Q94A97 (UBC35_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ubiquitin-conjugating enzyme E2 35
EC=6.3.2.19

Alternative name(s):
Ubiquitin carrier protein 35

Gene names

Name:	UBC35
Synonyms:	UBC13A, UBG13A
Ordered Locus Names:	At1g78870
ORF Names:	F9K20.8

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	153 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the synthesis of non-canonical poly-ubiquitin chains that are linked through 'Lys-63'. This type of poly-ubiquitination does not lead to protein degradation by the proteasome. Mediates transcriptional activation of target genes. Required for postreplication repair of UV-damaged DNA and for adaptating root developmental programs to suboptimal availability of iron. Ref.1 Ref.6 Ref.9
Catalytic activity	ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
Pathway	Protein modification; protein ubiquitination.
Subunit structure	Interacts with yeast and human Mms2, with the RING domain of RGLG2 and with UEV1A, UEV1B, UEV1C and UEV1D. Ref.6 Ref.7 Ref.8
Tissue specificity	Ubiquitously expressed at low level. Mainly expressed in the vasculature. Ref.1 Ref.6 Ref.9
Induction	Not induced by salt, abscisic acid, mannitol, H2O2, low temperature, MMS or iron. Ref.6 Ref.9
Disruption phenotype	No visible phenotype under normal growth conditions or in phosphate-deficient plants. Unable to form branched root hairs in response to iron-deficient conditions. Ref.9
Miscellaneous	Partly functionally redundant with UBC36.
Sequence similarities	Belongs to the ubiquitin-conjugating enzyme family.
Sequence caution	The sequence AAC83026.1 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	postreplication repair Inferred from genetic interaction Ref.8. Source: TAIR response to cadmium ion Inferred from expression pattern PubMed 16502469. Source: TAIR response to iron ion Inferred from mutant phenotype Ref.9. Source: TAIR root epidermal cell differentiation Inferred from genetic interaction Ref.9. Source: TAIR ubiquitin-dependent protein catabolic process Inferred from direct assay Ref.1. Source: TAIR
Cellular_component	UBC13-MMS2 complex Inferred from physical interaction Ref.8. Source: TAIR
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ubiquitin-protein ligase activity Inferred from direct assay Ref.1. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
UBE2V2	Q15819	3	EBI-994120,EBI-714329	From a different organism.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q94A97-1)

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: Q94A97-2)

The sequence of this isoform differs from the canonical sequence as follows:
     51-51: G → GR

Note: Derived from EST data. May be due to a competing donor splice site. No experimental confirmation available.

Isoform 3 (identifier: Q94A97-3)

The sequence of this isoform differs from the canonical sequence as follows:
     109-112: SIQA → RYMS
     113-153: Missing.

Note: Derived from EST data. May be due to an intron retention. No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 153	153	Ubiquitin-conjugating enzyme E2 35		PRO_0000345200
Sites
	Active site	89	1	Glycyl thioester intermediate By similarity
Natural variations
	Alternative sequence	51	1	G → GR in isoform 2.		VSP_034929
	Alternative sequence	109 – 112	4	SIQA → RYMS in isoform 3.		VSP_034930
	Alternative sequence	113 – 153	41	Missing in isoform 3.		VSP_034931

