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Protein

E3 ubiquitin-protein ligase COP1

Gene

COP1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

E3 ubiquitin-protein ligase that acts as a repressor of photomorphogenesis and as an activator of etiolation in darkness. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Represses photomorphogenesis in darkness by mediating ubiquitination and subsequent proteasomal degradation of light-induced transcription factors such as HY5, HYH and LAF1. Down-regulates MYB21, probably via ubiquitination process. Light stimuli abrogate the repression of photomorphogenesis, possibly due to its localization to the cytoplasm. Could play a role in switching between skotomorphogenetic and photomorphogenetic pathways.2 Publications

Pathwayi: protein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri52 – 90RING-typePROSITE-ProRule annotationAdd BLAST39

GO - Molecular functioni

  • identical protein binding Source: IntAct
  • ligase activity Source: UniProtKB-KW
  • ubiquitin protein ligase activity Source: GO_Central
  • ubiquitin-protein transferase activity Source: TAIR
  • zinc ion binding Source: InterPro

GO - Biological processi

  • anthocyanin-containing compound metabolic process Source: TAIR
  • DNA repair Source: TAIR
  • entrainment of circadian clock Source: TAIR
  • photomorphogenesis Source: TAIR
  • photoperiodism, flowering Source: TAIR
  • positive regulation of proteasomal ubiquitin-dependent protein catabolic process Source: GO_Central
  • red, far-red light phototransduction Source: UniProtKB-KW
  • regulation of stomatal movement Source: TAIR
  • shade avoidance Source: TAIR
  • skotomorphogenesis Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Phytochrome signaling pathway, Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-ATH-349425. Autodegradation of the E3 ubiquitin ligase COP1.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase COP1 (EC:6.3.2.-)
Alternative name(s):
Constitutive photomorphogenesis protein 1
Gene namesi
Name:COP1
Ordered Locus Names:At2g32950
ORF Names:T21L14.11
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G32950.

Subcellular locationi

  • Nucleus
  • Cytoplasm

  • Note: Localizes to the nucleus in darkness but is gradually relocated to the cytoplasm upon illumination. Localizes to subnuclear foci (speckle) and in dispersed nuclear localization in the dark.

GO - Cellular componenti

  • Cul4-RING E3 ubiquitin ligase complex Source: TAIR
  • cytoplasm Source: UniProtKB-SubCell
  • nuclear body Source: TAIR
  • nuclear ubiquitin ligase complex Source: TAIR
  • nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi52C → S: Abolishes LAF1 ubiquitination and degradation; when associated with S-55. 1 Publication1
Mutagenesisi55C → S: Abolishes LAF1 ubiquitination and degradation; when associated with S-52. 1 Publication1
Mutagenesisi294 – 296RKK → SKT: Abolishes localization to the nucleus. 1 Publication3
Mutagenesisi312 – 314KRR → TRS: Abolishes localization to the nucleus. 1 Publication3
Mutagenesisi422K → E: 5-fold increase in interaction with HY5, weak interaction with BBX24/STO and BBX25/STH, and at low light intensity shorter hypocotyl. 1 Publication1
Mutagenesisi465R → E: No interaction with BBX24/STO and BBX25/STH, and at low light intensity shorter hypocotyl. 1 Publication1
Mutagenesisi467W → A: No interaction with HY5, BBX24/STO and BBX25/STH and at low light intensity shorter hypocotyl. 1 Publication1
Mutagenesisi523 – 584Missing in COP1-8; no interaction with SPA1 and lethal. Add BLAST62
Mutagenesisi524G → E in COP1-9; no interaction with HY5, SPA1, BBX25/STH or BBX24/STO and lethal. 1
Mutagenesisi550K → E: No interaction with HY5, BBX24/STO and BBX25/STH and at low light intensity shorter hypocotyl. 1 Publication1
Mutagenesisi592E → R: Better interaction with HY5, BBX24/STO and BBX25/STH and slightly longer hypocotyls. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000558811 – 675E3 ubiquitin-protein ligase COP1Add BLAST675

Post-translational modificationi

Autoubiquitinated.4 Publications

Keywords - PTMi

Ubl conjugation

Proteomic databases

PaxDbiP43254.

