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Q9SB00

- PHR_ARATH

UniProt

Q9SB00 - PHR_ARATH

Protein

Deoxyribodipyrimidine photo-lyase

Gene

PHR1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 78 (01 Oct 2014)
      Sequence version 1 (01 May 2000)
      Previous versions | rss
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    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

    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

    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

    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.
    OMAiEWTETPE.
    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

    MASTVSVQPG RIRILKKGSW QPLDQTVGPV VYWMFRDQRL KDNWALIHAV    50
    DLANRTNAPV AVVFNLFDQF LDAKARQLGF MLKGLRQLHH QIDSLQIPFF 100
    LLQGDAKETI PNFLTECGAS HLVTDFSPLR EIRRCKDEVV KRTSDSLAIH 150
    EVDAHNVVPM WAASSKLEYS ARTIRGKINK LLPDYLIEFP KLEPPKKKWT 200
    GMMDKKLVDW DSLIDKVVRE GAEVPEIEWC VPGEDAGIEV LMGNKDGFLT 250
    KRLKNYSTDR NNPIKPKALS GLSPYLHFGQ VSAQRCALEA RKVRSTSPQA 300
    VDTFLEELIV RRELSDNFCY YQPHYDSLKG AWEWARKSLM DHASDKREHI 350
    YSLEQLEKGL TADPLWNASQ LEMVYQGKMH GFMRMYWAKK ILEWTKGPEE 400
    ALSISIYLNN KYEIDGRDPS GYVGCMWSIC GVHDQGWKER PVFGKIRYMN 450
    YAGCKRKFNV DSYISYVKSL VSVTKKKRKA EEQLTRDSVD PKITIV 496
    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.

    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi T52112.
    RefSeqi NP_563906.1. NM_101109.1. [Q9SB00-2 ]
    NP_849651.1. NM_179320.1. [Q9SB00-1 ]
    UniGenei At.19160.
    At.70097.

    3D structure databases

    ProteinModelPortali Q9SB00.
    SMRi Q9SB00. Positions 8-470.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 3702.AT1G12370.2-P.

    Proteomic databases

    PaxDbi Q9SB00.
    PRIDEi Q9SB00.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT1G12370.2 ; AT1G12370.2 ; AT1G12370 . [Q9SB00-1 ]
    GeneIDi 837792.
    KEGGi ath:AT1G12370.

    Organism-specific databases

    TAIRi AT1G12370.

    Phylogenomic databases

    eggNOGi COG0415.
    HOGENOMi HOG000016456.
    InParanoidi Q9SB00.
    KOi K01669.
    OMAi EWTETPE.
    PhylomeDBi Q9SB00.

    Enzyme and pathway databases

    BioCyci ARA:AT1G12370-MONOMER.

    Gene expression databases

    Genevestigatori Q9SB00.

    Family and domain databases

    Gene3Di 3.40.50.620. 1 hit.
    InterProi IPR008148. DNA_photolyase_2.
    IPR006050. DNA_photolyase_N.
    IPR005101. Photolyase_FAD-bd/Cryptochr_C.
    IPR014729. Rossmann-like_a/b/a_fold.
    [Graphical view ]
    PANTHERi PTHR10211. PTHR10211. 1 hit.
    Pfami PF00875. DNA_photolyase. 1 hit.
    PF03441. FAD_binding_7. 1 hit.
    [Graphical view ]
    SUPFAMi SSF48173. SSF48173. 1 hit.
    SSF52425. SSF52425. 1 hit.
    TIGRFAMsi TIGR00591. phr2. 1 hit.
    PROSITEi PS01083. DNA_PHOTOLYASES_2_1. 1 hit.
    PS01084. DNA_PHOTOLYASES_2_2. 1 hit.
    PS51645. PHR_CRY_ALPHA_BETA. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 78 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