EzCatDB: T00085
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DB codeT00085
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
CSA1dnp
MACiEM0183

CATH domainRelated DB codes (homologues)
1.10.579.10 : DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3T00249
1.25.40.80 : Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeatT00249
3.40.50.620 : Rossmann foldS00314,S00549,S00316,S00317,S00318,S00315,T00249,D00300,M00177,M00178,T00106,T00114

Enzyme Name
UniProtKBKEGG

P00914
Protein nameDeoxyribodipyrimidine 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
RefSeqNP_415236.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_488988.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF00875 (DNA_photolyase)
PF03441 (FAD_binding_7)
[Graphical view]


UniProtKB:Accession NumberP00914
Entry namePHR_ECOLI
ActivityCyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA).
SubunitMonomer.
Subcellular location
CofactorBinds 1 FAD per subunit.,Binds 1 5,10-methenyltetrahydrofolate non-covalently per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00016C00445C03103C08249
CompoundFAD5,10-MethenyltetrahydrofolateCyclobutadipyrimidinePyrimidine 5'-deoxynucleotide
Typeamide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,nucleotideamino acids,amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl groupnucleotidenucleotide
ChEBI16238


8676
PubChem643975
439237

46173772
            
1dnpA01UnboundBound:MHFUnboundUnbound
1dnpB01UnboundBound:MHFUnboundUnbound
1dnpA02Bound:FADUnboundUnboundUnbound
1dnpB02Bound:FADUnboundUnboundUnbound
1dnpA03UnboundUnboundUnboundUnbound
1dnpB03UnboundUnboundUnboundUnbound

Active-site residues
resource
literature & Catalytic Site Atlas
pdbCatalytic residues
         
1dnpA01 
1dnpB01 
1dnpA02 
1dnpB02 
1dnpA03TRP 306;TRP 359;GLY 373;TRP 382
1dnpB03TRP 306;TRP 359;GLY 373;TRP 382

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.260-261
[5]Scheme II, p.8922-89232
[7]p.559-561
[9]p.209-210
[11]p.8629-8630
[12]p.6327-6328
[15]p.902-904
[18]Fig.4, Fig.5, p.8024-8027
[19]p.12263-12664
[20]

[21]Fig.11, Fig.12
[22]Fig, p.p.1858-1859
[23]p.1869-1872
[26]p.3863-3865
[27]Fig.1
[29]p.491-496, Fig.1, Fig.3, Fig.4
[30]p.3797-3798
[31]Fig.3, p.242-246

