Q9SDY5 (RCE1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	RCE1
Ordered Locus Names:	At4g36800
ORF Names:	C7A10.560

Organism

Arabidopsis thaliana (Mouse-ear cress)

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	184 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Accepts the ubiquitin-like protein NEDD8/RUB1 from the ECR1-AXR1 E1 complex and catalyzes its covalent attachment to other proteins. Ref.1 Ref.7
Catalytic activity	ATP + NEDD8 + protein lysine = AMP + diphosphate + protein N-NEDD8yllysine.
Pathway	Protein modification; protein neddylation.
Subunit structure	Interacts with RBX1. Ref.7
Tissue specificity	Expressed in shoot, root and floral meristems, and in vascular tissues of leaves. Ref.7
Miscellaneous	Reduction in RCE1 levels leads to reduced organ length and defects in gravitropism.
Sequence similarities	Belongs to the ubiquitin-conjugating enzyme family. UBC12 subfamily.
Sequence caution	The sequence CAB16820.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence CAB80346.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Ubl conjugation pathway
Coding sequence diversity	Alternative splicing
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	response to auxin stimulus Inferred from mutant phenotype Ref.7. Source: TAIR
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW NEDD8 ligase activity Traceable author statement Ref.7. Source: TAIR protein binding Inferred from physical interaction Ref.7. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RBX1A	Q940X7	2	EBI-595116,EBI-532404

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q9SDY5-1)

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: Q9SDY5-2)

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.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 184	184	NEDD8-conjugating enzyme Ubc12		PRO_0000082494
Sites
	Active site	113	1	Glycyl thioester intermediate By similarity
Natural variations
	Alternative sequence	102 – 184	83	YHPNI…FPRCI → GLSSFYMPYIVYSFYFKIVC VVETLCWFSCLGLSSQYRFG RKRLPEHL in isoform 2.		VSP_034924

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: 9F541991CED5C1E4	FASTA	184	20,787
	10 20 30 40 50 60 MIGLFKVKEK QREQAQNATR GGASVKKQSA GELRLHKDIS ELNLPSSCSI SFPNGKDDLM 70 80 90 100 110 120 NFEVSIKPDD GYYHNGTFVF TFQVSPVYPH EAPKVKCKTK VYHPNIDLEG NVCLNILRED 130 140 150 160 170 180 WKPVLNINTV IYGLFHLFTE PNSEDPLNHD AAAVLRDNPK LFETNVRRAM TGGYVGQTFF PRCI
	Isoform 2 [UniParc]. Checksum: F8E0DCAEDC3E9FB0	FASTA	149	17,007
	10 20 30 40 50 60 MIGLFKVKEK QREQAQNATR GGASVKKQSA GELRLHKDIS ELNLPSSCSI SFPNGKDDLM 70 80 90 100 110 120 NFEVSIKPDD GYYHNGTFVF TFQVSPVYPH EAPKVKCKTK VGLSSFYMPY IVYSFYFKIV 130 140 CVVETLCWFS CLGLSSQYRF GRKRLPEHL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 10611386] [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: 9461215] [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: 10617198] [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: 14593172] [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: 12682009] [Abstract] Cited for: TISSUE SPECIFICITY, FUNCTION, INTERACTION WITH RBX1.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
IPI	IPI00539822. IPI00786235.
PIR	E85434.
RefSeq	NP_568008.4. NM_119844.5.
UniGene	At.11882. At.24761. At.43436.
3D structure databases
ProteinModelPortal	Q9SDY5.
SMR	Q9SDY5. Positions 29-184.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9SDY5. 4 interactions.
STRING	Q9SDY5.
Proteomic databases
PRIDE	Q9SDY5.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT4G36800.1; AT4G36800.1; AT4G36800. AT4G36800.2; AT4G36800.2; AT4G36800.
GeneID	829833.
GenomeReviews	Gene locus AT4G36800 in contig CT486007_GR.
KEGG	ath:AT4G36800.
Organism-specific databases
TAIR	At4g36800.
Phylogenomic databases
eggNOG	KOG0420.
GeneTree	EPGT00050000004359.
HOGENOM	HBG318790.
PhylomeDB	Q9SDY5.
ProtClustDB	CLSN2688235.
Gene expression databases
Genevestigator	Q9SDY5.
GermOnline	AT4G36800. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR000608. UBQ-conjugat_E2. IPR023313. UBQ-conjugating_AS. IPR016135. UBQ-conjugating_enzyme/RWD. [Graphical view]
Gene3D	G3DSA:3.10.110.10. UBQ-conjugat_E2. 1 hit.
Pfam	PF00179. UQ_con. 1 hit. [Graphical view]
SUPFAM	SSF54495. UBQ-conjugat/RWD-like. 1 hit.
PROSITE	PS00183. UBIQUITIN_CONJUGAT_1. 1 hit. PS50127. UBIQUITIN_CONJUGAT_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RCE1_ARATH

Accession

Primary (citable) accession number: Q9SDY5
Secondary accession number(s): O23202, Q0WLB1

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 6, 2005
Last sequence update:	May 1, 2000
Last modified:	September 21, 2011
This is version 77 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program