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B9DHA6

- RL40A_ARATH

UniProt

B9DHA6 - RL40A_ARATH

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Protein

Ubiquitin-60S ribosomal protein L40-1

Gene

RPL40A

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli

Functioni

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).By similarity
60S ribosomal protein L40-1: component of the 60S subunit of the ribosome.

GO - Molecular functioni

  1. structural constituent of ribosome Source: InterPro

GO - Biological processi

  1. translation Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Enzyme and pathway databases

ReactomeiREACT_106068. Autodegradation of Cdh1 by Cdh1:APC/C.
REACT_107429. Orc1 removal from chromatin.
REACT_185297. Separation of Sister Chromatids.
REACT_185305. APC/C:Cdc20 mediated degradation of Cyclin B.
REACT_187631. SRP-dependent cotranslational protein targeting to membrane.
REACT_187719. ER-Phagosome pathway.
REACT_187829. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_187848. Antigen processing: Ubiquitination & Proteasome degradation.
REACT_187954. Senescence-Associated Secretory Phenotype (SASP).
REACT_190928. Endosomal Sorting Complex Required For Transport (ESCRT).
REACT_190931. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_229741. Fanconi Anemia pathway.
REACT_231757. activated TAK1 mediates p38 MAPK activation.
REACT_232663. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_235587. Hh ligand biogenesis disease.
REACT_238761. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_240263. Ubiquitin-dependent degradation of Cyclin D1.
REACT_240283. Peptide chain elongation.
REACT_241531. APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1.
REACT_244054. Autodegradation of the E3 ubiquitin ligase COP1.
REACT_245715. Cyclin D associated events in G1.
REACT_246136. Hedgehog ligand biogenesis.
REACT_248654. Eukaryotic Translation Termination.
REACT_252436. CDK-mediated phosphorylation and removal of Cdc6.
REACT_261170. JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1.
REACT_262398. Formation of a pool of free 40S subunits.
REACT_94347. APC/C:Cdc20 mediated degradation of Securin.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-60S ribosomal protein L40-1
Cleaved into the following 2 chains:
Alternative name(s):
CEP52
Gene namesi
Name:RPL40A
Synonyms:UBQ2
Ordered Locus Names:At2g36170
ORF Names:F9C22.10
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 2

Organism-specific databases

TAIRiAT2G36170.

Subcellular locationi

Chain Ubiquitin : Cytoplasm By similarity. Nucleus By similarity

GO - Cellular componenti

  1. cytosolic large ribosomal subunit Source: TAIR
  2. nucleolus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 7676UbiquitinPRO_0000396865Add
BLAST
Chaini77 – 1285260S ribosomal protein L40-1PRO_0000138758Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki11 – 11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki29 – 29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki33 – 33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki48 – 48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki63 – 63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki76 – 76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)PROSITE-ProRule annotation

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PaxDbiB9DHA6.
PRIDEiB9DHA6.

Expressioni

Gene expression databases

ExpressionAtlasiB9DHA6. baseline and differential.

Interactioni

Subunit structurei

Ribosomal protein L40-1 is part of the 60S ribosomal subunit.By similarity

Protein-protein interaction databases

BioGridi3533. 1 interaction.
9743. 12 interactions.

Structurei

3D structure databases

ProteinModelPortaliB9DHA6.
SMRiB9DHA6. Positions 1-128.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 7676Ubiquitin-likePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

In the N-terminal section; belongs to the ubiquitin family.Curated
In the C-terminal section; belongs to the ribosomal protein L40e family.Curated
Contains 1 ubiquitin-like domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG5272.
InParanoidiB9DHA6.
KOiK02927.

Family and domain databases

InterProiIPR001975. Ribosomal_L40e.
IPR011332. Ribosomal_zn-bd.
IPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
[Graphical view]
PfamiPF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
SSF57829. SSF57829. 1 hit.
PROSITEiPS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

B9DHA6-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL
60 70 80 90 100
EDGRTLADYN IQKESTLHLV LRLRGGIIEP SLMMLARKYN QDKMICRKCY
110 120
ARLHPRAVNC RKKKCGHSNQ LRPKKKIK
Length:128
Mass (Da):14,733
Last modified:March 24, 2009 - v1
Checksum:i2E4EB17A20A6D28B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiB36571.
RefSeqiNP_565836.1. NM_129175.2.
NP_566969.1. NM_115119.3.
UniGeneiAt.23108.
At.24656.
At.35280.