references
[1]
PubMed ID6087879
JournalBiochemistry
Year1984
Volume23
Pages2673-9
AuthorsJorns MS, Sancar GB, Sancar A
TitleIdentification of a neutral flavin radical and characterization of a second chromophore in Escherichia coli DNA photolyase.
[2]
PubMed ID2827744
JournalBiochemistry
Year1987
Volume26
Pages7121-7
AuthorsPayne G, Heelis PF, Rohrs BR, Sancar A
TitleThe active form of Escherichia coli DNA photolyase contains a fully reduced flavin and not a flavin radical, both in vivo and in vitro.
[3]
PubMed ID3539940
JournalJ Biol Chem
Year1987
Volume262
Pages486-91
AuthorsJorns MS, Baldwin ET, Sancar GB, Sancar A
TitleAction mechanism of Escherichia coli DNA photolyase. II. Role of the chromophores in catalysis.
[4]
CommentsREVIEW
JournalTrends Biochem Sci
Year1987
Volume12
Pages259-61
AuthorsSancar GB, Sancar A
TitleStructure and function of DNA photolyases.
Related UniProtKBP00914
[5]
PubMed ID3069130
JournalBiochemistry
Year1988
Volume27
Pages8915-23
AuthorsJordan SP, Jorns MS
TitleEvidence for a singlet intermediate in catalysis by Escherichia coli DNA photolyase and evaluation of substrate binding determinants.
[6]
PubMed ID2656701
JournalJ Biol Chem
Year1989
Volume264
Pages9649-56
AuthorsHamm-Alvarez S, Sancar A, Rajagopalan KV
TitleRole of enzyme-bound 5,10-methenyltetrahydropteroylpolyglutamate in catalysis by Escherichia coli DNA photolyase.
[7]
PubMed ID2405908
JournalBiochemistry
Year1990
Volume29
Pages552-61
AuthorsJorns MS, Wang BY, Jordan SP, Chanderkar LP
TitleChromophore function and interaction in Escherichia coli DNA photolyase: reconstitution of the apoenzyme with pterin and/or flavin derivatives.
[8]
CommentsMUTAGENESIS OF TRP-278.
Medline ID90344791
PubMed ID2200511
JournalBiochemistry
Year1990
Volume29
Pages5698-706
AuthorsLi YF, Sancar A
TitleActive site of Escherichia coli DNA photolyase: mutations at Trp277 alter the selectivity of the enzyme without affecting the quantum yield of photorepair.
Related UniProtKBP00914
[9]
PubMed ID2282137
JournalBiofactors
Year1990
Volume2
Pages207-11
AuthorsJorns MS
TitleDNA photorepair: chromophore composition and function in two classes of DNA photolyases.
[10]
PubMed ID2211728
JournalJ Biol Chem
Year1990
Volume265
Pages18656-62
AuthorsHamm-Alvarez S, Sancar A, Rajagopalan KV
TitleThe folate cofactor of Escherichia coli DNA photolyase acts catalytically.
[11]
PubMed ID1716150
JournalBiochemistry
Year1991
Volume30
Pages8623-30
AuthorsKim ST, Sancar A
TitleEffect of base, pentose, and phosphodiester backbone structures on binding and repair of pyrimidine dimers by Escherichia coli DNA photolyase.
[12]
PubMed ID2059637
JournalBiochemistry
Year1991
Volume30
Pages6322-9
AuthorsLi YF, Heelis PF, Sancar A
TitleActive site of DNA photolyase: tryptophan-306 is the intrinsic hydrogen atom donor essential for flavin radical photoreduction and DNA repair in vitro.
[13]
PubMed ID1840665
JournalNucleic Acids Res
Year1991
Volume19
Pages4885-90
AuthorsLi YF, Sancar A
TitleCloning, sequencing, expression and characterization of DNA photolyase from Salmonella typhimurium.
[14]
PubMed ID1643047
JournalBiochemistry
Year1992
Volume31
Pages7134-42
AuthorsRamsey AJ, Alderfer JL, Jorns MS
TitleEnergy transduction during catalysis by Escherichia coli DNA photolyase.
[15]
PubMed ID1736305
JournalProc Natl Acad Sci U S A
Year1992
Volume89
Pages900-4
AuthorsKim ST, Li YF, Sancar A
TitleThe third chromophore of DNA photolyase: Trp-277 of Escherichia coli DNA photolyase repairs thymine dimers by direct electron transfer.
[16]
PubMed ID8515468
JournalJ Mol Biol
Year1993
Volume231
Pages1122-5
AuthorsPark HW, Sancar A, Deisenhofer J
TitleCrystallization and preliminary crystallographic analysis of Escherichia coli DNA photolyase.
[17]
PubMed ID8252071
