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P0CH08

- RL401_YEAST

UniProt

P0CH08 - RL401_YEAST

Protein

Ubiquitin-60S ribosomal protein L40

Gene

RPL40A

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 39 (01 Oct 2014)
      Sequence version 1 (10 Aug 2010)
      Previous versions | rss
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    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. Ribosomal protein L40 is essential for translation of a subset of cellular transcripts, including stress response transcripts, such as DDR2.1 Publication

    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-31397-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:RPL40A
    Synonyms:UBI1
    Ordered Locus Names:YIL148W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IX

    Organism-specific databases

    SGDiS000001410. RPL40A.

    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_0000396454Add
    BLAST
    Chaini77 – 1285260S ribosomal protein L40PRO_0000138775Add
    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

    MaxQBiP0CH08.
    PRIDEiP0CH08.

    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).2 Publications

    Protein-protein interaction databases

    BioGridi34225. 145 interactions.
    34844. 62 interactions.

    Structurei

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1VW8electron microscopy6.10n1-128[»]
    1VWUelectron microscopy6.10n1-128[»]
    3IZSelectron microscopy-p77-128[»]
    3U5EX-ray3.00m1-128[»]
    3U5IX-ray3.00m1-128[»]
    4B6Aelectron microscopy8.10m1-128[»]
    4BYNelectron microscopy4.30m1-128[»]
    4BYUelectron microscopy6.60m1-128[»]
    ProteinModelPortaliP0CH08.
    SMRiP0CH08. 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

    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.

    P0CH08-1 [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
    X05728 Genomic DNA. Translation: CAA29195.1.
    X05729 Genomic DNA. Translation: CAA29196.1.
    Z38059 Genomic DNA. Translation: CAA86130.1.
    BK006942 Genomic DNA. Translation: DAA08405.1.
    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
    X05728 Genomic DNA. Translation: CAA29195.1 .
    X05729 Genomic DNA. Translation: CAA29196.1 .
    Z38059 Genomic DNA. Translation: CAA86130.1 .
    BK006942 Genomic DNA. Translation: DAA08405.1 .
    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
    1VW8 electron microscopy 6.10 n 1-128 [» ]
    1VWU electron microscopy 6.10 n 1-128 [» ]
    3IZS electron microscopy - p 77-128 [» ]
    3U5E X-ray 3.00 m 1-128 [» ]
    3U5I X-ray 3.00 m 1-128 [» ]
    4B6A electron microscopy 8.10 m 1-128 [» ]
    4BYN electron microscopy 4.30 m 1-128 [» ]
    4BYU electron microscopy 6.60 m 1-128 [» ]
    ProteinModelPortali P0CH08.
    SMRi P0CH08. Positions 1-74, 77-128.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 34225. 145 interactions.
    34844. 62 interactions.

    2D gel databases

    SWISS-2DPAGE P61864.

    Proteomic databases

    MaxQBi P0CH08.
    PRIDEi P0CH08.

    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 S000001410. RPL40A.

    Phylogenomic databases

    KOi K02927.
    OrthoDBi EOG7D5B06.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-31397-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "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.
    5. "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.
    6. "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).
    7. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS] (L40).
    8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS] (L40).
    9. Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-6; LYS-11; LYS-27; LYS-29; LYS-33; LYS-48 AND LYS-63.
      Strain: SUB592.
    10. "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.
    11. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. "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].
    13. "A ribosome-specialized translation initiation pathway is required for cap-dependent translation of vesicular stomatitis virus mRNAs."
      Lee A.S., Burdeinick-Kerr R., Whelan S.P.
      Proc. Natl. Acad. Sci. U.S.A. 110:324-329(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBUNIT.
    14. "Crystal structure of the eukaryotic ribosome."
      Ben-Shem A., Jenner L., Yusupova G., Yusupov M.
      Science 330:1203-1209(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (4.0 ANGSTROMS) OF 80S RIBOSOME.
    15. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 77-128 WITHIN THE 60S RIBOSOMAL SUBUNIT.
    16. "Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit."
      Greber B.J., Boehringer D., Montellese C., Ban N.
      Nat. Struct. Mol. Biol. 19:1228-1233(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY ELECTRON MICROSCOPY (8.1 ANGSTROMS) OF 77-128 WITHIN THE 60S RIBOSOMAL SUBUNIT.

    Entry informationi

    Entry nameiRL401_YEAST
    AccessioniPrimary (citable) accession number: P0CH08
    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 39 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 IX
      Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names

    External Data

    Dasty 3