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Protein

NEDD8-conjugating enzyme Ubc12

Gene

RCE1

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

Functioni

Accepts the ubiquitin-like protein NEDD8/RUB1 from the ECR1-AXR1 E1 complex and catalyzes its covalent attachment to other proteins.2 Publications

Catalytic activityi

ATP + NEDD8 + protein lysine = AMP + diphosphate + protein N-NEDD8yllysine.

Pathwayi: protein neddylation

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei113 – 1131Glycyl thioester intermediatePROSITE-ProRule annotation

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ligase activity Source: UniProtKB-KW
  • NEDD8 transferase activity Source: TAIR

GO - Biological processi

  • protein neddylation Source: GO_Central
  • response to auxin Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Ubl conjugation pathway

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciARA:AT4G36800-MONOMER.
ARA:GQT-910-MONOMER.
UniPathwayiUPA00885.

Names & Taxonomyi

Protein namesi
Recommended name:
NEDD8-conjugating enzyme Ubc12 (EC:6.3.2.-)
Alternative name(s):
RUB1 carrier protein 1
RUB1-conjugating enzyme 1
RUB1-protein ligase 1
Gene namesi
Name:RCE1
Ordered Locus Names:At4g36800
ORF Names:C7A10.560
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G36800.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 184184NEDD8-conjugating enzyme Ubc12PRO_0000082494Add
BLAST

Proteomic databases

PaxDbiQ9SDY5.
PRIDEiQ9SDY5.

Expressioni

Tissue specificityi

Expressed in shoot, root and floral meristems, and in vascular tissues of leaves.1 Publication

Gene expression databases

GenevisibleiQ9SDY5. AT.

Interactioni

Subunit structurei

Interacts with RBX1.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
RBX1AQ940X72EBI-595116,EBI-532404

Protein-protein interaction databases

BioGridi15114. 5 interactions.
IntActiQ9SDY5. 4 interactions.
STRINGi3702.AT4G36800.1.

Structurei

3D structure databases

ProteinModelPortaliQ9SDY5.
SMRiQ9SDY5. Positions 29-184.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ubiquitin-conjugating enzyme family. UBC12 subfamily.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0420. Eukaryota.
ENOG410XS81. LUCA.
HOGENOMiHOG000233456.
InParanoidiQ9SDY5.
KOiK10579.
OMAiLFHLFTQ.
PhylomeDBiQ9SDY5.

Family and domain databases

Gene3Di3.10.110.10. 1 hit.
InterProiIPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]
PfamiPF00179. UQ_con. 1 hit.
[Graphical view]
SUPFAMiSSF54495. SSF54495. 1 hit.
PROSITEiPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9SDY5-1) [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

        10         20         30         40         50
MIGLFKVKEK QREQAQNATR GGASVKKQSA GELRLHKDIS ELNLPSSCSI
60 70 80 90 100
SFPNGKDDLM NFEVSIKPDD GYYHNGTFVF TFQVSPVYPH EAPKVKCKTK
110 120 130 140 150
VYHPNIDLEG NVCLNILRED WKPVLNINTV IYGLFHLFTE PNSEDPLNHD
160 170 180
AAAVLRDNPK LFETNVRRAM TGGYVGQTFF PRCI
Length:184
Mass (Da):20,787
Last modified:May 1, 2000 - v1
Checksum:i9F541991CED5C1E4
GO
Isoform 2 (identifier: Q9SDY5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     102-184: YHPNIDLEGN...VGQTFFPRCI → GLSSFYMPYI...FGRKRLPEHL

Note: May be due to intron retention. No experimental confirmation available.
Show »
Length:149
Mass (Da):17,007
Checksum:iF8E0DCAEDC3E9FB0
GO

Sequence cautioni

The sequence CAB16820.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAB80346.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei102 – 18483YHPNI…FPRCI → GLSSFYMPYIVYSFYFKIVC VVETLCWFSCLGLSSQYRFG RKRLPEHL in isoform 2. 1 PublicationVSP_034924Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF202771 mRNA. Translation: AAF19827.1.
Z99708 Genomic DNA. Translation: CAB16820.1. Sequence problems.
AL161590 Genomic DNA. Translation: CAB80346.1. Sequence problems.
CP002687 Genomic DNA. Translation: AEE86703.1.
CP002687 Genomic DNA. Translation: AEE86704.1.
AY048210 mRNA. Translation: AAK82473.1.
AY097381 mRNA. Translation: AAM19897.1.
AK230295 mRNA. Translation: BAF02096.1.
PIRiE85434.
RefSeqiNP_001154289.1. NM_001160817.1. [Q9SDY5-1]
NP_568008.4. NM_119844.5. [Q9SDY5-1]
UniGeneiAt.11882.
At.24761.
At.43436.

