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B9DHA6 (RL40A_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 40. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length128 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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.

60S ribosomal protein L40-1: 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 a 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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 7676Ubiquitin
PRO_0000396865
Chain77 – 1285260S ribosomal protein L40-1
PRO_0000138758

Regions

Domain1 – 7676Ubiquitin-like

Amino acid modifications

Cross-link11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) By similarity

Sequences

Sequence LengthMass (Da)Tools
B9DHA6 [UniParc].

Last modified March 24, 2009. Version 1.
Checksum: 2E4EB17A20A6D28B

FASTA12814,733
        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 

« Hide

References

« Hide '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. expand/collapse author list , 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. expand/collapse author list , 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.
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.
PIRB36571.
RefSeqNP_565836.1. NM_129175.2.
NP_566969.1. NM_115119.3.
UniGeneAt.23108.
At.24656.
At.35280.

3D structure databases

ProteinModelPortalB9DHA6.
SMRB9DHA6. Positions 1-74, 89-128.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid3533. 1 interaction.
9743. 9 interactions.

Proteomic databases

PaxDbB9DHA6.
PRIDEB9DHA6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT2G36170.1; AT2G36170.1; AT2G36170.
AT3G52590.1; AT3G52590.1; AT3G52590.
GeneID818189.
824425.
KEGGath:AT2G36170.
ath:AT3G52590.

Organism-specific databases

GeneFarm382. 38.
TAIRAT2G36170.

Phylogenomic databases

eggNOGCOG5272.
KOK02927.
ProtClustDBCLSN2688722.

Gene expression databases

ArrayExpressB9DHA6.

Family and domain databases

InterProIPR001975. Ribosomal_L40e.
IPR011332. Ribosomal_zn-bd.
IPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR019954. Ubiquitin_CS.
[Graphical view]
PfamPF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]
PRINTSPR00348. UBIQUITIN.
SMARTSM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMSSF57829. SSF57829. 1 hit.
PROSITEPS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameRL40A_ARATH
AccessionPrimary (citable) accession number: B9DHA6
Secondary accession number(s): O80715 expand/collapse secondary AC list , 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: April 16, 2014
This is version 40 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Ribosomal proteins

Ribosomal proteins families and list of entries

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names