PTM databases

iPTMnetiP43254.

Expressioni

Gene expression databases

GenevisibleiP43254. AT.

Interactioni

Subunit structurei

Homodimer. Interacts with HY5, HYH, BBX24/STO, BBX25/STH, CIP8, COP10, SPA1, SPA2, SPA3, SPA4 and UVR8 and phosphorylated PHYA. Light induces dissociation of the SPA1/COP1 complex. Interacts with HRT/RPP8 and triggers it to the 26s proteasome. Binds to CRY2; this competitive interaction prevents triggering to proteasome of other binding proteins (PubMed:20624951).12 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself5EBI-301649,EBI-301649
Q388433EBI-301649,EBI-2119970
BBX25Q9SID13EBI-301649,EBI-631960
CIP8Q9SPL26EBI-301649,EBI-301644
COQ390578EBI-301649,EBI-1639724
COL3Q9SK533EBI-301649,EBI-1995108
COP10Q9LJD73EBI-301649,EBI-2429853
CRY1Q431254EBI-301649,EBI-300703
CRY2Q965242EBI-301649,EBI-531555
HFR1Q9FE226EBI-301649,EBI-626001
HY5O246468EBI-301649,EBI-301660
HYHQ8W191-13EBI-301649,EBI-11463635
LAF1Q9M0K43EBI-301649,EBI-1543309
RAX2Q9SJL73EBI-301649,EBI-2292310
SPA1Q9SYX217EBI-301649,EBI-626992
SPA3Q9LJR37EBI-301649,EBI-626921
SPA4Q94BM714EBI-301649,EBI-626943
UVR8Q9FN033EBI-301649,EBI-2407499

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi3204. 54 interactors.
DIPiDIP-32850N.
IntActiP43254. 28 interactors.
MINTiMINT-189205.
STRINGi3702.AT2G32950.1.

Structurei

Secondary structure

1675
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi355 – 362Combined sources8
Turni367 – 369Combined sources3
Beta strandi374 – 379Combined sources6
Beta strandi383 – 390Combined sources8
Beta strandi393 – 399Combined sources7
Helixi400 – 405Combined sources6
Beta strandi414 – 418Combined sources5
Beta strandi423 – 428Combined sources6
Beta strandi430 – 432Combined sources3
Beta strandi435 – 440Combined sources6
Beta strandi445 – 449Combined sources5
Turni450 – 453Combined sources4
Beta strandi454 – 459Combined sources6
Beta strandi466 – 471Combined sources6
Beta strandi473 – 475Combined sources3
Beta strandi478 – 483Combined sources6
Beta strandi486 – 492Combined sources7
Beta strandi499 – 503Combined sources5
Beta strandi508 – 513Combined sources6
Beta strandi520 – 525Combined sources6
Beta strandi530 – 534Combined sources5
Beta strandi542 – 545Combined sources4
Beta strandi552 – 567Combined sources16
Turni568 – 570Combined sources3
Beta strandi571 – 576Combined sources6
Turni577 – 580Combined sources4
Beta strandi581 – 586Combined sources6
Beta strandi592 – 594Combined sources3
Beta strandi598 – 600Combined sources3
Beta strandi602 – 607Combined sources6
Beta strandi612 – 618Combined sources7
Beta strandi625 – 629Combined sources5
Helixi633 – 636Combined sources4
Turni637 – 639Combined sources3
Turni641 – 644Combined sources4
Beta strandi647 – 652Combined sources6
Beta strandi656 – 663Combined sources8
Beta strandi668 – 674Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5IGOX-ray1.60A/B/C/D349-675[»]
ProteinModelPortaliP43254.
SMRiP43254.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati369 – 408WD 1Add BLAST40
Repeati418 – 458WD 2Add BLAST41
Repeati461 – 501WD 3Add BLAST41
Repeati503 – 543WD 4Add BLAST41
Repeati547 – 585WD 5Add BLAST39
Repeati588 – 627WD 6Add BLAST40
Repeati642 – 674WD 7Add BLAST33