Genome annotation databases

EnsemblPlantsiAT2G36170.1; AT2G36170.1; AT2G36170.
AT3G52590.1; AT3G52590.1; AT3G52590.
GeneIDi818189.
824425.
KEGGiath:AT2G36170.
ath:AT3G52590.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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 .
PIRi B36571.
RefSeqi NP_565836.1. NM_129175.2.
NP_566969.1. NM_115119.3.
UniGenei At.23108.
At.24656.
At.35280.

3D structure databases

ProteinModelPortali B9DHA6.
SMRi B9DHA6. Positions 1-128.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 3533. 1 interaction.
9743. 12 interactions.

Proteomic databases

PaxDbi B9DHA6.
PRIDEi B9DHA6.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT2G36170.1 ; AT2G36170.1 ; AT2G36170 .
AT3G52590.1 ; AT3G52590.1 ; AT3G52590 .
GeneIDi 818189.
824425.
KEGGi ath:AT2G36170.
ath:AT3G52590.

Organism-specific databases

GeneFarmi 382. 38.
TAIRi AT2G36170.

Phylogenomic databases

eggNOGi COG5272.
InParanoidi B9DHA6.
KOi K02927.

Enzyme and pathway databases

Reactomei REACT_106068. Autodegradation of Cdh1 by Cdh1:APC/C.
REACT_107429. Orc1 removal from chromatin.
REACT_185297. Separation of Sister Chromatids.
REACT_185305. APC/C:Cdc20 mediated degradation of Cyclin B.
REACT_187631. SRP-dependent cotranslational protein targeting to membrane.
REACT_187719. ER-Phagosome pathway.
REACT_187829. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_187848. Antigen processing: Ubiquitination & Proteasome degradation.
REACT_187954. Senescence-Associated Secretory Phenotype (SASP).
REACT_190928. Endosomal Sorting Complex Required For Transport (ESCRT).
REACT_190931. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_229741. Fanconi Anemia pathway.
REACT_231757. activated TAK1 mediates p38 MAPK activation.
REACT_232663. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_235587. Hh ligand biogenesis disease.
REACT_238761. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_240263. Ubiquitin-dependent degradation of Cyclin D1.
REACT_240283. Peptide chain elongation.
REACT_241531. APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1.
REACT_244054. Autodegradation of the E3 ubiquitin ligase COP1.
REACT_245715. Cyclin D associated events in G1.
REACT_246136. Hedgehog ligand biogenesis.
REACT_248654. Eukaryotic Translation Termination.
REACT_252436. CDK-mediated phosphorylation and removal of Cdc6.
REACT_261170. JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1.
REACT_262398. Formation of a pool of free 40S subunits.
REACT_94347. APC/C:Cdc20 mediated degradation of Securin.

Gene expression databases

ExpressionAtlasi B9DHA6. baseline and differential.

Family and domain databases

InterProi IPR001975. Ribosomal_L40e.
IPR011332. Ribosomal_zn-bd.
IPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
[Graphical view ]
Pfami PF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view ]
PRINTSi PR00348. UBIQUITIN.
SMARTi SM00213. UBQ. 1 hit.
[Graphical view ]
SUPFAMi SSF54236. SSF54236. 1 hit.
SSF57829. SSF57829. 1 hit.
PROSITEi PS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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.
    Strain: cv. Landsberg erecta.

Entry informationi

Entry nameiRL40A_ARATH
AccessioniPrimary (citable) accession number: B9DHA6
Secondary accession number(s): O80715
, P19232, P59263, Q38875, Q9LDJ2, Q9LYW1, Q9M0W3, Q9M1P9, Q9S7X3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 10, 2010
Last sequence update: March 24, 2009
Last modified: November 26, 2014
This is version 47 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. Ribosomal proteins
    Ribosomal proteins families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3