JournalPlant J
Year1993
Volume4
Pages705-9
AuthorsBatschauer A
TitleA plant gene for photolyase: an enzyme catalyzing the repair of UV-light-induced DNA damage.
[18]
PubMed ID8396257
JournalProc Natl Acad Sci U S A
Year1993
Volume90
Pages8023-7
AuthorsKim ST, Sancar A, Essenmacher C, Babcock GT
TitleTime-resolved EPR studies with DNA photolyase: excited-state FADH0 abstracts an electron from Trp-306 to generate FADH-, the catalytically active form of the cofactor.
[19]
PubMed ID7918492
JournalBiochemistry
Year1994
Volume33
Pages12656-64
AuthorsRaibekas AA, Jorns MS
TitleAffinity probing of flavin binding sites. 2. Identification of a reactive cysteine in the flavin domain of Escherichia coli DNA photolyase.
[20]
PubMed ID7857939
JournalBiochemistry
Year1995
Volume34
Pages2284-8
AuthorsRustandi RR, Jorns MS
TitlePhotoinduced spin-polarized radical pair formation in a DNA photolyase.substrate complex at low temperature.
[21]
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.
[22]
PubMed ID7604259
JournalScience
Year1995
Volume268
Pages1858-9
AuthorsHearst JE
TitleThe structure of photolyase: using photon energy for DNA repair.
[23]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID95327928
PubMed ID7604260
JournalScience
Year1995
Volume268
Pages1866-72
AuthorsPark HW, Kim ST, Sancar A, Deisenhofer J
TitleCrystal structure of DNA photolyase from Escherichia coli.
Related PDB1dnp
Related UniProtKBP00914
[24]
PubMed ID8672500
JournalBiochemistry
Year1996
Volume35
Pages7968-73
AuthorsLipman RS, Jorns MS
TitleAn unnatural folate stereoisomer is catalytically competent in DNA photolyase.
[25]
PubMed ID9685377
JournalJ Biol Chem
Year1998
Volume273
Pages20276-84
AuthorsVande Berg BJ, Sancar GB
TitleEvidence for dinucleotide flipping by DNA photolyase.
[26]
PubMed ID10194296
JournalBiochemistry
Year1999
Volume38
Pages3857-66
AuthorsGindt YM, Vollenbroek E, Westphal K, Sackett H, Sancar A, Babcock GT
TitleOrigin of the transient electron paramagnetic resonance signals in DNA photolyase.
[27]
PubMed ID10606505
JournalBiochemistry
Year1999
Volume38
Pages16740-8
AuthorsKay CW, Feicht R, Schulz K, Sadewater P, Sancar A, Bacher A, Mobius K, Richter G, Weber S
TitleEPR, ENDOR, and TRIPLE resonance spectroscopy on the neutral flavin radical in Escherichia coli DNA photolyase.
[28]
PubMed ID11463661
JournalBiophys J
Year2001
Volume81
Pages1195-204
AuthorsWeber S, Richter G, Schleicher E, Bacher A, Mobius K, Kay CW
TitleSubstrate binding to DNA photolyase studied by electron paramagnetic resonance spectroscopy.
[29]
PubMed ID11578921
JournalCurr Opin Chem Biol
Year2001
Volume5
Pages491-8
AuthorsCarell T, Burgdorf LT, Kundu LM, Cichon M
TitleThe mechanism of action of DNA photolyases.
[30]
PubMed ID11457111
JournalJ Am Chem Soc
Year2001
Volume123
Pages3790-8
AuthorsWeber S, Mobius K, Richter G, Kay CW
TitleThe electronic structure of the flavin cofactor in DNA photolyase.
[31]
PubMed ID11371177
JournalJ Theor Biol
Year2001
Volume210
Pages237-48
AuthorsMedvedev D, Stuchebrukhov AA
TitleDNA repair mechanism by photolyase: electron transfer path from the photolyase catalytic cofactor FADH(-) to DNA thymine dimer.

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 light-harvesting cofactor, a pterin derivative (5,10-methenyltetrahydrofolate; MTHF), whereas type-II enzyme contains FADHs and a light-harvesting cofactor, 8-hydroxy-5-deazariboflavin (8-HDF).
This enzyme belongs to the type-I enzyme group.
According to the literature [22], [29], the reaction of this enzyme proceeds as follows:
(A) Excitation of MTHF by visible light, producing *MTHF
(B) Excitation energy transfer from *MHTF 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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