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P0CX53

- RL12A_YEAST

UniProt

P0CX53 - RL12A_YEAST

Protein

60S ribosomal protein L12-A

Gene

RPL12A

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 29 (01 Oct 2014)
      Sequence version 1 (28 Jun 2011)
      Previous versions | rss
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    Functioni

    This protein binds directly to 26S ribosomal RNA.

    GO - Molecular functioni

    1. RNA binding Source: UniProtKB-KW
    2. structural constituent of ribosome Source: SGD

    GO - Biological processi

    1. cytoplasmic translation Source: SGD
    2. ribosomal large subunit assembly Source: SGD

    Keywords - Molecular functioni

    Ribonucleoprotein, Ribosomal protein

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30172-MONOMER.
    ReactomeiREACT_188965. SRP-dependent cotranslational protein targeting to membrane.
    REACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
    REACT_189183. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
    REACT_217188. Formation of a pool of free 40S subunits.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    60S ribosomal protein L12-A
    Alternative name(s):
    L15
    YL23
    Gene namesi
    Name:RPL12A
    Synonyms:RPL15B
    Ordered Locus Names:YEL054C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome V

    Organism-specific databases

    CYGDiYEL054c.
    SGDiS000000780. RPL12A.

    Subcellular locationi

    Cytoplasm 1 Publication

    GO - Cellular componenti

    1. cytosolic large ribosomal subunit Source: SGD

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi67 – 671R → K: Abolishes monomethylation by RMT2. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 16516460S ribosomal protein L12-APRO_0000104467Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N,N-dimethylproline; by NTM12 Publications
    Modified residuei4 – 41N6,N6,N6-trimethyllysine; by RKM22 Publications
    Modified residuei11 – 111N6,N6,N6-trimethyllysine; by RKM21 Publication
    Modified residuei25 – 251Phosphoserine1 Publication
    Modified residuei38 – 381Phosphoserine2 Publications
    Modified residuei67 – 671N5-methylarginine; by RMT22 Publications

    Post-translational modificationi

    It appears that the main modified species for L12 contains 6 methyl groups, 2 on Pro-2, 3 on Lys-4 and 1 on Arg-67. Although not reproduced with a second method, methylation at Lys-11 cannot be ruled out.4 Publications

    Keywords - PTMi

    Methylation, Phosphoprotein

    Proteomic databases

    MaxQBiP0CX53.
    PRIDEiP0CX53.

    Interactioni

    Subunit structurei

    Component of the large 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

    BioGridi32476. 91 interactions.
    36675. 86 interactions.
    IntActiP0CX53. 1 interaction.
    MINTiMINT-8285568.

    Structurei

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1K5Ymodel-K13-143[»]
    1S1Ielectron microscopy11.70K13-143[»]
    3IZSelectron microscopy-J1-165[»]
    3J16electron microscopy-H1-165[»]
    3J65electron microscopy8.70I1-165[»]
    3O5HX-ray4.00L1-165[»]
    ProteinModelPortaliP0CX53.
    SMRiP0CX53. Positions 7-144.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0CX53.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ribosomal protein L11P family.Curated

    Phylogenomic databases

    HOGENOMiHOG000082125.
    KOiK02870.
    OrthoDBiEOG71VT57.

    Family and domain databases

    Gene3Di1.10.10.250. 1 hit.
    3.30.1550.10. 1 hit.
    HAMAPiMF_00736. Ribosomal_L11.
    InterProiIPR000911. Ribosomal_L11/L12.
    IPR020783. Ribosomal_L11_C.
    IPR020785. Ribosomal_L11_CS.
    IPR020784. Ribosomal_L11_N.
    [Graphical view]
    PANTHERiPTHR11661. PTHR11661. 1 hit.
    PfamiPF00298. Ribosomal_L11. 1 hit.
    PF03946. Ribosomal_L11_N. 1 hit.
    [Graphical view]
    SMARTiSM00649. RL11. 1 hit.
    [Graphical view]
    SUPFAMiSSF46906. SSF46906. 1 hit.
    SSF54747. SSF54747. 1 hit.
    PROSITEiPS00359. RIBOSOMAL_L11. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P0CX53-1 [UniParc]FASTAAdd to Basket

