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Protein

Deoxyribodipyrimidine photo-lyase

Gene

PHR

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutylpyrimidine dimers (CPDs), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation. Required for plant survival in the presence of UV-B light. Not involved in the repair of (6-4) photoproducts.6 Publications

Catalytic activityi

Cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA).

Cofactori

FAD1 PublicationNote: Binds 1 FAD per subunit.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei268 – 2681FADBy similarity
Binding sitei319 – 3191DNASequence analysis
Sitei378 – 3781Electron transfer via tryptophanyl radicalSequence analysis
Sitei399 – 3991Electron transfer via tryptophanyl radicalSequence analysis
Sitei406 – 4061Electron transfer via tryptophanyl radicalSequence analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi281 – 2855FADBy similarity
Nucleotide bindingi319 – 3279FADBy similarity
Nucleotide bindingi427 – 4293FADBy similarity

GO - Molecular functioni

  • deoxyribodipyrimidine photo-lyase activity Source: UniProtKB
  • DNA binding Source: UniProtKB-KW
  • nucleotide binding Source: UniProtKB-KW

GO - Biological processi

  • DNA repair Source: UniProtKB
  • photoreactive repair Source: GO_Central
  • UV protection Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

DNA-binding, FAD, Flavoprotein, Nucleotide-binding

Enzyme and pathway databases

BRENDAi4.1.99.3. 4460.

Names & Taxonomyi

Protein namesi
Recommended name:
Deoxyribodipyrimidine photo-lyase (EC:4.1.99.3)
Alternative name(s):
DNA photolyase
OsCPDII
Photoreactivating enzyme
Gene namesi
Name:PHR
Ordered Locus Names:Os10g0167600, LOC_Os10g08580
ORF Names:OSJNAb0015J03.12
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryza
Proteomesi
  • UP000059680 Componenti: Chromosome 10, cultivar: Nipponbare

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 506506Deoxyribodipyrimidine photo-lyasePRO_0000407852Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei312 – 3121Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ6F6A2.

PTM databases

iPTMnetiQ6F6A2.

Expressioni

Gene expression databases

ExpressionAtlasiQ6F6A2. baseline and differential.
GenevisibleiQ6F6A2. OS.

Interactioni

Protein-protein interaction databases

STRINGi39947.LOC_Os10g08580.1.

Structurei

Secondary structure

1
506
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi23 – 253Combined sources
Beta strandi26 – 305Combined sources
Beta strandi40 – 467Combined sources
Helixi54 – 6512Combined sources
Beta strandi70 – 756Combined sources
Helixi82 – 843Combined sources
Helixi87 – 10620Combined sources
Beta strandi111 – 1166Combined sources
Helixi120 – 1278Combined sources
Beta strandi131 – 1355Combined sources
Helixi141 – 15717Combined sources
Beta strandi161 – 1666Combined sources
Helixi174 – 1774Combined sources
Helixi185 – 1939Combined sources
Helixi196 – 1994Combined sources
Helixi222 – 23110Combined sources
Helixi246 – 2549Combined sources
Turni256 – 2583Combined sources
Helixi260 – 2634Combined sources
Helixi265 – 2673Combined sources
Helixi268 – 2714Combined sources
Helixi278 – 2803Combined sources
Helixi285 – 2895Combined sources
Helixi295 – 30511Combined sources
Helixi306 – 3083Combined sources
Helixi310 – 32011Combined sources
Helixi322 – 33312Combined sources
Turni335 – 3384Combined sources
Helixi340 – 3423Combined sources
Helixi345 – 3539Combined sources
Turni354 – 3563Combined sources
Helixi365 – 3695Combined sources
Helixi376 – 38813Combined sources
Helixi393 – 40513Combined sources
Beta strandi407 – 4093Combined sources
Helixi410 – 42415Combined sources
Helixi431 – 44212Combined sources
Turni453 – 4553Combined sources
Helixi463 – 4697Combined sources
Helixi472 – 48918Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3UMVX-ray1.70A/B1-506[»]
ProteinModelPortaliQ6F6A2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini38 – 171134Photolyase/cryptochrome alpha/betaAdd
BLAST

