EzCatDB: T00249
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DB codeT00249
CATH domainDomain 13.40.50.620 : Rossmann foldCatalytic domain
Domain 21.25.40.80 : Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeatCatalytic domain
Domain 31.10.579.10 : DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3Catalytic domain
E.C.4.1.99.3

CATH domainRelated DB codes (homologues)
1.10.579.10 : DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3T00085
1.25.40.80 : Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeatT00085
3.40.50.620 : Rossmann foldS00314,S00549,S00316,S00317,S00318,S00315,T00085,D00300,M00177,M00178,T00106,T00114

Enzyme Name
UniProtKBKEGG

P05327P61497
Protein nameDeoxyribodipyrimidine photo-lyaseDeoxyribodipyrimidine photo-lyasedeoxyribodipyrimidine 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)
SynonymsEC 4.1.99.3
DNA photolyase
Photoreactivating enzyme
EC 4.1.99.3
DNA photolyase
Photoreactivating enzyme
RefSeqYP_172102.1 (Protein)
NC_006576.1 (DNA/RNA sequence)
YP_145341.1 (Protein)
NC_006462.1 (DNA/RNA sequence)
PfamPF00875 (DNA_photolyase)
PF03441 (FAD_binding_7)
[Graphical view]
PF00875 (DNA_photolyase)
PF03441 (FAD_binding_7)
[Graphical view]


UniProtKB:Accession NumberP05327P61497
Entry namePHR_SYNP6PHR_THET8
ActivityCyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA).Cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA).
SubunitMonomer.Monomer (By similarity).
Subcellular location

CofactorBinds 1 FAD per subunit.,Binds 1 coenzyme F420 (8-HDF / 7,8-didemethyl-8-hydroxy- 5-deazaflavin) non-covalently per subunit.Binds 1 FAD per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00016C00876C03103C08249
CompoundFADCoenzyme F420CyclobutadipyrimidinePyrimidine 5'-deoxynucleotide
Typeamide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,nucleotideamino acids,amide group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,carboxyl group,peptide/protein,phosphate group/phosphate ionnucleotidenucleotide
ChEBI16238
16848

8676
PubChem643975


46173772
            
1owlA01UnboundUnboundUnboundUnbound
1owmA01UnboundUnboundUnboundUnbound
1ownA01UnboundUnboundUnboundUnbound
1owoA01UnboundUnboundUnboundUnbound
1owpA01UnboundUnboundUnboundUnbound
1qnfA01UnboundAnalogue:HDFUnboundUnbound
1tezA01UnboundAnalogue:HDFUnboundUnbound
1tezB01UnboundAnalogue:HDFUnboundUnbound
1tezC01UnboundAnalogue:HDFUnboundUnbound
1tezD01UnboundAnalogue:HDFUnboundUnbound
1iqrA01UnboundUnboundUnboundUnbound
1iquA01UnboundUnboundUnboundUnbound
2j07A01UnboundAnalogue:HDFUnboundUnbound
2j08A01UnboundAnalogue:IRFUnboundUnbound
2j09A01UnboundAnalogue:FMNUnboundUnbound
1owlA02Bound:FADUnboundUnboundUnbound
1owmA02Bound:FADUnboundUnboundUnbound
1ownA02Bound:FADUnboundUnboundUnbound
1owoA02Bound:FADUnboundUnboundUnbound
1owpA02Bound:FADUnboundUnboundUnbound
1qnfA02Bound:FADUnboundUnboundUnbound
1tezA02Bound:FADUnboundUnboundAnalogue:A-T-C-G-G-C-T-TCP-C-G-C(chain I)
1tezB02Bound:FADUnboundUnboundAnalogue:A-T-C-G-G-C-T-TCP-C-G-C(chain K)
1tezC02Bound:FADUnboundUnboundUnbound
1tezD02Bound:FADUnboundUnboundUnbound
1iqrA02Bound:FADUnboundUnboundUnbound
1iquA02Bound:FADUnboundUnboundAnalogue:TDR
2j07A02Bound:FADUnboundUnboundUnbound
2j08A02Bound:FADUnboundUnboundUnbound
2j09A02Bound:FADUnboundUnboundUnbound
1owlA03UnboundUnboundUnboundUnbound
1owmA03UnboundUnboundUnboundUnbound
1ownA03UnboundUnboundUnboundUnbound
1owoA03UnboundUnboundUnboundUnbound
1owpA03UnboundUnboundUnboundUnbound
1qnfA03UnboundUnboundUnboundUnbound
1tezA03UnboundUnboundUnboundUnbound
1tezB03UnboundUnboundUnboundUnbound
1tezC03UnboundUnboundUnboundUnbound
1tezD03UnboundUnboundUnboundUnbound
1iqrA03UnboundUnboundUnboundUnbound
1iquA03UnboundUnboundUnboundUnbound
2j07A03UnboundUnboundUnboundUnbound
2j08A03UnboundUnboundUnboundUnbound
2j09A03UnboundUnboundUnboundUnbound

