B9DHA6 (RL40A_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ubiquitin-60S ribosomal protein L40-1

Cleaved into the following 2 chains:

1. Ubiquitin
2. 60S ribosomal protein L40-1
   Alternative name(s):
   CEP52

Gene names

Name:	RPL40A
Synonyms:	UBQ2
Ordered Locus Names:	At2g36170
ORF Names:	F9C22.10

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	128 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling By similarity. Ribosomal protein L40-1 is a component of the 60S subunit of the ribosome.
Subunit structure	Ribosomal protein L40-1 is part of the 60S ribosomal subunit By similarity.
Subcellular location	Ubiquitin: Cytoplasm By similarity. Nucleus By similarity. 60S ribosomal protein L40-1: Cytoplasm By similarity.
Miscellaneous	Ubiquitin is encoded by 16 different genes. Ubiquitin is generally synthesized as a polyubiquitin precursor with tandem head to tail repeats. Often, there is one to three additional amino-acids after the last repeat, removed in the mature protein. Alternatively, ubiquitin extension protein is synthesized as a single copy of ubiquitin fused to a ribosomal protein (either L40 or S27A) or to an ubiquitin-related protein (either RUB1 or RUB2). Following translation, extension protein is cleaved from ubiquitin.
Sequence similarities	In the N-terminal section; belongs to the ubiquitin family. In the C-terminal section; belongs to the ribosomal protein L40e family. Contains 1 ubiquitin-like domain.

Ontologies

Keywords
Cellular component	Cytoplasm Nucleus
Molecular function	Ribonucleoprotein Ribosomal protein
PTM	Isopeptide bond Ubl conjugation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	translation Inferred from electronic annotation. Source: InterPro
Cellular_component	cytosolic large ribosomal subunit Inferred from direct assay PubMed 17934214. Source: TAIR nucleolus Inferred from direct assay PubMed 15496452. Source: TAIR
Molecular_function	structural constituent of ribosome Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 76	76	Ubiquitin		PRO_0000396865
	Chain	77 – 128	52	60S ribosomal protein L40-1		PRO_0000138758
Regions
	Domain	1 – 76	76	Ubiquitin-like
Amino acid modifications
	Cross-link	11		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
	Cross-link	29		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
	Cross-link	33		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
	Cross-link	48		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
	Cross-link	63		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
	Cross-link	76		Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) By similarity

Sequences

	Sequence		Length	Mass (Da)
	B9DHA6 [UniParc]. Last modified March 24, 2009. Version 1. Checksum: 2E4EB17A20A6D28B	FASTA	128	14,733
	10 20 30 40 50 60 MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLADYN 70 80 90 100 110 120 IQKESTLHLV LRLRGGIIEP SLMMLARKYN QDKMICRKCY ARLHPRAVNC RKKKCGHSNQ LRPKKKIK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Ubiquitin extension proteins of Arabidopsis thaliana. Structure, localization, and expression of their promoters in transgenic tobacco." Callis J., Raasch J.A., Vierstra R.D. J. Biol. Chem. 265:12486-12493(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: cv. Columbia.
[2]	"Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana." Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D., Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V., Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S., Cronin L.A. , Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C. Nature 402:761-768(1999) [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]. Strain: cv. Columbia.
[5]	"Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs." Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K. DNA Res. 16:155-164(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia. Tissue: Rosette leaf.
[6]	"The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome." Barakat A., Szick-Miranda K., Chang I.-F., Guyot R., Blanc G., Cooke R., Delseny M., Bailey-Serres J. Plant Physiol. 127:398-415(2001) [PubMed] [Europe PMC] [Abstract] Cited for: GENE FAMILY ORGANIZATION, NOMENCLATURE.
[7]	"Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants." Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K. Mol. Cell. Proteomics 6:601-610(2007) [PubMed] [Europe PMC] [Abstract] Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-11; LYS-29; LYS-33; LYS-48 AND LYS-63, MASS SPECTROMETRY. Strain: cv. Landsberg erecta.

Cross-references

Sequence databases
EMBL GenBank DDBJ	J05508 Genomic DNA. Translation: AAA32905.1. AC006921 Genomic DNA. No translation available. AC007135 Genomic DNA. Translation: AAM15407.1. CP002685 Genomic DNA. Translation: AEC09212.1. AF360311 mRNA. Translation: AAK26021.1. AY056360 mRNA. Translation: AAL07246.1. AK317456 mRNA. Translation: BAH20123.1.
IPI	IPI00533306.
PIR	B36571.
RefSeq	NP_565836.1. NM_129175.2. NP_566969.1. NM_115119.3.
UniGene	At.23108. At.24656. At.35280.
3D structure databases
ProteinModelPortal	B9DHA6.
SMR	B9DHA6. Positions 1-74, 89-128.
ModBase	Search...
Proteomic databases
PaxDb	B9DHA6.
PRIDE	B9DHA6.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT2G36170.1; AT2G36170.1; AT2G36170. AT3G52590.1; AT3G52590.1; AT3G52590.
GeneID	818189. 824425.
KEGG	ath:AT2G36170. ath:AT3G52590.
Organism-specific databases
GeneFarm	382. 38.
TAIR	At2g36170.
Phylogenomic databases
eggNOG	COG5272.
KO	K02927.
ProtClustDB	CLSN2688722.
Gene expression databases
ArrayExpress	B9DHA6.
Family and domain databases
InterPro	IPR001975. Ribosomal_L40e. IPR000626. Ubiquitin. IPR019954. Ubiquitin_CS. IPR019956. Ubiquitin_subgr. IPR019955. Ubiquitin_supergroup. [Graphical view]
Pfam	PF01020. Ribosomal_L40e. 1 hit. PF00240. ubiquitin. 1 hit. [Graphical view]
PRINTS	PR00348. UBIQUITIN.
SMART	SM00213. UBQ. 1 hit. [Graphical view]
PROSITE	PS00299. UBIQUITIN_1. 1 hit. PS50053. UBIQUITIN_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RL40A_ARATH

Accession

Primary (citable) accession number: B9DHA6
Secondary accession number(s): O80715 , P19232, P59263, Q38875, Q9LDJ2, Q9LYW1, Q9M0W3, Q9M1P9, Q9S7X3

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 10, 2010
Last sequence update:	March 24, 2009
Last modified:	May 1, 2013
This is version 31 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program