Sequence similaritiesi

Belongs to the DNA photolyase class-2 family.Curated

Phylogenomic databases

eggNOGiKOG0133. Eukaryota.
COG0415. LUCA.
InParanoidiQ6F6A2.
KOiK01669.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
InterProiIPR005101. Cryptochr/Photolyase_FAD-bd.
IPR008148. DNA_photolyase_2.
IPR032673. DNA_photolyase_2_CS.
IPR006050. DNA_photolyase_N.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
PANTHERiPTHR10211:SF0. PTHR10211:SF0. 1 hit.
PfamiPF00875. DNA_photolyase. 1 hit.
[Graphical view]
SUPFAMiSSF48173. SSF48173. 1 hit.
SSF52425. SSF52425. 1 hit.
TIGRFAMsiTIGR00591. phr2. 1 hit.
PROSITEiPS01083. DNA_PHOTOLYASES_2_1. 1 hit.
PS01084. DNA_PHOTOLYASES_2_2. 1 hit.
PS51645. PHR_CRY_ALPHA_BETA. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q6F6A2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPPTSVSPPR TAPGPANPSP AHPSRVRVIH PGGGKPGGPV VYWMLRDQRL
60 70 80 90 100
ADNWALLHAA GLAAASASPL AVAFALFPRP FLLSARRRQL GFLLRGLRRL
110 120 130 140 150
AADAAARHLP FFLFTGGPAE IPALVRRLGA STLVADFSPL RPVREALDAV
160 170 180 190 200
VGDLRREAPG VAVHQVDAHN VVPVWTASAK MEYSAKTFRG KVSKVMDEYL
210 220 230 240 250
VEFPELPAVV PWDREQPEGV DWDALIARVC SEAENVPEID WCEPGEEAAI
260 270 280 290 300
EALLGSKDGF LTKRIKSYET DRNDPTKPRA LSGLSPYLHF GHISAQRCAL
310 320 330 340 350
EAKKCRHLSP KSVDAFLEEL VVRRELADNF CYYQPQYDSL SGAWEWARKT
360 370 380 390 400
LMDHAADKRE HIYTREQLEN AKTHDPLWNA SQLEMVHHGK MHGFMRMYWA
410 420 430 440 450
KKILEWTSGP EEALSTAIYL NDKYEIDGRD PSGYVGCMWS ICGLHDQGWK
460 470 480 490 500
ERPVFGKIRY MNYAGCKRKF DVDAYISYVK RLAGQSKKRN AEESPNPVVK

LSKSQH
Length:506
Mass (Da):56,637
Last modified:August 16, 2004 - v1
Checksum:i954450951EE78EA4
GO

Sequence cautioni

The sequence AAN04184.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence BAH94769.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti126 – 1261R → Q in BAC76449 (PubMed:12764611).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB096003 mRNA. Translation: BAC76449.2.
AB099694 Genomic DNA. Translation: BAD26607.1.
AB198744 Genomic DNA. Translation: BAE06248.1.
AB210109 mRNA. Translation: BAE45635.1.
AC131375 Genomic DNA. Translation: AAN04184.1. Sequence problems.
DP000086 Genomic DNA. Translation: ABB46863.1.
AP008216 Genomic DNA. Translation: BAH94769.1. Sequence problems.
AP014966 Genomic DNA. Translation: BAT10044.1.
RefSeqiXP_015614933.1. XM_015759447.1.
UniGeneiOs.46278.

Genome annotation databases

GeneIDi9272017.
KEGGiosa:9272017.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB096003 mRNA. Translation: BAC76449.2.
AB099694 Genomic DNA. Translation: BAD26607.1.
AB198744 Genomic DNA. Translation: BAE06248.1.
AB210109 mRNA. Translation: BAE45635.1.
AC131375 Genomic DNA. Translation: AAN04184.1. Sequence problems.
DP000086 Genomic DNA. Translation: ABB46863.1.
AP008216 Genomic DNA. Translation: BAH94769.1. Sequence problems.
AP014966 Genomic DNA. Translation: BAT10044.1.
RefSeqiXP_015614933.1. XM_015759447.1.
UniGeneiOs.46278.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3UMVX-ray1.70A/B1-506[»]
ProteinModelPortaliQ6F6A2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi39947.LOC_Os10g08580.1.

PTM databases

iPTMnetiQ6F6A2.

Proteomic databases

PaxDbiQ6F6A2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi9272017.
KEGGiosa:9272017.

Phylogenomic databases

eggNOGiKOG0133. Eukaryota.
COG0415. LUCA.
InParanoidiQ6F6A2.
KOiK01669.

Enzyme and pathway databases

BRENDAi4.1.99.3. 4460.