Genome annotation databases

EnsemblPlantsiAT4G36800.1; AT4G36800.1; AT4G36800. [Q9SDY5-1]
AT4G36800.2; AT4G36800.2; AT4G36800. [Q9SDY5-1]
GeneIDi829833.
KEGGiath:AT4G36800.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF202771 mRNA. Translation: AAF19827.1.
Z99708 Genomic DNA. Translation: CAB16820.1. Sequence problems.
AL161590 Genomic DNA. Translation: CAB80346.1. Sequence problems.
CP002687 Genomic DNA. Translation: AEE86703.1.
CP002687 Genomic DNA. Translation: AEE86704.1.
AY048210 mRNA. Translation: AAK82473.1.
AY097381 mRNA. Translation: AAM19897.1.
AK230295 mRNA. Translation: BAF02096.1.
PIRiE85434.
RefSeqiNP_001154289.1. NM_001160817.1. [Q9SDY5-1]
NP_568008.4. NM_119844.5. [Q9SDY5-1]
UniGeneiAt.11882.
At.24761.
At.43436.

3D structure databases

ProteinModelPortaliQ9SDY5.
SMRiQ9SDY5. Positions 29-184.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi15114. 5 interactions.
IntActiQ9SDY5. 4 interactions.
STRINGi3702.AT4G36800.1.

Proteomic databases

PaxDbiQ9SDY5.
PRIDEiQ9SDY5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G36800.1; AT4G36800.1; AT4G36800. [Q9SDY5-1]
AT4G36800.2; AT4G36800.2; AT4G36800. [Q9SDY5-1]
GeneIDi829833.
KEGGiath:AT4G36800.

Organism-specific databases

TAIRiAT4G36800.

Phylogenomic databases

eggNOGiKOG0420. Eukaryota.
ENOG410XS81. LUCA.
HOGENOMiHOG000233456.
InParanoidiQ9SDY5.
KOiK10579.
OMAiLFHLFTQ.
PhylomeDBiQ9SDY5.

Enzyme and pathway databases

UniPathwayiUPA00885.
BioCyciARA:AT4G36800-MONOMER.
ARA:GQT-910-MONOMER.

Miscellaneous databases

PROiQ9SDY5.

Gene expression databases

GenevisibleiQ9SDY5. AT.

Family and domain databases

Gene3Di3.10.110.10. 1 hit.
InterProiIPR000608. UBQ-conjugat_E2.
IPR023313. UBQ-conjugating_AS.
IPR016135. UBQ-conjugating_enzyme/RWD.
[Graphical view]
PfamiPF00179. UQ_con. 1 hit.
[Graphical view]
SUPFAMiSSF54495. SSF54495. 1 hit.
PROSITEiPS00183. UBIQUITIN_CONJUGAT_1. 1 hit.
PS50127. UBIQUITIN_CONJUGAT_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The Arabidopsis cullin AtCUL1 is modified by the ubiquitin-related protein RUB1."
    del Pozo J.C., Estelle M.
    Proc. Natl. Acad. Sci. U.S.A. 96:15342-15347(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION.
  2. "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana."
    Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C., Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P., Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.
    , Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R., De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M., Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M., Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A., Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D., Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A., Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S., Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G., Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.
    Nature 391:485-488(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1999) [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 1).
    Strain: cv. Columbia.
  6. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Strain: cv. Columbia.
  7. "The RUB/Nedd8 conjugation pathway is required for early development in Arabidopsis."
    Dharmasiri S., Dharmasiri N., Hellmann H., Estelle M.
    EMBO J. 22:1762-1770(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, FUNCTION, INTERACTION WITH RBX1.

Entry informationi

Entry nameiRCE1_ARATH
AccessioniPrimary (citable) accession number: Q9SDY5
Secondary accession number(s): O23202, Q0WLB1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: May 1, 2000
Last modified: February 17, 2016
This is version 107 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Reduction in RCE1 levels leads to reduced organ length and defects in gravitropism.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.