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni67 – 177CLS (cytoplasmic localization signal)Add BLAST111
Regioni120 – 177SNLS (subnuclear localization signal)Add BLAST58

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili134 – 201Sequence analysisAdd BLAST68

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi294 – 317Bipartite nuclear localization signalAdd BLAST24
Motifi522 – 536DWD box 1Add BLAST15
Motifi563 – 578DWD box 2Add BLAST16

Domaini

The coiled-coil domain (134-201) is necessary for SPA1, SPA3 or SPA4 binding. The DWD box is required for interaction with DDB1A (By similarity).By similarity

Sequence similaritiesi

Contains 1 RING-type zinc finger.PROSITE-ProRule annotation
Contains 7 WD repeats.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri52 – 90RING-typePROSITE-ProRule annotationAdd BLAST39

Keywords - Domaini

Coiled coil, Repeat, WD repeat, Zinc-finger

Phylogenomic databases

eggNOGiENOG410ISDP. Eukaryota.
ENOG410XNTU. LUCA.
HOGENOMiHOG000006123.
InParanoidiP43254.
KOiK10143.
OMAiFSTRMTR.
OrthoDBiEOG093603KX.
PhylomeDBiP43254.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
3.30.40.10. 1 hit.
InterProiIPR033313. RFWD2/COP1.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PANTHERiPTHR22847:SF451. PTHR22847:SF451. 2 hits.
PfamiPF00400. WD40. 2 hits.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
SM00320. WD40. 7 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS00678. WD_REPEATS_1. 1 hit.
PS50082. WD_REPEATS_2. 2 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
PS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P43254-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEEISTDPVV PAVKPDPRTS SVGEGANRHE NDDGGSGGSE IGAPDLDKDL
60 70 80 90 100
LCPICMQIIK DAFLTACGHS FCYMCIITHL RNKSDCPCCS QHLTNNQLYP
110 120 130 140 150
NFLLDKLLKK TSARHVSKTA SPLDQFREAL QRGCDVSIKE VDNLLTLLAE
160 170 180 190 200
RKRKMEQEEA ERNMQILLDF LHCLRKQKVD ELNEVQTDLQ YIKEDINAVE
210 220 230 240 250
RHRIDLYRAR DRYSVKLRML GDDPSTRNAW PHEKNQIGFN SNSLSIRGGN
260 270 280 290 300
FVGNYQNKKV EGKAQGSSHG LPKKDALSGS DSQSLNQSTV SMARKKRIHA
310 320 330 340 350
QFNDLQECYL QKRRQLADQP NSKQENDKSV VRREGYSNGL ADFQSVLTTF
360 370 380 390 400
TRYSRLRVIA EIRHGDIFHS ANIVSSIEFD RDDELFATAG VSRCIKVFDF
410 420 430 440 450
SSVVNEPADM QCPIVEMSTR SKLSCLSWNK HEKNHIASSD YEGIVTVWDV
460 470 480 490 500
TTRQSLMEYE EHEKRAWSVD FSRTEPSMLV SGSDDCKVKV WCTRQEASVI
510 520 530 540 550
NIDMKANICC VKYNPGSSNY IAVGSADHHI HYYDLRNISQ PLHVFSGHKK
560 570 580 590 600
AVSYVKFLSN NELASASTDS TLRLWDVKDN LPVRTFRGHT NEKNFVGLTV
610 620 630 640 650
NSEYLACGSE TNEVYVYHKE ITRPVTSHRF GSPDMDDAEE EAGSYFISAV
660 670
CWKSDSPTML TANSQGTIKV LVLAA
Length:675
Mass (Da):76,188
Last modified:January 23, 2002 - v2
Checksum:iE6D9A1B702EAE8F0
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti292M → I in AAA32772 (PubMed:1423630).Curated1
Sequence conflicti361E → Q in CAA04168 (PubMed:9744100).Curated1
Sequence conflicti381R → P in CAA04168 (PubMed:9744100).Curated1
Sequence conflicti403V → F in AAA32772 (PubMed:1423630).Curated1
Sequence conflicti456L → R in AAA32772 (PubMed:1423630).Curated1
Sequence conflicti515P → R in CAA04169 (PubMed:9744100).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L24437 mRNA. Translation: AAA32772.1.
AC003033 Genomic DNA. Translation: AAB91983.1.
CP002685 Genomic DNA. Translation: AEC08766.1.
BT025337 mRNA. Translation: ABF57293.1.
AJ000535 Genomic DNA. Translation: CAA04168.1.
AJ000536 Genomic DNA. Translation: CAA04169.1.
PIRiT01112.
RefSeqiNP_180854.1. NM_128855.4.
UniGeneiAt.298.

