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P04456

- RL25_YEAST

UniProt

P04456 - RL25_YEAST

Protein

60S ribosomal protein L25

Gene

RPL25

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 140 (01 Oct 2014)
      Sequence version 4 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    This protein binds to a specific region on the 26S rRNA.

    GO - Molecular functioni

    1. nucleotide binding Source: InterPro
    2. protein binding Source: IntAct
    3. RNA binding Source: SGD
    4. rRNA binding Source: UniProtKB-KW
    5. 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, rRNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-33522-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 L25
    Alternative name(s):
    RP16L
    YL25
    YP42'
    Gene namesi
    Name:RPL25
    Ordered Locus Names:YOL127W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XV

    Organism-specific databases

    SGDiS000005487. RPL25.

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytosolic large ribosomal subunit Source: SGD

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed2 Publications
    Chaini2 – 14214160S ribosomal protein L25PRO_0000129483Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Cross-linki61 – 61Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)

    Keywords - PTMi

    Isopeptide bond, Ubl conjugation

    Proteomic databases

    MaxQBiP04456.
    PaxDbiP04456.
    PeptideAtlasiP04456.

    Expressioni

    Gene expression databases

    GenevestigatoriP04456.

    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

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    BTT1P403143EBI-15308,EBI-3802
    EGD1Q026424EBI-15308,EBI-6371
    NPL3Q015602EBI-15308,EBI-12114

    Protein-protein interaction databases

    BioGridi34248. 154 interactions.
    DIPiDIP-7137N.
    IntActiP04456. 54 interactions.
    MINTiMINT-1488162.
    STRINGi4932.YOL127W.

    Structurei

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1K5Ymodel-T60-136[»]
    1S1Ielectron microscopy11.70T60-142[»]
    1VW8electron microscopy6.10Y1-142[»]
    1VWUelectron microscopy6.10Y1-142[»]
    2WW9electron microscopy8.60K1-142[»]
    2WWAelectron microscopy8.90K1-142[»]
    2WWBelectron microscopy6.48K1-142[»]
    3IZSelectron microscopy-X1-142[»]
    3J65electron microscopy8.70W1-142[»]
    3O58X-ray4.00W1-142[»]
    3O5HX-ray4.00W1-142[»]
    3U5EX-ray3.00X1-142[»]
    3U5IX-ray3.00X1-142[»]
    4B6Aelectron microscopy8.10X1-142[»]
    4BYNelectron microscopy4.30X2-142[»]
    4BYUelectron microscopy6.60X2-142[»]
    4CUWelectron microscopy3.70X1-142[»]
    ProteinModelPortaliP04456.
    SMRiP04456. Positions 23-142.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04456.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ribosomal protein L23P family.Curated

    Phylogenomic databases

    eggNOGiCOG0089.
    GeneTreeiENSGT00390000003263.
    HOGENOMiHOG000231365.
    KOiK02893.
    OMAiKAVPHYN.
    OrthoDBiEOG7Z0K8S.

    Family and domain databases

    Gene3Di3.30.70.330. 1 hit.
    HAMAPiMF_01369_A. Ribosomal_L23_A.
    InterProiIPR012677. Nucleotide-bd_a/b_plait.
    IPR012678. Ribosomal_L23/L15e_core_dom.
    IPR001014. Ribosomal_L23/L25_CS.
    IPR005633. Ribosomal_L23/L25_N.
    IPR013025. Ribosomal_L25/23.
    [Graphical view]
    PfamiPF00276. Ribosomal_L23. 1 hit.
    PF03939. Ribosomal_L23eN. 1 hit.
    [Graphical view]
    SUPFAMiSSF54189. SSF54189. 1 hit.
    PROSITEiPS00050. RIBOSOMAL_L23. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P04456-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAPSAKATAA KKAVVKGTNG KKALKVRTSA TFRLPKTLKL ARAPKYASKA    50
    VPHYNRLDSY KVIEQPITSE TAMKKVEDGN ILVFQVSMKA NKYQIKKAVK 100
    ELYEVDVLKV NTLVRPNGTK KAYVRLTADY DALDIANRIG YI 142
    Length:142
    Mass (Da):15,758
    Last modified:January 23, 2007 - v4
    Checksum:iE40ED3A4FB8CA9F5
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti106 – 1127DVLKVNT → NI in CAA25506. (PubMed:6091033)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U41293 Genomic DNA. Translation: AAC49465.1.
    X01014 Genomic DNA. Translation: CAA25506.1.
    Z74869 Genomic DNA. Translation: CAA99146.1.
    BK006948 Genomic DNA. Translation: DAA10657.1.
    PIRiS63443. R5BY25.
    RefSeqiNP_014514.1. NM_001183381.1.

