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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. Mediates the ubiquitination-dependent degradation of HY5 in the darkness during seedling development (e.g. hypocotyl growth) (PubMed:26474641). Represses CIP7 in darkness (PubMed:9668129).4 Publications

Miscellaneous

Plants lacking COP1 are not viable.
Although plants lack TRIB proteins, a human TRIB1 peptide binds to a highly conserved surface on the top face of the beta propeller, indicating a general mode for recognition of peptide motifs by COP1.1 Publication

Catalytic activityi

S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6-ubiquitinyl-[acceptor protein]-L-lysine.1 Publication

Pathwayi: protein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.1 Publication
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei422Human TRIB1 COP1-binding motif1 Publication1
Binding sitei441Human TRIB1 COP1-binding motif1 Publication1

Regions

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

GO - Molecular functioni

  • identical protein binding Source: IntAct
  • metal ion binding Source: UniProtKB-KW
  • ubiquitin-protein transferase activity Source: TAIR

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
  • red, far-red light phototransduction Source: UniProtKB-KW
  • regulation of stomatal movement Source: TAIR
  • shade avoidance Source: TAIR
  • skotomorphogenesis Source: TAIR

Keywordsi

Molecular functionTransferase
Biological processPhytochrome signaling pathway, Ubl conjugation pathway
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-ATH-349425. Autodegradation of the E3 ubiquitin ligase COP1.
R-ATH-8951664. Neddylation.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase COP11 Publication (EC:2.3.2.271 Publication)
Alternative name(s):
Constitutive photomorphogenesis protein 11 Publication
RING-type E3 ubiquitin transferase COP11 Publication
Gene namesi
Name:COP11 Publication
Ordered Locus Names:At2g32950Imported
ORF Names:T21L14.11Imported
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

AraportiAT2G32950.
TAIRilocus:2059359. AT2G32950.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

The double mutant shw1 cop1 displays an enhanced photomorphogenic growth in the darkness as well as abnormal accumulation of HY5.1 Publication

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

ExpressionAtlasiP43254. baseline and differential.
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). Binds to SHW1 in the nucleus (PubMed:26474641). Bonds to CIP7 (PubMed:9668129). Interacts with CSU2 (PubMed:26714275). Binds to CIP1 (PubMed:7753789).16 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi3204. 58 interactors.
DIPiDIP-32850N.
ELMiP43254.
IntActiP43254. 30 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[»]
5KWNX-ray1.42A349-675[»]
ProteinModelPortaliP43254.
SMRiP43254.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

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

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni67 – 177CLS (cytoplasmic localization signal)Add BLAST111
Regioni120 – 177SNLS (subnuclear localization signal)Add BLAST58
Regioni593 – 595Binding of human TRIB1 COP1-binding-motif1 Publication3

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

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.
OMAiPICFEMI.
OrthoDBiEOG093603KX.
PhylomeDBiP43254.

Family and domain databases

Gene3Di2.130.10.10. 2 hits.
3.30.40.10. 1 hit.
InterProiView protein in InterPro
IPR015943. WD40/YVTN_repeat-like_dom_sf.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
IPR036322. WD40_repeat_dom_sf.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
PfamiView protein in Pfam
PF00400. WD40. 2 hits.
SMARTiView protein in SMART
SM00184. RING. 1 hit.
SM00320. WD40. 7 hits.
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiView protein in PROSITE
PS00678. 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.

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.

Similar proteinsi

Entry informationi

Entry nameiCOP1_ARATH
AccessioniPrimary (citable) accession number: P43254
Secondary accession number(s): O23974
, O23975, O48770, Q1JPL6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: January 23, 2002
Last modified: November 22, 2017
This is version 174 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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