Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Deoxyribodipyrimidine photo-lyase

Gene

PHR1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript 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 sitei256 – 2561FADBy similarity
Binding sitei307 – 3071DNASequence Analysis
Sitei366 – 3661Electron transfer via tryptophanyl radicalSequence Analysis
Sitei387 – 3871Electron transfer via tryptophanyl radicalSequence Analysis
Sitei394 – 3941Electron transfer via tryptophanyl radicalSequence Analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi269 – 2735FADBy similarity
Nucleotide bindingi307 – 3159FADBy similarity
Nucleotide bindingi415 – 4173FADBy similarity

GO - Molecular functioni

  1. deoxyribodipyrimidine photo-lyase activity Source: UniProtKB-EC
  2. DNA binding Source: UniProtKB-KW
  3. DNA photolyase activity Source: TAIR
  4. nucleotide binding Source: UniProtKB-KW

GO - Biological processi

  1. photoreactive repair Source: TAIR
  2. UV protection Source: TAIR
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

BioCyciARA:AT1G12370-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Deoxyribodipyrimidine photo-lyase (EC:4.1.99.3)
Alternative name(s):
AtCPDII
DNA photolyase
Photoreactivating enzyme 1
Protein UV RESISTANCE 2
Gene namesi
Name:PHR1
Synonyms:UVR2
Ordered Locus Names:At1g12370
ORF Names:F5O11.9
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 1

Organism-specific databases

TAIRiAT1G12370.

Subcellular locationi

Nucleus 1 Publication

GO - Cellular componenti

  1. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

No visible phenotype under white light, but inhibition of growth and leaf necrosis under white light and UV-B. Increasesd accumulation of CPDs under UV-B.4 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 496496Deoxyribodipyrimidine photo-lyasePRO_0000407851Add
BLAST

Proteomic databases

PaxDbiQ9SB00.
PRIDEiQ9SB00.

Expressioni

Tissue specificityi

Highly expressed in flowers. Expressed in roots and stems.1 Publication

Inductioni

By high-fluence white light, UV-A and UV-B.2 Publications

Gene expression databases

GenevestigatoriQ9SB00.

Interactioni

Protein-protein interaction databases

STRINGi3702.AT1G12370.2-P.

Structurei

3D structure databases

ProteinModelPortaliQ9SB00.
SMRiQ9SB00. Positions 8-470.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini28 – 160133Photolyase/cryptochrome alpha/betaAdd
BLAST

Sequence similaritiesi

Belongs to the DNA photolyase class-2 family.Curated

Phylogenomic databases

eggNOGiCOG0415.
HOGENOMiHOG000016456.
InParanoidiQ9SB00.
KOiK01669.
OMAiLADNFCF.
PhylomeDBiQ9SB00.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
InterProiIPR008148. DNA_photolyase_2.
IPR006050. DNA_photolyase_N.
IPR005101. Photolyase_FAD-bd/Cryptochr_C.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
PANTHERiPTHR10211. PTHR10211. 1 hit.
PfamiPF00875. DNA_photolyase. 1 hit.
PF03441. FAD_binding_7. 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]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q9SB00-1) [UniParc]FASTAAdd to Basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MASTVSVQPG RIRILKKGSW QPLDQTVGPV VYWMFRDQRL KDNWALIHAV
60 70 80 90 100
DLANRTNAPV AVVFNLFDQF LDAKARQLGF MLKGLRQLHH QIDSLQIPFF
110 120 130 140 150
LLQGDAKETI PNFLTECGAS HLVTDFSPLR EIRRCKDEVV KRTSDSLAIH
160 170 180 190 200
EVDAHNVVPM WAASSKLEYS ARTIRGKINK LLPDYLIEFP KLEPPKKKWT
210 220 230 240 250
GMMDKKLVDW DSLIDKVVRE GAEVPEIEWC VPGEDAGIEV LMGNKDGFLT
260 270 280 290 300
KRLKNYSTDR NNPIKPKALS GLSPYLHFGQ VSAQRCALEA RKVRSTSPQA
310 320 330 340 350
VDTFLEELIV RRELSDNFCY YQPHYDSLKG AWEWARKSLM DHASDKREHI
360 370 380 390 400
YSLEQLEKGL TADPLWNASQ LEMVYQGKMH GFMRMYWAKK ILEWTKGPEE
410 420 430 440 450
ALSISIYLNN KYEIDGRDPS GYVGCMWSIC GVHDQGWKER PVFGKIRYMN
460 470 480 490
YAGCKRKFNV DSYISYVKSL VSVTKKKRKA EEQLTRDSVD PKITIV
Length:496
Mass (Da):57,055
Last modified:May 1, 2000 - v1
Checksum:i0EEC0511BE8F5639
GO
Isoform 2 (identifier: Q9SB00-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     365-370: Missing.

Note: No experimental confirmation available.