    « Hide

    MPPKFDPNEV KYLYLRAVGG EVGASAALAP KIGPLGLSPK KVGEDIAKAT    50
    KEFKGIKVTV QLKIQNRQAA ASVVPSASSL VITALKEPPR DRKKDKNVKH 100
    SGNIQLDEII EIARQMRDKS FGRTLASVTK EILGTAQSVG CRVDFKNPHD 150
    IIEGINAGEI EIPEN 165
    Length:165
    Mass (Da):17,823
    Last modified:June 28, 2011 - v1
    Checksum:i0B23A483781DFBE5
    GO

    Mass spectrometryi

    Molecular mass is 17764.712 Da from positions 2 - 106. Determined by ESI. Monoisotopic mass with either 6 methylation modifications or 1 acetylation and 3 methylation modifications.1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X51519 Genomic DNA. Translation: CAA35891.1.
    U18795 Genomic DNA. Translation: AAB65033.1.
    AY693201 Genomic DNA. Translation: AAT93220.1.
    BK006939 Genomic DNA. Translation: DAA07600.1.
    PIRiS13665.
    RefSeqiNP_010706.3. NM_001180726.3.
    NP_010860.1. NM_001178869.1.

    Genome annotation databases

    EnsemblFungiiYDR418W; YDR418W; YDR418W.
    YEL054C; YEL054C; YEL054C.
    GeneIDi852026.
    856656.
    KEGGisce:YDR418W.
    sce:YEL054C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X51519 Genomic DNA. Translation: CAA35891.1 .
    U18795 Genomic DNA. Translation: AAB65033.1 .
    AY693201 Genomic DNA. Translation: AAT93220.1 .
    BK006939 Genomic DNA. Translation: DAA07600.1 .
    PIRi S13665.
    RefSeqi NP_010706.3. NM_001180726.3.
    NP_010860.1. NM_001178869.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1K5Y model - K 13-143 [» ]
    1S1I electron microscopy 11.70 K 13-143 [» ]
    3IZS electron microscopy - J 1-165 [» ]
    3J16 electron microscopy - H 1-165 [» ]
    3J65 electron microscopy 8.70 I 1-165 [» ]
    3O5H X-ray 4.00 L 1-165 [» ]
    ProteinModelPortali P0CX53.
    SMRi P0CX53. Positions 7-144.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32476. 91 interactions.
    36675. 86 interactions.
    IntActi P0CX53. 1 interaction.
    MINTi MINT-8285568.

    Proteomic databases

    MaxQBi P0CX53.
    PRIDEi P0CX53.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDR418W ; YDR418W ; YDR418W .
    YEL054C ; YEL054C ; YEL054C .
    GeneIDi 852026.
    856656.
    KEGGi sce:YDR418W.
    sce:YEL054C.

    Organism-specific databases

    CYGDi YEL054c.
    SGDi S000000780. RPL12A.

    Phylogenomic databases

    HOGENOMi HOG000082125.
    KOi K02870.
    OrthoDBi EOG71VT57.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30172-MONOMER.
    Reactomei REACT_188965. SRP-dependent cotranslational protein targeting to membrane.
    REACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
    REACT_189183. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
    REACT_217188. Formation of a pool of free 40S subunits.

    Miscellaneous databases

    EvolutionaryTracei P0CX53.
    NextBioi 970252.