Active-site residues
resource
literature [39] & Catalytic Site Atlas
pdbCatalytic residues
         
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 
1owlA03TRP 314;TRP 367;GLY 381;TRP 390
1owmA03TRP 314;TRP 367;GLY 381;TRP 390
1ownA03TRP 314;TRP 367;GLY 381;TRP 390
1owoA03TRP 314;TRP 367;GLY 381;TRP 390
1owpA03TRP 314;TRP 367;GLY 381;TRP 390
1qnfA03TRP 314;TRP 367;GLY 381;TRP 390
1tezA03TRP 314;TRP 367;GLY 381;TRP 390
1tezB03TRP 314;TRP 367;GLY 381;TRP 390
1tezC03TRP 314;TRP 367;GLY 381;TRP 390
1tezD03TRP 314;TRP 367;GLY 381;TRP 390
1iqrA03TRP 275;TRP 328;GLY 342;TRP 351
1iquA03TRP 275;TRP 328;GLY 342;TRP 351
2j07A03TRP 275;TRP 328;GLY 342;TRP 351
2j08A03TRP 275;TRP 328;GLY 342;TRP 351
2j09A03TRP 275;TRP 328;GLY 342;TRP 351

References for Catalytic Mechanism
ReferencesSectionsNo. 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]
CommentsREVIEW
JournalTrends Biochem Sci
Year1987
Volume12
Pages259-61
AuthorsSancar GB, Sancar A
TitleStructure and function of DNA photolyases.
Related UniProtKBP00914
[2]
PubMed ID2282137
JournalBiofactors
Year1990
Volume2
Pages207-11
AuthorsJorns MS
TitleDNA photorepair: chromophore composition and function in two classes of DNA photolyases.
[3]
PubMed ID8377184
JournalJ Mol Biol
Year1993
Volume233
Pages167-9
AuthorsMiki K, Tamada T, Nishida H, Inaka K, Yasui A, de Ruiter PE, Eker AP
TitleCrystallization and preliminary X-ray diffraction studies of photolyase (photoreactivating enzyme) from the cyanobacterium Anacystis nidulans.
[4]
PubMed ID8524158
JournalMethods Enzymol
Year1995
Volume258
Pages319-43
AuthorsKim ST, Heelis PF, Sancar A
TitleRole of tryptophans in substrate binding and catalysis by DNA photolyase.
[5]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID98025052
PubMed ID9360600
JournalNat Struct Biol
Year1997
Volume4
Pages887-91
AuthorsTamada T, Kitadokoro K, Higuchi Y, Inaka K, Yasui A, de Ruiter PE, Eker AP, Miki K
TitleCrystal structure of DNA photolyase from Anacystis nidulans.
Related PDB1qnf
Related UniProtKBP05327
[6]
PubMed ID10747389
JournalChemistry
Year2000
Volume6
Pages62-72
AuthorsButenandt J, Epple R, Wallenborn EU, Eker AP, Gramlich V, Carell T
TitleA comparative repair study of thymine- and uracil-photodimers with model compounds and a photolyase repair enzyme.
[7]
PubMed ID10946225
JournalMutat Res
Year2000
Volume460
Pages143-9
AuthorsDeisenhofer J
TitleDNA photolyases and cryptochromes.
[8]
PubMed ID11707580
JournalProc Natl Acad Sci U S A
Year2001
Volume98
Pages13560-5
AuthorsKomori H, Masui R, Kuramitsu S, Yokoyama S, Shibata T, Inoue Y, Miki K
TitleCrystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism.
Related PDB1iqr,1iqu
[9]
PubMed ID12169694
JournalJ Biol Chem
Year2002
Volume277
Pages38339-44
AuthorsChristine KS, MacFarlane AW 4th, Yang K, Stanley RJ
TitleCyclobutylpyrimidine dimer base flipping by DNA photolyase.
[10]
PubMed ID15213381
JournalActa Crystallogr D Biol Crystallogr
Year2004
Volume60
Pages1205-13
AuthorsKort R, Komori H, Adachi S, Miki K, Eker A
TitleDNA apophotolyase from Anacystis nidulans: 1.8 A structure, 8-HDF reconstitution and X-ray-induced FAD reduction.
Related PDB1owl,1owm,1own,1owo,1owp
[11]
PubMed ID15576622
JournalScience
Year2004
Volume306
Pages1789-93
AuthorsMees A, Klar T, Gnau P, Hennecke U, Eker AP, Carell T, Essen LO
TitleCrystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair.
Related PDB1tez
[12]
PubMed ID17051659
JournalChembiochem
Year2006
Volume7
Pages1798-806
AuthorsKlar T, Kaiser G, Hennecke U, Carell T, Batschauer A, Essen LO
TitleNatural and non-natural antenna chromophores in the DNA photolyase from Thermus thermophilus.
Related PDB2j07,2j08,2j09

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-

createdupdated
2004-07-092009-02-26


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Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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