Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P0CH09

- RL402_YEAST

UniProt

P0CH09 - RL402_YEAST

Protein

Ubiquitin-60S ribosomal protein L40

Gene

RPL40B

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 38 (01 Oct 2014)
      Sequence version 1 (10 Aug 2010)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    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-6-linked may be involved in DNA repair; 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: component of the 60S subunit of the ribosome.

    GO - Molecular functioni

    1. protein tag Source: SGD
    2. structural constituent of ribosome Source: SGD

    GO - Biological processi

    1. cytoplasmic translation Source: SGD
    2. protein ubiquitination Source: SGD
    3. ribosomal large subunit assembly Source: SGD
    4. ribosomal large subunit export from nucleus Source: SGD
    5. ribosome biogenesis Source: SGD

    Keywords - Molecular functioni

    Ribonucleoprotein, Ribosomal protein

    Enzyme and pathway databases

    BioCyciYEAST:G3O-32057-MONOMER.
    ReactomeiREACT_100522. Regulation of activated PAK-2p34 by proteasome mediated degradation.
    REACT_188965. SRP-dependent cotranslational protein targeting to membrane.
    REACT_189025. ER-Phagosome pathway.
    REACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
    REACT_189060. Antigen processing: Ubiquitination & Proteasome degradation.
    REACT_189183. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
    REACT_189189. Endosomal Sorting Complex Required For Transport (ESCRT).
    REACT_217188. Formation of a pool of free 40S subunits.
    REACT_83036. Orc1 removal from chromatin.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin-60S ribosomal protein L40
    Cleaved into the following 2 chains:
    Alternative name(s):
    CEP52
    Gene namesi
    Name:RPL40B
    Synonyms:UBI2
    Ordered Locus Names:YKR094C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XI

    Organism-specific databases

    SGDiS000001802. RPL40B.

    Subcellular locationi

    Chain Ubiquitin : Cytoplasm By similarity. Nucleus By similarity

    GO - Cellular componenti

    1. cytosolic large ribosomal subunit Source: SGD
    2. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi29 – 291K → R: Deficiency in ubiquitin-protein conjugate formation. 2 Publications
    Mutagenesisi48 – 481K → R: Deficiency in ubiquitin-protein conjugate formation. 2 Publications
    Mutagenesisi63 – 631K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 7676UbiquitinPRO_0000396455Add
    BLAST
    Chaini77 – 1285260S ribosomal protein L40PRO_0000396456Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Cross-linki6 – 6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
    Cross-linki11 – 11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
    Cross-linki27 – 27Glycyl 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)2 Publications
    Cross-linki63 – 63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
    Cross-linki76 – 76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

    Keywords - PTMi

    Isopeptide bond, Ubl conjugation

    Proteomic databases

    PRIDEiP0CH09.

    2D gel databases

    SWISS-2DPAGEP61864.

    Expressioni

    Gene expression databases

    GenevestigatoriP61864.

    Interactioni

    Subunit structurei

    Ribosomal protein L40 is part of the 60S ribosomal subunit. Mature ribosomes consist of a small (40S) and a large (60S) subunit. The 40S subunit contains 32 different proteins (encoded by 56 genes) and 1 molecule of RNA (18S). The 60S subunit contains 46 different proteins (encoded by 81 genes) and 3 molecules of RNA (25S, 5.8S and 5S).1 Publication

    Protein-protein interaction databases

    BioGridi34225. 145 interactions.
    34844. 62 interactions.
    MINTiMINT-2788967.

    Structurei

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4CUWelectron microscopy3.70m1-128[»]
    ProteinModelPortaliP0CH09.
    SMRiP0CH09. 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

    GeneTreeiENSGT00750000117491.
    KOiK02927.
    OrthoDBiEOG7D5B06.

    Family and domain databases

    InterProiIPR001975. Ribosomal_L40e.
    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.
    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.

    P0CH09-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL    50
    EDGRTLSDYN IQKESTLHLV LRLRGGIIEP SLKALASKYN CDKSVCRKCY 100
    ARLPPRATNC RKRKCGHTNQ LRPKKKLK 128
    Length:128
    Mass (Da):14,554
    Last modified:August 10, 2010 - v1
    Checksum:i84BD137A4B1F7797
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X73541 Genomic DNA. Translation: CAA51949.1.
    Z28319 Genomic DNA. Translation: CAA82173.1.
    BK006944 Genomic DNA. Translation: DAA09244.1.
    PIRiA29456.
    RefSeqiNP_012118.1. NM_001179496.1.
    NP_013020.3. NM_001179884.3.