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified December 1, 2001. Version 1. Checksum: 66FDD14FA347A8D0	FASTA	153	17,192
	10 20 30 40 50 60 MANSNLPRRI IKETQRLLSE PAPGISASPS EDNMRYFNVM ILGPTQSPYE GGVFKLELFL 70 80 90 100 110 120 PEEYPMAAPK VRFLTKIYHP NIDKLGRICL DILKDKWSPA LQIRTVLLSI QALLSAPNPD 130 140 150 DPLSENIAKH WKSNEAEAVD TAKEWTRLYA SGA
	Isoform 2 [UniParc]. Checksum: E5616F62F3894F92	FASTA	154	17,348
	10 20 30 40 50 60 MANSNLPRRI IKETQRLLSE PAPGISASPS EDNMRYFNVM ILGPTQSPYE GRGVFKLELF 70 80 90 100 110 120 LPEEYPMAAP KVRFLTKIYH PNIDKLGRIC LDILKDKWSP ALQIRTVLLS IQALLSAPNP 130 140 150 DDPLSENIAK HWKSNEAEAV DTAKEWTRLY ASGA
	Isoform 3 [UniParc]. Checksum: 99FC71C2CB9C008F	FASTA	112	12,851
	10 20 30 40 50 60 MANSNLPRRI IKETQRLLSE PAPGISASPS EDNMRYFNVM ILGPTQSPYE GGVFKLELFL 70 80 90 100 110 PEEYPMAAPK VRFLTKIYHP NIDKLGRICL DILKDKWSPA LQIRTVLLRY MS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Genome analysis and functional characterization of the E2 and RING-type E3 ligase ubiquitination enzymes of Arabidopsis." Kraft E., Stone S.L., Ma L., Su N., Gao Y., Lau O.-S., Deng X.-W., Callis J. Plant Physiol. 139:1597-1611(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, TISSUE SPECIFICITY, GENE FAMILY, NOMENCLATURE.
[2]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"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.
[5]	"Full-length cDNA from Arabidopsis thaliana." Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A. Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[6]	"Arabidopsis thaliana UBC13: implication of error-free DNA damage tolerance and Lys63-linked polyubiquitylation in plants." Wen R., Newton L., Li G., Wang H., Xiao W. Plant Mol. Biol. 61:241-253(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH YEAST AND HUMAN MMS2, TISSUE SPECIFICITY, INDUCTION.
[7]	"Ubiquitin lysine 63 chain forming ligases regulate apical dominance in Arabidopsis." Yin X.-J., Volk S., Ljung K., Mehlmer N., Dolezal K., Ditengou F., Hanano S., Davis S.J., Schmelzer E., Sandberg G., Teige M., Palme K., Pickart C., Bachmair A. Plant Cell 19:1898-1911(2007) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RGLG2.
[8]	"Arabidopsis UEV1D promotes lysine-63-linked polyubiquitination and is involved in DNA damage response." Wen R., Torres-Acosta J.A., Pastushok L., Lai X., Pelzer L., Wang H., Xiao W. Plant Cell 20:213-227(2008) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH UEV1A; UEV1B; UEV1C AND UEV1D.
[9]	"A lysine-63-linked ubiquitin chain-forming conjugase, UBC13, promotes the developmental responses to iron deficiency in Arabidopsis roots." Li W., Schmidt W. Plant J. 62:330-343(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INDUCTION BY IRON, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE.
+	Additional computationally mapped references.

Web resources

PlantsUBQ

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

Cross-references

Sequence databases
EMBL GenBank DDBJ	DQ027048 mRNA. Translation: AAY44874.1. AC005679 Genomic DNA. Translation: AAC83026.1. Sequence problems. CP002684 Genomic DNA. Translation: AEE36164.1. CP002684 Genomic DNA. Translation: AEE36165.1. CP002684 Genomic DNA. Translation: AEE36166.1. AY049261 mRNA. Translation: AAK83603.1. BT000544 mRNA. Translation: AAN18113.1. AY085854 mRNA. Translation: AAM63067.1.
IPI	IPI00517808. IPI00530602. IPI00656884.
PIR	B96818.
RefSeq	NP_001031298.1. NM_001036221.2. NP_565192.1. NM_106535.3. NP_849902.2. NM_179571.2.
UniGene	At.46456.
3D structure databases
HSSP	HSSP built from PDB template 2C2V based on UniProtKB P61088.
ProteinModelPortal	Q94A97.
SMR	Q94A97. Positions 6-150.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q94A97. 2 interactions.
Proteomic databases
PaxDb	Q94A97.
PRIDE	Q94A97.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT1G78870.2; AT1G78870.2; AT1G78870.
GeneID	844224.
KEGG	ath:AT1G78870.
Organism-specific databases
TAIR	At1g78870.
Phylogenomic databases
eggNOG	COG5078.
HOGENOM	HOG000233455.
InParanoid	Q94A97.
KO	K10580.
OMA	ELWKINE.
PhylomeDB	Q94A97.
ProtClustDB	CLSN2687835.
Enzyme and pathway databases
UniPathway	UPA00143.
Gene expression databases
Genevestigator	Q94A97.
Family and domain databases
Gene3D	3.10.110.10. 1 hit.
InterPro	IPR000608. UBQ-conjugat_E2. IPR023313. UBQ-conjugating_AS. IPR016135. UBQ-conjugating_enzyme/RWD. [Graphical view]
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

UBC35_ARATH

Accession

Primary (citable) accession number: Q94A97
Secondary accession number(s): Q2V4C1, Q9ZVA6

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 22, 2008
Last sequence update:	December 1, 2001
Last modified:	May 1, 2013
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program