Show »
Length:490
Mass (Da):56,355
Checksum:i3B6A483B371C47FD
GO

Sequence cautioni

The sequence AAF79657.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti23 – 231L → S in AAC08008. (PubMed:9061951)Curated
Sequence conflicti23 – 231L → S in CAA67683. 1 PublicationCurated
Sequence conflicti303 – 3031T → I in AAC08008. (PubMed:9061951)Curated
Sequence conflicti303 – 3031T → I in CAA67683. 1 PublicationCurated
Sequence conflicti374 – 3741V → L in AAC08008. (PubMed:9061951)Curated
Sequence conflicti374 – 3741V → L in CAA67683. 1 PublicationCurated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei365 – 3706Missing in isoform 2. 1 PublicationVSP_040972

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF053365 mRNA. Translation: AAC08008.1.
X99301 mRNA. Translation: CAA67683.1.
AB010875 Genomic DNA. Translation: BAA74701.1.
AC025416 Genomic DNA. Translation: AAF79657.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE28871.1.
CP002684 Genomic DNA. Translation: AEE28872.1.
AY034961 mRNA. Translation: AAK59467.1.
AY113909 mRNA. Translation: AAM44957.1.
PIRiT52112.
RefSeqiNP_563906.1. NM_101109.1. [Q9SB00-2]
NP_849651.1. NM_179320.1. [Q9SB00-1]
UniGeneiAt.19160.
At.70097.

Genome annotation databases

EnsemblPlantsiAT1G12370.2; AT1G12370.2; AT1G12370. [Q9SB00-1]
GeneIDi837792.
KEGGiath:AT1G12370.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF053365 mRNA. Translation: AAC08008.1.
X99301 mRNA. Translation: CAA67683.1.
AB010875 Genomic DNA. Translation: BAA74701.1.
AC025416 Genomic DNA. Translation: AAF79657.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE28871.1.
CP002684 Genomic DNA. Translation: AEE28872.1.
AY034961 mRNA. Translation: AAK59467.1.
AY113909 mRNA. Translation: AAM44957.1.
PIRiT52112.
RefSeqiNP_563906.1. NM_101109.1. [Q9SB00-2]
NP_849651.1. NM_179320.1. [Q9SB00-1]
UniGeneiAt.19160.
At.70097.

3D structure databases

ProteinModelPortaliQ9SB00.
SMRiQ9SB00. Positions 8-470.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT1G12370.2-P.

Proteomic databases

PaxDbiQ9SB00.
PRIDEiQ9SB00.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G12370.2; AT1G12370.2; AT1G12370. [Q9SB00-1]
GeneIDi837792.
KEGGiath:AT1G12370.

Organism-specific databases

TAIRiAT1G12370.

Phylogenomic databases

eggNOGiCOG0415.
HOGENOMiHOG000016456.
InParanoidiQ9SB00.
KOiK01669.
OMAiLADNFCF.
PhylomeDBiQ9SB00.

Enzyme and pathway databases

BioCyciARA:AT1G12370-MONOMER.

Gene expression databases

GenevestigatoriQ9SB00.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
InterProiIPR008148. DNA_photolyase_2.
IPR006050. DNA_photolyase_N.
IPR005101. Photolyase_FAD-bd/Cryptochr_C.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
PANTHERiPTHR10211. PTHR10211. 1 hit.
PfamiPF00875. DNA_photolyase. 1 hit.
PF03441. FAD_binding_7. 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. "An enzyme similar to animal type II photolyases mediates photoreactivation in Arabidopsis."
    Ahmad M., Jarillo J.A., Klimczak L.J., Landry L.G., Peng T., Last R.L., Cashmore A.R.
    Plant Cell 9:199-207(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, TISSUE SPECIFICITY, INDUCTION, DISRUPTION PHENOTYPE.
  2. "The cloning and sequence analysis of a putative type II CPD photolyases from Arabidopsis thaliana."
    Taylor R., Tobin A., Bray C.
    Submitted (SEP-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  3. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Strain: cv. Columbia.
  6. "An Arabidopsis photolyase mutant is hypersensitive to ultraviolet-B radiation."
    Landry L.G., Stapleton A.E., Lim J., Hoffman P., Hays J.B., Walbot V., Last R.L.
    Proc. Natl. Acad. Sci. U.S.A. 94:328-332(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
  7. Cited for: FUNCTION, DISRUPTION PHENOTYPE.
  8. "UV-damage-mediated induction of homologous recombination in Arabidopsis is dependent on photosynthetically active radiation."
    Ries G., Buchholz G., Frohnmeyer H., Hohn B.
    Proc. Natl. Acad. Sci. U.S.A. 97:13425-13429(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
  9. "An ultraviolet-B-resistant mutant with enhanced DNA repair in Arabidopsis."
    Tanaka A., Sakamoto A., Ishigaki Y., Nikaido O., Sun G., Hase Y., Shikazono N., Tano S., Watanabe H.
    Plant Physiol. 129:64-71(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  10. "Increased DNA repair in Arabidopsis plants overexpressing CPD photolyase."
    Kaiser G., Kleiner O., Beisswenger C., Batschauer A.
    Planta 230:505-515(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  11. Cited for: FUNCTION, COFACTOR.

Entry informationi

Entry nameiPHR_ARATH
AccessioniPrimary (citable) accession number: Q9SB00
Secondary accession number(s): O24374, Q94CC5, Q9LNA9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 3, 2011
Last sequence update: May 1, 2000
Last modified: January 7, 2015
This is version 81 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 PHR1 decreases CPDs accumulation during UV-B treatment.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.