    Genome annotation databases

    EnsemblFungiiYIL148W; YIL148W; YIL148W.
    YKR094C; YKR094C; YKR094C.
    GeneIDi853969.
    854658.
    KEGGisce:YIL148W.
    sce:YKR094C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X73541 Genomic DNA. Translation: CAA51949.1 .
    Z28319 Genomic DNA. Translation: CAA82173.1 .
    BK006944 Genomic DNA. Translation: DAA09244.1 .
    PIRi A29456.
    RefSeqi NP_012118.1. NM_001179496.1.
    NP_013020.3. NM_001179884.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4CUW electron microscopy 3.70 m 1-128 [» ]
    ProteinModelPortali P0CH09.
    SMRi P0CH09. Positions 1-74, 77-128.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 34225. 145 interactions.
    34844. 62 interactions.
    MINTi MINT-2788967.

    2D gel databases

    SWISS-2DPAGE P61864.

    Proteomic databases

    PRIDEi P0CH09.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YIL148W ; YIL148W ; YIL148W .
    YKR094C ; YKR094C ; YKR094C .
    GeneIDi 853969.
    854658.
    KEGGi sce:YIL148W.
    sce:YKR094C.

    Organism-specific databases

    SGDi S000001802. RPL40B.

    Phylogenomic databases

    GeneTreei ENSGT00750000117491.
    KOi K02927.
    OrthoDBi EOG7D5B06.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-32057-MONOMER.
    Reactomei REACT_100522. Regulation of activated PAK-2p34 by proteasome mediated degradation.
    REACT_188965. SRP-dependent cotranslational protein targeting to membrane.
    REACT_189025. ER-Phagosome pathway.
    REACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
    REACT_189060. Antigen processing: Ubiquitination & Proteasome degradation.
    REACT_189183. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
    REACT_189189. Endosomal Sorting Complex Required For Transport (ESCRT).
    REACT_217188. Formation of a pool of free 40S subunits.
    REACT_83036. Orc1 removal from chromatin.

    Miscellaneous databases

    NextBioi 975410.

    Gene expression databases

    Genevestigatori P61864.

    Family and domain databases

    InterProi IPR001975. Ribosomal_L40e.
    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.
    PROSITEi PS00299. UBIQUITIN_1. 1 hit.
    PS50053. UBIQUITIN_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The yeast ubiquitin genes: a family of natural gene fusions."
      Oezkaynak E., Finley D., Solomon M.J., Varshavsky A.
      EMBO J. 6:1429-1439(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "The complete sequence of a 15,820 bp segment of Saccharomyces cerevisiae chromosome XI contains the UBI2 and MPL1 genes and three new open reading frames."
      Bou G., Esteban P.F., Baladron V., Gonzalez G.A., Cantalejo J.G., Remacha M.A., Jimenez A., del Rey F., Ballesta J.P.G., Revuelta J.L.
      Yeast 9:1349-1354(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "Complete DNA sequence of yeast chromosome XI."
      Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C.
      , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W.
      Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    5. "A proteolytic pathway that recognizes ubiquitin as a degradation signal."
      Johnson E.S., Ma P.C.M., Ota I.M., Varshavsky A.
      J. Biol. Chem. 270:17442-17456(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF LYS-29; LYS-48 AND LYS-63.
    6. "A ubiquitin mutant with specific defects in DNA repair and multiubiquitination."
      Spence J., Sadis S., Haas A.L., Finley D.
      Mol. Cell. Biol. 15:1265-1273(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF LYSINE RESIDUES IN UBIQUITIN.
    7. "The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae."
      Planta R.J., Mager W.H.
      Yeast 14:471-477(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NOMENCLATURE, SUBUNIT (L40).
    8. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS] (L40).
    9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS] (L40).
    10. Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-6; LYS-11; LYS-27; LYS-29; LYS-33; LYS-48 AND LYS-63.
      Strain: SUB592.
    11. "A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery."
      Hitchcock A.L., Auld K., Gygi S.P., Silver P.A.
      Proc. Natl. Acad. Sci. U.S.A. 100:12735-12740(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-11; LYS-48 AND LYS-63.
    12. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    13. "Sites of ubiquitin attachment in Saccharomyces cerevisiae."
      Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
      Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiRL402_YEAST
    AccessioniPrimary (citable) accession number: P0CH09
    Secondary accession number(s): D6VVD9
    , P04838, P14796, P61864, Q6LA96
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 10, 2010
    Last sequence update: August 10, 2010
    Last modified: October 1, 2014
    This is version 38 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Ubiquitin is encoded by 4 different genes. UBI1 and UBI2 genes code for a single copy of ubiquitin fused to the ribosomal proteins L40. UBI3 is a polyprotein with one copy of ubiquitin fused to ribosomal protein S37. UBI4 is a polyprotein containing 5 exact head to tail repeats of ubiquitin.
    The 60S ribosomal protein L40 is present with 40000 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. Ribosomal proteins
      Ribosomal proteins families and list of entries
    3. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome XI
      Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

    External Data

    Dasty 3