Gene expression databases

ExpressionAtlasiQ6F6A2. baseline and differential.
GenevisibleiQ6F6A2. OS.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
InterProiIPR005101. Cryptochr/Photolyase_FAD-bd.
IPR008148. DNA_photolyase_2.
IPR032673. DNA_photolyase_2_CS.
IPR006050. DNA_photolyase_N.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
PANTHERiPTHR10211:SF0. PTHR10211:SF0. 1 hit.
PfamiPF00875. DNA_photolyase. 1 hit.
[Graphical view]
SUPFAMiSSF48173. SSF48173. 1 hit.
SSF52425. SSF52425. 1 hit.
TIGRFAMsiTIGR00591. phr2. 1 hit.
PROSITEiPS01083. DNA_PHOTOLYASES_2_1. 1 hit.
PS01084. DNA_PHOTOLYASES_2_2. 1 hit.
PS51645. PHR_CRY_ALPHA_BETA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A gene for a Class II DNA photolyase from Oryza sativa: cloning of the cDNA by dilution-amplification."
    Hirouchi T., Nakajima S., Najrana T., Tanaka M., Matsunaga T., Hidema J., Teranishi M., Fujino T., Kumagai T., Yamamoto K.
    Mol. Genet. Genomics 269:508-516(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION.
    Strain: cv. Sasanishiki.
  2. "Ultraviolet-B sensitivities in Japanese lowland rice cultivars: cyclobutane pyrimidine dimer photolyase activity and gene mutation."
    Teranishi M., Iwamatsu Y., Hidema J., Kumagai T.
    Plant Cell Physiol. 45:1848-1856(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: cv. Nohrin.
  3. "qUVR-10, a major quantitative trait locus for ultraviolet-B resistance in rice, encodes cyclobutane pyrimidine dimer photolyase."
    Ueda T., Sato T., Hidema J., Hirouchi T., Yamamoto K., Kumagai T., Yano M.
    Genetics 171:1941-1950(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
  4. "Biochemical and biological properties of DNA photolyases derived from utraviolet-sensitive rice cultivars."
    Ymamoto A., Hirouchi T., Mori T., Teranishi M., Hidema J., Morioka H., Kumagai T., Yamamoto K.
    Genes Genet. Syst. 82:311-319(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION.
    Strain: cv. Gulfmont.
  5. "In-depth view of structure, activity, and evolution of rice chromosome 10."
    Yu Y., Rambo T., Currie J., Saski C., Kim H.-R., Collura K., Thompson S., Simmons J., Yang T.-J., Nah G., Patel A.J., Thurmond S., Henry D., Oates R., Palmer M., Pries G., Gibson J., Anderson H.
    , Paradkar M., Crane L., Dale J., Carver M.B., Wood T., Frisch D., Engler F., Soderlund C., Palmer L.E., Teytelman L., Nascimento L., De la Bastide M., Spiegel L., Ware D., O'Shaughnessy A., Dike S., Dedhia N., Preston R., Huang E., Ferraro K., Kuit K., Miller B., Zutavern T., Katzenberger F., Muller S., Balija V., Martienssen R.A., Stein L., Minx P., Johnson D., Cordum H., Mardis E., Cheng Z., Jiang J., Wilson R., McCombie W.R., Wing R.A., Yuan Q., Ouyang S., Liu J., Jones K.M., Gansberger K., Moffat K., Hill J., Tsitrin T., Overton L., Bera J., Kim M., Jin S., Tallon L., Ciecko A., Pai G., Van Aken S., Utterback T., Reidmuller S., Bormann J., Feldblyum T., Hsiao J., Zismann V., Blunt S., de Vazeille A.R., Shaffer T., Koo H., Suh B., Yang Q., Haas B., Peterson J., Pertea M., Volfovsky N., Wortman J., White O., Salzberg S.L., Fraser C.M., Buell C.R., Messing J., Song R., Fuks G., Llaca V., Kovchak S., Young S., Bowers J.E., Paterson A.H., Johns M.A., Mao L., Pan H., Dean R.A.
    Science 300:1566-1569(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  7. "The rice annotation project database (RAP-DB): 2008 update."
    The rice annotation project (RAP)
    Nucleic Acids Res. 36:D1028-D1033(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION.
    Strain: cv. Nipponbare.
  8. Cited for: GENOME REANNOTATION.
    Strain: cv. Nipponbare.
  9. "Increase in CPD photolyase activity functions effectively to prevent growth inhibition caused by UVB radiation."
    Hidema J., Taguchi T., Ono T., Teranishi M., Yamamoto K., Kumagai T.
    Plant J. 50:70-79(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. "The native cyclobutane pyrimidine dimer photolyase of rice is phosphorylated."
    Teranishi M., Nakamura K., Morioka H., Yamamoto K., Hidema J.
    Plant Physiol. 146:1941-1951(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, PHOSPHORYLATION AT SER-312, IDENTIFICATION BY MASS SPECTROMETRY.
  11. Cited for: FUNCTION, COFACTOR.

Entry informationi

Entry nameiPHR_ORYSJ
AccessioniPrimary (citable) accession number: Q6F6A2
Secondary accession number(s): A0A0P0XT34
, C7J833, Q3LGA3, Q84LN6, Q8LM09
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 3, 2011
Last sequence update: August 16, 2004
Last modified: May 11, 2016
This is version 71 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Over-expression of PHR decreases growth inhibition, leaf necrosis and CPDs accumulation under UV-B treatment.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.