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Q9SB00 (PHR_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 77. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Deoxyribodipyrimidine photo-lyase

EC=4.1.99.3
Alternative name(s):
AtCPDII
DNA photolyase
Photoreactivating enzyme 1
Protein UV RESISTANCE 2
Gene names
Name:PHR1
Synonyms:UVR2
Ordered Locus Names:At1g12370
ORF Names:F5O11.9
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length496 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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. Ref.1 Ref.6 Ref.7 Ref.8 Ref.10 Ref.11

Catalytic activity

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

Cofactor

Binds 1 FAD per subunit. Ref.11

Subcellular location

Nucleus Ref.10.

Tissue specificity

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

Induction

By high-fluence white light, UV-A and UV-B. Ref.1 Ref.9

Disruption phenotype

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. Ref.1 Ref.6 Ref.7 Ref.8

Miscellaneous

Over-expression of PHR1 decreases CPDs accumulation during UV-B treatment.

Sequence similarities

Belongs to the DNA photolyase class-2 family.

Contains 1 photolyase/cryptochrome alpha/beta domain.

Sequence caution

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

Ontologies

Keywords
   Biological processDNA damage
DNA repair
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   LigandDNA-binding
FAD
Flavoprotein
Nucleotide-binding
   Molecular functionLyase
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processUV protection

Inferred from mutant phenotype Ref.6. Source: TAIR

photoreactive repair

Inferred from mutant phenotype Ref.1Ref.7. Source: TAIR

   Cellular_componentnucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA photolyase activity

Inferred from direct assay Ref.6Ref.1. Source: TAIR

deoxyribodipyrimidine photo-lyase activity

Inferred from electronic annotation. Source: UniProtKB-EC

nucleotide binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9SB00-1)

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.
Isoform 2 (identifier: Q9SB00-2)

The sequence of this isoform differs from the canonical sequence as follows:
     365-370: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 496496Deoxyribodipyrimidine photo-lyase
PRO_0000407851

Regions

Domain28 – 160133Photolyase/cryptochrome alpha/beta
Nucleotide binding269 – 2735FAD By similarity
Nucleotide binding307 – 3159FAD By similarity
Nucleotide binding415 – 4173FAD By similarity

Sites

Binding site2561FAD By similarity
Binding site3071DNA Potential
Site3661Electron transfer via tryptophanyl radical Potential
Site3871Electron transfer via tryptophanyl radical Potential
Site3941Electron transfer via tryptophanyl radical Potential

Natural variations

Alternative sequence365 – 3706Missing in isoform 2.
VSP_040972

Experimental info

Sequence conflict231L → S in AAC08008. Ref.1
Sequence conflict231L → S in CAA67683. Ref.2
Sequence conflict3031T → I in AAC08008. Ref.1
Sequence conflict3031T → I in CAA67683. Ref.2
Sequence conflict3741V → L in AAC08008. Ref.1
Sequence conflict3741V → L in CAA67683. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 1, 2000. Version 1.
Checksum: 0EEC0511BE8F5639

FASTA49657,055
        10         20         30         40         50         60 
MASTVSVQPG RIRILKKGSW QPLDQTVGPV VYWMFRDQRL KDNWALIHAV DLANRTNAPV 

        70         80         90        100        110        120 
AVVFNLFDQF LDAKARQLGF MLKGLRQLHH QIDSLQIPFF LLQGDAKETI PNFLTECGAS 

       130        140        150        160        170        180 
HLVTDFSPLR EIRRCKDEVV KRTSDSLAIH EVDAHNVVPM WAASSKLEYS ARTIRGKINK 

       190        200        210        220        230        240 
LLPDYLIEFP KLEPPKKKWT GMMDKKLVDW DSLIDKVVRE GAEVPEIEWC VPGEDAGIEV 

       250        260        270        280        290        300 
LMGNKDGFLT KRLKNYSTDR NNPIKPKALS GLSPYLHFGQ VSAQRCALEA RKVRSTSPQA 

       310        320        330        340        350        360 
VDTFLEELIV RRELSDNFCY YQPHYDSLKG AWEWARKSLM DHASDKREHI YSLEQLEKGL 

       370        380        390        400        410        420 
TADPLWNASQ LEMVYQGKMH GFMRMYWAKK ILEWTKGPEE ALSISIYLNN KYEIDGRDPS 

       430        440        450        460        470        480 
GYVGCMWSIC GVHDQGWKER PVFGKIRYMN YAGCKRKFNV DSYISYVKSL VSVTKKKRKA 

       490 
EEQLTRDSVD PKITIV 

« Hide

Isoform 2 [UniParc].

Checksum: 3B6A483B371C47FD
Show »

FASTA49056,355

References

« Hide 'large scale' references
[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. expand/collapse author list , 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. expand/collapse author list , 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]"Photorepair mutants of Arabidopsis."
Jiang C.Z., Yee J., Mitchell D.L., Britt A.B.
Proc. Natl. Acad. Sci. U.S.A. 94:7441-7445(1997) [PubMed] [Europe PMC] [Abstract]
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]"Light-induced activation of class II cyclobutane pyrimidine dimer photolyases."
Okafuji A., Biskup T., Hitomi K., Getzoff E.D., Kaiser G., Batschauer A., Bacher A., Hidema J., Teranishi M., Yamamoto K., Schleicher E., Weber S.
DNA Repair 9:495-505(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, COFACTOR.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRT52112.
RefSeqNP_563906.1. NM_101109.1. [Q9SB00-2]
NP_849651.1. NM_179320.1. [Q9SB00-1]
UniGeneAt.19160.
At.70097.

3D structure databases

ProteinModelPortalQ9SB00.
SMRQ9SB00. Positions 8-470.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING3702.AT1G12370.2-P.

Proteomic databases

PaxDbQ9SB00.
PRIDEQ9SB00.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT1G12370.2; AT1G12370.2; AT1G12370. [Q9SB00-1]
GeneID837792.
KEGGath:AT1G12370.

Organism-specific databases

TAIRAT1G12370.

Phylogenomic databases

eggNOGCOG0415.
HOGENOMHOG000016456.
InParanoidQ9SB00.
KOK01669.
OMAEWTETPE.
PhylomeDBQ9SB00.

Enzyme and pathway databases

BioCycARA:AT1G12370-MONOMER.

Gene expression databases

GenevestigatorQ9SB00.

Family and domain databases

Gene3D3.40.50.620. 1 hit.
InterProIPR008148. DNA_photolyase_2.
IPR006050. DNA_photolyase_N.
IPR005101. Photolyase_FAD-bd/Cryptochr_C.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
PANTHERPTHR10211. PTHR10211. 1 hit.
PfamPF00875. DNA_photolyase. 1 hit.
PF03441. FAD_binding_7. 1 hit.
[Graphical view]
SUPFAMSSF48173. SSF48173. 1 hit.
SSF52425. SSF52425. 1 hit.
TIGRFAMsTIGR00591. phr2. 1 hit.
PROSITEPS01083. DNA_PHOTOLYASES_2_1. 1 hit.
PS01084. DNA_PHOTOLYASES_2_2. 1 hit.
PS51645. PHR_CRY_ALPHA_BETA. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePHR_ARATH
AccessionPrimary (citable) accession number: Q9SB00
Secondary accession number(s): O24374, Q94CC5, Q9LNA9
Entry history
Integrated into UniProtKB/Swiss-Prot: May 3, 2011
Last sequence update: May 1, 2000
Last modified: May 14, 2014
This is version 77 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names