    Genome annotation databases

    EnsemblFungiiYOL127W; YOL127W; YOL127W.
    GeneIDi853993.
    KEGGisce:YOL127W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U41293 Genomic DNA. Translation: AAC49465.1 .
    X01014 Genomic DNA. Translation: CAA25506.1 .
    Z74869 Genomic DNA. Translation: CAA99146.1 .
    BK006948 Genomic DNA. Translation: DAA10657.1 .
    PIRi S63443. R5BY25.
    RefSeqi NP_014514.1. NM_001183381.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1K5Y model - T 60-136 [» ]
    1S1I electron microscopy 11.70 T 60-142 [» ]
    1VW8 electron microscopy 6.10 Y 1-142 [» ]
    1VWU electron microscopy 6.10 Y 1-142 [» ]
    2WW9 electron microscopy 8.60 K 1-142 [» ]
    2WWA electron microscopy 8.90 K 1-142 [» ]
    2WWB electron microscopy 6.48 K 1-142 [» ]
    3IZS electron microscopy - X 1-142 [» ]
    3J65 electron microscopy 8.70 W 1-142 [» ]
    3O58 X-ray 4.00 W 1-142 [» ]
    3O5H X-ray 4.00 W 1-142 [» ]
    3U5E X-ray 3.00 X 1-142 [» ]
    3U5I X-ray 3.00 X 1-142 [» ]
    4B6A electron microscopy 8.10 X 1-142 [» ]
    4BYN electron microscopy 4.30 X 2-142 [» ]
    4BYU electron microscopy 6.60 X 2-142 [» ]
    4CUW electron microscopy 3.70 X 1-142 [» ]
    ProteinModelPortali P04456.
    SMRi P04456. Positions 23-142.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 34248. 154 interactions.
    DIPi DIP-7137N.
    IntActi P04456. 54 interactions.
    MINTi MINT-1488162.
    STRINGi 4932.YOL127W.

    Proteomic databases

    MaxQBi P04456.
    PaxDbi P04456.
    PeptideAtlasi P04456.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YOL127W ; YOL127W ; YOL127W .
    GeneIDi 853993.
    KEGGi sce:YOL127W.

    Organism-specific databases

    SGDi S000005487. RPL25.

    Phylogenomic databases

    eggNOGi COG0089.
    GeneTreei ENSGT00390000003263.
    HOGENOMi HOG000231365.
    KOi K02893.
    OMAi KAVPHYN.
    OrthoDBi EOG7Z0K8S.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-33522-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 P04456.
    NextBioi 975479.
    PROi P04456.

    Gene expression databases

    Genevestigatori P04456.

    Family and domain databases

    Gene3Di 3.30.70.330. 1 hit.
    HAMAPi MF_01369_A. Ribosomal_L23_A.
    InterProi IPR012677. Nucleotide-bd_a/b_plait.
    IPR012678. Ribosomal_L23/L15e_core_dom.
    IPR001014. Ribosomal_L23/L25_CS.
    IPR005633. Ribosomal_L23/L25_N.
    IPR013025. Ribosomal_L25/23.
    [Graphical view ]
    Pfami PF00276. Ribosomal_L23. 1 hit.
    PF03939. Ribosomal_L23eN. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54189. SSF54189. 1 hit.
    PROSITEi PS00050. RIBOSOMAL_L23. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: Carlsbergensis.
    2. "Sequence analysis of a 13.4 kbp fragment from the left arm of chromosome XV reveals a malate dehydrogenase gene, a putative Ser/Thr protein kinase, the ribosomal L25 gene and four new open reading frames."
      Casamayor A., Khalid H., Balcells L., Aldea M., Casas C., Herrero E., Arino J.
      Yeast 12:1013-1020(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 96604 / S288c / FY1679.
    3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
      Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
      , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
      Nature 387:98-102(1997) [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. "NH2-terminal acetylation of ribosomal proteins of Saccharomyces cerevisiae."
      Takakura H., Tsunasawa S., Miyagi M., Warner J.R.
      J. Biol. Chem. 267:5442-5445(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-21.
    6. "The action of N-terminal acetyltransferases on yeast ribosomal proteins."
      Arnold R.J., Polevoda B., Reilly J.P., Sherman F.
      J. Biol. Chem. 274:37035-37040(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: CLEAVAGE OF INITIATOR METHIONINE.
    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. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
      Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
      Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    9. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "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].
    12. "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 60-136, ELECTRON MICROSCOPY.
    13. "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 60-142, ELECTRON MICROSCOPY.
    14. "A proteomic strategy for gaining insights into protein sumoylation in yeast."
      Denison C., Rudner A.D., Gerber S.A., Bakalarski C.E., Moazed D., Gygi S.P.
      Mol. Cell. Proteomics 4:246-254(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-61.
      Strain: EJY251-11b.
    15. "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.
    16. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 80S RIBOSOME.

    Entry informationi

    Entry nameiRL25_YEAST
    AccessioniPrimary (citable) accession number: P04456
    Secondary accession number(s): D6W1U1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 13, 1987
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 140 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    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 XV
      Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

    External Data

    Dasty 3