DB code: T00085

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 1dnp
M-CSA 1dnp
MACiE M0183

CATH domain Related DB codes (homologues)
1.10.579.10 : DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 T00249
1.25.40.80 : Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat T00249
3.40.50.620 : Rossmann fold S00314 S00549 S00316 S00317 S00318 S00315 T00249 D00300 M00177 M00178 T00106 T00114

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P00914 Deoxyribodipyrimidine photo-lyase
EC 4.1.99.3
DNA photolyase
Photoreactivating enzyme
NP_415236.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_488988.1 (Protein)
NC_007779.1 (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
P00914 PHR_ECOLI Cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA). Monomer. Binds 1 FAD per subunit. Binds 1 5,10-methenyltetrahydrofolate non-covalently per subunit.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00016 C00445 C03103 C08249
E.C.
Compound FAD 5,10-Methenyltetrahydrofolate 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,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl group nucleotide nucleotide
ChEBI 16238
8676
PubChem 643975
439237
46173772
1dnpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:MHF Unbound Unbound
1dnpB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:MHF Unbound Unbound
1dnpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
1dnpB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound
1dnpA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1dnpB03 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 & Catalytic Site Atlas

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1dnpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dnpB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dnpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dnpB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dnpA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 306;TRP 359;GLY 373;TRP 382
1dnpB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TRP 306;TRP 359;GLY 373;TRP 382

