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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

FAD2 PublicationsNote: Binds 1 FAD per subunit.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei268FADCombined sources1 Publication1
Sitei378Electron transfer via tryptophanyl radicalSequence analysis1
Binding sitei390FADCombined sources1 Publication1
Sitei399Electron transfer via tryptophanyl radicalSequence analysis1
Sitei406Electron transfer via tryptophanyl radicalSequence analysis1
Binding sitei421FADCombined sources1 Publication1
Binding sitei427FAD; via carbonyl oxygenCombined sources1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi282 – 285FADCombined sources1 Publication4
Nucleotide bindingi319 – 327FADBy similarity9
Nucleotide bindingi427 – 429FADBy similarity3

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

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004078521 – 506Deoxyribodipyrimidine photo-lyaseAdd BLAST506

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei312Phosphoserine1 Publication1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ6F6A2.
PRIDEiQ6F6A2.

PTM databases

iPTMnetiQ6F6A2.

Expressioni

Tissue specificityi

Expressed in proliferating tissues. Highly expressed in roots and shoot apical meristem (SAM). Expressed in leaves, flag leaves, and panicle.1 Publication

Inductioni

Induced by gamma irradiation.1 Publication

Gene expression databases

GenevisibleiQ6F6A2. OS.

Interactioni

Protein-protein interaction databases

DIPiDIP-62040N.
STRINGi39947.LOC_Os10g08580.1.

Structurei

Secondary structure

1506
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi23 – 25Combined sources3
Beta strandi26 – 30Combined sources5
Beta strandi40 – 46Combined sources7
Helixi54 – 65Combined sources12
Beta strandi70 – 75Combined sources6
Helixi82 – 84Combined sources3
Helixi87 – 106Combined sources20
Beta strandi111 – 116Combined sources6
Helixi120 – 127Combined sources8
Beta strandi131 – 135Combined sources5
Helixi141 – 157Combined sources17
Beta strandi161 – 166Combined sources6
Helixi174 – 177Combined sources4
Helixi185 – 193Combined sources9
Helixi196 – 199Combined sources4
Helixi222 – 231Combined sources10
Helixi246 – 254Combined sources9
Turni256 – 258Combined sources3
Helixi260 – 263Combined sources4
Helixi265 – 267Combined sources3
Helixi268 – 271Combined sources4
Helixi278 – 280Combined sources3
Helixi285 – 289Combined sources5
Helixi295 – 305Combined sources11
Helixi306 – 308Combined sources3
Helixi310 – 320Combined sources11
Helixi322 – 333Combined sources12
Turni335 – 338Combined sources4
Helixi340 – 342Combined sources3
Helixi345 – 353Combined sources9
Turni354 – 356Combined sources3
Helixi365 – 369Combined sources5
Helixi376 – 388Combined sources13
Helixi393 – 405Combined sources13
Beta strandi407 – 409Combined sources3
Helixi410 – 424Combined sources15
Helixi431 – 442Combined sources12
Turni453 – 455Combined sources3
Helixi463 – 469Combined sources7
Helixi472 – 489Combined sources18

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3UMVX-ray1.70A/B1-506[»]
ProteinModelPortaliQ6F6A2.
SMRiQ6F6A2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini38 – 171Photolyase/cryptochrome alpha/betaAdd BLAST134

Sequence similaritiesi

Belongs to the DNA photolyase class-2 family.Curated

Phylogenomic databases

eggNOGiKOG0133. Eukaryota.
COG0415. LUCA.
InParanoidiQ6F6A2.
KOiK01669.
OrthoDBiEOG0936088L.

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

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti126R → Q in BAC76449 (PubMed:12764611).Curated1

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3UMVX-ray1.70A/B1-506[»]
ProteinModelPortaliQ6F6A2.
SMRiQ6F6A2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-62040N.
STRINGi39947.LOC_Os10g08580.1.

PTM databases

iPTMnetiQ6F6A2.

Proteomic databases

PaxDbiQ6F6A2.
PRIDEiQ6F6A2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi9272017.
KEGGiosa:9272017.

Phylogenomic databases

eggNOGiKOG0133. Eukaryota.
COG0415. LUCA.
InParanoidiQ6F6A2.
KOiK01669.
OrthoDBiEOG0936088L.

Enzyme and pathway databases

BRENDAi4.1.99.3. 4460.

Gene expression databases

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...

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: November 2, 2016
This is version 75 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.