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P0CH07

- RL402_SCHPO

UniProt

P0CH07 - RL402_SCHPO

Protein

Ubiquitin-60S ribosomal protein L40

Gene

ubi2

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 33 (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.

    GO - Molecular functioni

    1. structural constituent of ribosome Source: PomBase

    GO - Biological processi

    1. cytoplasmic translation Source: PomBase
    2. ribosome biogenesis Source: PomBase
    3. translation Source: PomBase

    Keywords - Molecular functioni

    Ribonucleoprotein, Ribosomal protein

    Enzyme and pathway databases

    ReactomeiREACT_188294. SRP-dependent cotranslational protein targeting to membrane.
    REACT_188524. Antigen processing: Ubiquitination & Proteasome degradation.
    REACT_188542. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
    REACT_188549. Endosomal Sorting Complex Required For Transport (ESCRT).
    REACT_188560. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
    REACT_188568. ER-Phagosome pathway.
    REACT_206850. Formation of a pool of free 40S subunits.
    REACT_208775. SCF-beta-TrCP mediated degradation of Emi1.
    REACT_215140. CDK-mediated phosphorylation and removal of Cdc6.
    REACT_215320. Orc1 removal from chromatin.
    REACT_215930. GTP hydrolysis and joining of the 60S ribosomal subunit.
    REACT_218991. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
    REACT_81558. Regulation of activated PAK-2p34 by proteasome mediated degradation.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin-60S ribosomal protein L40
    Cleaved into the following 2 chains:
    Alternative name(s):
    CEP52
    Gene namesi
    Name:ubi2
    Synonyms:uep1
    ORF Names:SPAC1805.12c
    OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
    Taxonomic identifieri284812 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
    ProteomesiUP000002485: Chromosome I

    Organism-specific databases

    PomBaseiSPAC1805.12c.

    Subcellular locationi

    Chain Ubiquitin : Cytoplasm By similarity. Nucleus By similarity

    GO - Cellular componenti

    1. cytosol Source: PomBase
    2. cytosolic large ribosomal subunit Source: PomBase
    3. nucleolus Source: PomBase
    4. nucleus Source: PomBase

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 7676UbiquitinPRO_0000396452Add
    BLAST
    Chaini77 – 1285260S ribosomal protein L40PRO_0000396453Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Cross-linki6 – 6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)
    Cross-linki11 – 11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)
    Cross-linki27 – 27Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)
    Cross-linki29 – 29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
    Cross-linki33 – 33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)
    Cross-linki48 – 48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
    Cross-linki63 – 63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
    Cross-linki76 – 76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)PROSITE-ProRule annotation

    Keywords - PTMi

    Isopeptide bond, Ubl conjugation

    Interactioni

    Subunit structurei

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

    Protein-protein interaction databases

    BioGridi278262. 3 interactions.
    278890. 14 interactions.

    Structurei

    Secondary structure

    128
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi1 – 77
    Beta strandi12 – 187
    Helixi23 – 3412
    Helixi38 – 403
    Beta strandi42 – 454
    Helixi56 – 594
    Beta strandi66 – 705

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4II2X-ray2.20B1-76[»]
    4II3X-ray2.90B/D1-76[»]
    ProteinModelPortaliP0CH07.
    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.
    PhylomeDBiP0CH07.

    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.

    P0CH07-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL    50
    EDGRTLSDYN IQKESTLHLV LRLRGGIIEP SLKALASKYN CEKQICRKCY 100
    ARLPPRATNC RKKKCGHTNQ LRPKKKLK 128
    Length:128
    Mass (Da):14,595
    Last modified:August 10, 2010 - v1
    Checksum:iA35EA817EFD46D38
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CU329670 Genomic DNA. Translation: CAB55853.1.
    PIRiT37547.
    RefSeqiNP_593923.1. NM_001019352.2.
    NP_594398.1. NM_001019821.2.

    Genome annotation databases

    EnsemblFungiiSPAC11G7.04.1; SPAC11G7.04.1:pep; SPAC11G7.04.
    SPAC1805.12c.1; SPAC1805.12c.1:pep; SPAC1805.12c.
    GeneIDi2541768.
    2542428.
    KEGGispo:SPAC11G7.04.
    spo:SPAC1805.12c.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CU329670 Genomic DNA. Translation: CAB55853.1 .
    PIRi T37547.
    RefSeqi NP_593923.1. NM_001019352.2.
    NP_594398.1. NM_001019821.2.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4II2 X-ray 2.20 B 1-76 [» ]
    4II3 X-ray 2.90 B/D 1-76 [» ]
    ProteinModelPortali P0CH07.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 278262. 3 interactions.
    278890. 14 interactions.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii SPAC11G7.04.1 ; SPAC11G7.04.1:pep ; SPAC11G7.04 .
    SPAC1805.12c.1 ; SPAC1805.12c.1:pep ; SPAC1805.12c .
    GeneIDi 2541768.
    2542428.
    KEGGi spo:SPAC11G7.04.
    spo:SPAC1805.12c.

    Organism-specific databases

    PomBasei SPAC1805.12c.

    Phylogenomic databases

    KOi K02927.
    OrthoDBi EOG7D5B06.
    PhylomeDBi P0CH07.

    Enzyme and pathway databases

    Reactomei REACT_188294. SRP-dependent cotranslational protein targeting to membrane.
    REACT_188524. Antigen processing: Ubiquitination & Proteasome degradation.
    REACT_188542. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
    REACT_188549. Endosomal Sorting Complex Required For Transport (ESCRT).
    REACT_188560. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
    REACT_188568. ER-Phagosome pathway.
    REACT_206850. Formation of a pool of free 40S subunits.
    REACT_208775. SCF-beta-TrCP mediated degradation of Emi1.
    REACT_215140. CDK-mediated phosphorylation and removal of Cdc6.
    REACT_215320. Orc1 removal from chromatin.
    REACT_215930. GTP hydrolysis and joining of the 60S ribosomal subunit.
    REACT_218991. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
    REACT_81558. Regulation of activated PAK-2p34 by proteasome mediated degradation.

    Miscellaneous databases

    NextBioi 20802859.
    PROi P0CH07.

    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 genome sequence of Schizosaccharomyces pombe."
      Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
      , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
      Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 972 / ATCC 24843.

    Entry informationi

    Entry nameiRL402_SCHPO
    AccessioniPrimary (citable) accession number: P0CH07
    Secondary accession number(s): O13697
    , O14257, P0C014, P0C015, Q76PD0, Q9HDZ4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 10, 2010
    Last sequence update: August 10, 2010
    Last modified: October 1, 2014
    This is version 33 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 5 different genes. Ubi1 and ubi2 are synthesized as a polyprotein with one copy of ubiquitin fused to ribosomal protein L40. Ubi3 and ubi5 are polyproteins with one copy of ubiquitin fused to ribosomal proteins S27a and s27b respectively. Ubi4 is a polyprotein containing 5 exact head to tail repeats of ubiquitin.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. Schizosaccharomyces pombe
      Schizosaccharomyces pombe: entries and gene names
    3. Ribosomal proteins
      Ribosomal proteins families and list of entries
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3