Genome annotation databases

EnsemblPlantsiAT2G32950.1; AT2G32950.1; AT2G32950.
GeneIDi817857.
GrameneiAT2G32950.1; AT2G32950.1; AT2G32950.
KEGGiath:AT2G32950.

Cross-referencesi

Web resourcesi

PlantsUBQ

A functional genomics database for the ubiquitin/26S proteasome proteolytic pathway in plants

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L24437 mRNA. Translation: AAA32772.1.
AC003033 Genomic DNA. Translation: AAB91983.1.
CP002685 Genomic DNA. Translation: AEC08766.1.
BT025337 mRNA. Translation: ABF57293.1.
AJ000535 Genomic DNA. Translation: CAA04168.1.
AJ000536 Genomic DNA. Translation: CAA04169.1.
PIRiT01112.
RefSeqiNP_180854.1. NM_128855.4.
UniGeneiAt.298.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5IGOX-ray1.60A/B/C/D349-675[»]
ProteinModelPortaliP43254.
SMRiP43254.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi3204. 54 interactors.
DIPiDIP-32850N.
IntActiP43254. 28 interactors.
MINTiMINT-189205.
STRINGi3702.AT2G32950.1.

PTM databases

iPTMnetiP43254.

Proteomic databases

PaxDbiP43254.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G32950.1; AT2G32950.1; AT2G32950.
GeneIDi817857.
GrameneiAT2G32950.1; AT2G32950.1; AT2G32950.
KEGGiath:AT2G32950.

Organism-specific databases

TAIRiAT2G32950.

Phylogenomic databases

eggNOGiENOG410ISDP. Eukaryota.
ENOG410XNTU. LUCA.
HOGENOMiHOG000006123.
InParanoidiP43254.
KOiK10143.
OMAiFSTRMTR.
OrthoDBiEOG093603KX.
PhylomeDBiP43254.

Enzyme and pathway databases

UniPathwayiUPA00143.
ReactomeiR-ATH-349425. Autodegradation of the E3 ubiquitin ligase COP1.

Miscellaneous databases

PROiP43254.

Gene expression databases

GenevisibleiP43254. AT.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
3.30.40.10. 1 hit.
InterProiIPR033313. RFWD2/COP1.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PANTHERiPTHR22847:SF451. PTHR22847:SF451. 2 hits.
PfamiPF00400. WD40. 2 hits.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
SM00320. WD40. 7 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS00678. WD_REPEATS_1. 1 hit.
PS50082. WD_REPEATS_2. 2 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
PS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCOP1_ARATH
AccessioniPrimary (citable) accession number: P43254
Secondary accession number(s): O23974
, O23975, O48770, Q1JPL6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: January 23, 2002
Last modified: November 30, 2016
This is version 163 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Plants lacking COP1 are not viable.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.