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1owmA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ownA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1owoA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1owpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qnfA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tezA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tezB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tezC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tezD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1iqrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1iquA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2j07A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2j08A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2j09A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1owlA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1owmA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ownA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1owoA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1owpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qnfA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tezA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tezB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tezC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tezD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1iqrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1iquA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2j07A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2j08A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2j09A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1owlA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 314;TRP 367;GLY 381;TRP 390
1owmA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 314;TRP 367;GLY 381;TRP 390
1ownA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 314;TRP 367;GLY 381;TRP 390
1owoA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 314;TRP 367;GLY 381;TRP 390
1owpA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 314;TRP 367;GLY 381;TRP 390
1qnfA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 314;TRP 367;GLY 381;TRP 390
1tezA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 314;TRP 367;GLY 381;TRP 390
1tezB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 314;TRP 367;GLY 381;TRP 390
1tezC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 314;TRP 367;GLY 381;TRP 390
1tezD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 314;TRP 367;GLY 381;TRP 390
1iqrA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 275;TRP 328;GLY 342;TRP 351
1iquA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 275;TRP 328;GLY 342;TRP 351
2j07A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 275;TRP 328;GLY 342;TRP 351
2j08A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 275;TRP 328;GLY 342;TRP 351
2j09A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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