    Family and domain databases

    Gene3Di 1.10.10.250. 1 hit.
    3.30.1550.10. 1 hit.
    HAMAPi MF_00736. Ribosomal_L11.
    InterProi IPR000911. Ribosomal_L11/L12.
    IPR020783. Ribosomal_L11_C.
    IPR020785. Ribosomal_L11_CS.
    IPR020784. Ribosomal_L11_N.
    [Graphical view ]
    PANTHERi PTHR11661. PTHR11661. 1 hit.
    Pfami PF00298. Ribosomal_L11. 1 hit.
    PF03946. Ribosomal_L11_N. 1 hit.
    [Graphical view ]
    SMARTi SM00649. RL11. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46906. SSF46906. 1 hit.
    SSF54747. SSF54747. 1 hit.
    PROSITEi PS00359. RIBOSOMAL_L11. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The 26S rRNA binding ribosomal protein equivalent to bacterial protein L11 is encoded by unspliced duplicated genes in Saccharomyces cerevisiae."
      Pucciarelli G., Remacha M., Ballesta J.P.G.
      Nucleic Acids Res. 18:4409-4416(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: Y166.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. "A novel SET domain methyltransferase in yeast: Rkm2-dependent trimethylation of ribosomal protein L12ab at lysine 10."
      Porras-Yakushi T.R., Whitelegge J.P., Clarke S.
      J. Biol. Chem. 281:35835-35845(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-16, METHYLATION AT LYS-4 AND LYS-11, IDENTIFICATION BY MASS SPECTROMETRY.
    6. "Yeast ribosomal proteins. VIII. Isolation of two proteins and sequence characterization of twenty-four proteins from cytoplasmic ribosomes."
      Otaka E., Higo K., Itoh T.
      Mol. Gen. Genet. 195:544-546(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: PARTIAL PROTEIN SEQUENCE OF 17-36.
    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.
    8. "Yeast ribosomal protein L12 is a substrate of protein-arginine methyltransferase 2."
      Chern M.-K., Chang K.-N., Liu L.-F., Tam T.-C.S., Liu Y.-C., Liang Y.-L., Tam M.F.
      J. Biol. Chem. 277:15345-15353(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY, METHYLATION AT ARG-67, MUTAGENESIS OF ARG-67.
    9. "Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR."
      Lee S.-W., Berger S.J., Martinovic S., Pasa-Tolic L., Anderson G.A., Shen Y., Zhao R., Smith R.D.
      Proc. Natl. Acad. Sci. U.S.A. 99:5942-5947(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: MASS SPECTROMETRY.
    10. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    11. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    12. "Identification of two SET domain proteins required for methylation of lysine residues in yeast ribosomal protein Rpl42ab."
      Webb K.J., Laganowsky A., Whitelegge J.P., Clarke S.G.
      J. Biol. Chem. 283:35561-35568(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: METHYLATION AT PRO-2; LYS-4 AND ARG-67.
    13. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-38, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    14. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-25 AND SER-38, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. "Identification of protein N-terminal methyltransferases in yeast and humans."
      Webb K.J., Lipson R.S., Al-Hadid Q., Whitelegge J.P., Clarke S.G.
      Biochemistry 49:5225-5235(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: METHYLATION AT PRO-2 BY NTM1/TAE1.
    16. "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].
    17. "Structure of the 80S ribosome from Saccharomyces cerevisiae -- tRNA-ribosome and subunit-subunit interactions."
      Spahn C.M.T., Beckmann R., Eswar N., Penczek P.A., Sali A., Blobel G., Frank J.
      Cell 107:373-386(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: 3D-STRUCTURE MODELING OF 13-143, ELECTRON MICROSCOPY.
    18. "Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation."
      Spahn C.M.T., Gomez-Lorenzo M.G., Grassucci R.A., Joergensen R., Andersen G.R., Beckmann R., Penczek P.A., Ballesta J.P.G., Frank J.
      EMBO J. 23:1008-1019(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: 3D-STRUCTURE MODELING OF 13-143, ELECTRON MICROSCOPY.

    Entry informationi

    Entry nameiRL12A_YEAST
    AccessioniPrimary (citable) accession number: P0CX53
    Secondary accession number(s): D3DLJ6, P05741, P17079
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 28, 2011
    Last sequence update: June 28, 2011
    Last modified: October 1, 2014
    This is version 29 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 68500 molecules/cell in log phase SD medium.1 Publication
    There are 2 genes for L12 in yeast.

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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 V
      Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

    External Data

    Dasty 3