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.260-261
[5]
Scheme II, p.8922-8923 2
[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]
Resource
Comments
Medline ID
PubMed ID 6087879
Journal Biochemistry
Year 1984
Volume 23
Pages 2673-9
Authors Jorns MS, Sancar GB, Sancar A
Title Identification of a neutral flavin radical and characterization of a second chromophore in Escherichia coli DNA photolyase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2827744
Journal Biochemistry
Year 1987
Volume 26
Pages 7121-7
Authors Payne G, Heelis PF, Rohrs BR, Sancar A
Title The active form of Escherichia coli DNA photolyase contains a fully reduced flavin and not a flavin radical, both in vivo and in vitro.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 3539940
Journal J Biol Chem
Year 1987
Volume 262
Pages 486-91
Authors Jorns MS, Baldwin ET, Sancar GB, Sancar A
Title Action mechanism of Escherichia coli DNA photolyase. II. Role of the chromophores in catalysis.
Related PDB
Related UniProtKB
[4]
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
[5]
Resource
Comments
Medline ID
PubMed ID 3069130
Journal Biochemistry
Year 1988
Volume 27
Pages 8915-23
Authors Jordan SP, Jorns MS
Title Evidence for a singlet intermediate in catalysis by Escherichia coli DNA photolyase and evaluation of substrate binding determinants.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 2656701
Journal J Biol Chem
Year 1989
Volume 264
Pages 9649-56
Authors Hamm-Alvarez S, Sancar A, Rajagopalan KV
Title Role of enzyme-bound 5,10-methenyltetrahydropteroylpolyglutamate in catalysis by Escherichia coli DNA photolyase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 2405908
Journal Biochemistry
Year 1990
Volume 29
Pages 552-61
Authors Jorns MS, Wang BY, Jordan SP, Chanderkar LP
Title Chromophore function and interaction in Escherichia coli DNA photolyase: reconstitution of the apoenzyme with pterin and/or flavin derivatives.
Related PDB
Related UniProtKB
[8]
Resource
Comments MUTAGENESIS OF TRP-278.
Medline ID 90344791
PubMed ID 2200511
Journal Biochemistry
Year 1990
Volume 29
Pages 5698-706
Authors Li YF, Sancar A
Title Active site of Escherichia coli DNA photolyase: mutations at Trp277 alter the selectivity of the enzyme without affecting the quantum yield of photorepair.
Related PDB
Related UniProtKB P00914
[9]
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
[10]
Resource
Comments
Medline ID
PubMed ID 2211728
Journal J Biol Chem
Year 1990
Volume 265
Pages 18656-62
Authors Hamm-Alvarez S, Sancar A, Rajagopalan KV
Title The folate cofactor of Escherichia coli DNA photolyase acts catalytically.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 1716150
Journal Biochemistry
Year 1991
Volume 30
Pages 8623-30
Authors Kim ST, Sancar A
Title Effect of base, pentose, and phosphodiester backbone structures on binding and repair of pyrimidine dimers by Escherichia coli DNA photolyase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 2059637
Journal Biochemistry
Year 1991
Volume 30
Pages 6322-9
Authors Li YF, Heelis PF, Sancar A
Title Active site of DNA photolyase: tryptophan-306 is the intrinsic hydrogen atom donor essential for flavin radical photoreduction and DNA repair in vitro.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 1840665
Journal Nucleic Acids Res
Year 1991
Volume 19
Pages 4885-90
Authors Li YF, Sancar A
Title Cloning, sequencing, expression and characterization of DNA photolyase from Salmonella typhimurium.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 1643047
Journal Biochemistry
Year 1992
Volume 31
Pages 7134-42
Authors Ramsey AJ, Alderfer JL, Jorns MS
Title Energy transduction during catalysis by Escherichia coli DNA photolyase.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 1736305
Journal Proc Natl Acad Sci U S A
Year 1992
Volume 89
Pages 900-4
Authors Kim ST, Li YF, Sancar A
Title The third chromophore of DNA photolyase: Trp-277 of Escherichia coli DNA photolyase repairs thymine dimers by direct electron transfer.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 8515468
Journal J Mol Biol
Year 1993
Volume 231
Pages 1122-5
Authors Park HW, Sancar A, Deisenhofer J
Title Crystallization and preliminary crystallographic analysis of Escherichia coli DNA photolyase.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 8252071
Journal Plant J
Year 1993
Volume 4
Pages 705-9
Authors Batschauer A
Title A plant gene for photolyase: an enzyme catalyzing the repair of UV-light-induced DNA damage.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 8396257
Journal Proc Natl Acad Sci U S A
Year 1993
Volume 90
Pages 8023-7
Authors Kim ST, Sancar A, Essenmacher C, Babcock GT
Title Time-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.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 7918492
Journal Biochemistry
Year 1994
Volume 33
Pages 12656-64
Authors Raibekas AA, Jorns MS
Title Affinity probing of flavin binding sites. 2. Identification of a reactive cysteine in the flavin domain of Escherichia coli DNA photolyase.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 7857939
Journal Biochemistry
Year 1995
Volume 34
Pages 2284-8
Authors Rustandi RR, Jorns MS
Title Photoinduced spin-polarized radical pair formation in a DNA photolyase.substrate complex at low temperature.
Related PDB
Related UniProtKB
[21]
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
[22]
Resource
Comments
Medline ID
PubMed ID 7604259
Journal Science
Year 1995
Volume 268
Pages 1858-9
Authors Hearst JE
Title The structure of photolyase: using photon energy for DNA repair.
Related PDB
Related UniProtKB
[23]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID 95327928
PubMed ID 7604260
Journal Science
Year 1995
Volume 268
Pages 1866-72
Authors Park HW, Kim ST, Sancar A, Deisenhofer J
Title Crystal structure of DNA photolyase from Escherichia coli.
Related PDB 1dnp
Related UniProtKB P00914
[24]
Resource
Comments
Medline ID
PubMed ID 8672500
Journal Biochemistry
Year 1996
Volume 35
Pages 7968-73
Authors Lipman RS, Jorns MS
Title An unnatural folate stereoisomer is catalytically competent in DNA photolyase.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 9685377
Journal J Biol Chem
Year 1998
Volume 273
Pages 20276-84
Authors Vande Berg BJ, Sancar GB
Title Evidence for dinucleotide flipping by DNA photolyase.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 10194296
Journal Biochemistry
Year 1999
Volume 38
Pages 3857-66
Authors Gindt YM, Vollenbroek E, Westphal K, Sackett H, Sancar A, Babcock GT
Title Origin of the transient electron paramagnetic resonance signals in DNA photolyase.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 10606505
Journal Biochemistry
Year 1999
Volume 38
Pages 16740-8
Authors Kay CW, Feicht R, Schulz K, Sadewater P, Sancar A, Bacher A, Mobius K, Richter G, Weber S
Title EPR, ENDOR, and TRIPLE resonance spectroscopy on the neutral flavin radical in Escherichia coli DNA photolyase.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 11463661
Journal Biophys J
Year 2001
Volume 81
Pages 1195-204
Authors Weber S, Richter G, Schleicher E, Bacher A, Mobius K, Kay CW
Title Substrate binding to DNA photolyase studied by electron paramagnetic resonance spectroscopy.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 11578921
Journal Curr Opin Chem Biol
Year 2001
Volume 5
Pages 491-8
Authors Carell T, Burgdorf LT, Kundu LM, Cichon M
Title The mechanism of action of DNA photolyases.
Related PDB
Related UniProtKB
[30]
Resource
Comments
Medline ID
PubMed ID 11457111
Journal J Am Chem Soc
Year 2001
Volume 123
Pages 3790-8
Authors Weber S, Mobius K, Richter G, Kay CW
Title The electronic structure of the flavin cofactor in DNA photolyase.
Related PDB
Related UniProtKB
[31]
Resource
Comments
Medline ID
PubMed ID 11371177
Journal J Theor Biol
Year 2001
Volume 210
Pages 237-48
Authors Medvedev D, Stuchebrukhov AA
Title DNA repair mechanism by photolyase: electron transfer path from the photolyase catalytic cofactor FADH(-) to DNA thymine dimer.
Related PDB
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 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-

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