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B9DHA6

- RL40A_ARATH

UniProt

B9DHA6 - RL40A_ARATH

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
  1. 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

    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_190928. Endosomal Sorting Complex Required For Transport (ESCRT).
    REACT_190931. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
    REACT_190947. AUF1 (hnRNP D0) destabilizes mRNA.
    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

    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

    ArrayExpressiB9DHA6.

    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 1-74, 77-128.
    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.
    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

    MQIFVKTLTG KTITLEVESS DTIDNVKAKI QDKEGIPPDQ QRLIFAGKQL    50
    EDGRTLADYN IQKESTLHLV LRLRGGIIEP SLMMLARKYN QDKMICRKCY 100
    ARLHPRAVNC RKKKCGHSNQ LRPKKKIK 128
    Length:128
    Mass (Da):14,733
    Last modified:March 24, 2009 - v1
    Checksum:i2E4EB17A20A6D28B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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 1-74, 77-128.
    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.
    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_190928. Endosomal Sorting Complex Required For Transport (ESCRT).
    REACT_190931. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
    REACT_190947. AUF1 (hnRNP D0) destabilizes mRNA.
    REACT_94347. APC/C:Cdc20 mediated degradation of Securin.

    Gene expression databases

    ArrayExpressi B9DHA6.

    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

    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: October 1, 2014
    This is version 45 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