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P42073

- REF2_YEAST

UniProt

P42073 - REF2_YEAST

Protein

RNA end formation protein 2

Gene

REF2

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 116 (01 Oct 2014)
      Sequence version 2 (01 Feb 1996)
      Previous versions | rss
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    Functioni

    RNA-binding component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB. Negative regulator of poly(A) synthesis. Component of the APT complex, which may be involved in polyadenylation-independent transcript 3'-end formation. REF2 is required for 3'-end formation of snoRNAs.4 Publications

    GO - Molecular functioni

    1. chromatin binding Source: SGD
    2. protein binding Source: IntAct
    3. RNA binding Source: SGD

    GO - Biological processi

    1. mRNA 3'-end processing Source: SGD
    2. negative regulation of mRNA polyadenylation Source: SGD
    3. snoRNA 3'-end processing Source: SGD
    4. termination of RNA polymerase II transcription, poly(A)-coupled Source: SGD

    Keywords - Biological processi

    mRNA processing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29782-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    RNA end formation protein 2
    Gene namesi
    Name:REF2
    Ordered Locus Names:YDR195W
    ORF Names:YD9346.06
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    CYGDiYDR195w.
    SGDiS000002603. REF2.

    Subcellular locationi

    Nucleus 1 Publication

    GO - Cellular componenti

    1. cytosol Source: SGD
    2. mRNA cleavage and polyadenylation specificity factor complex Source: SGD
    3. nucleus Source: SGD

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 533533RNA end formation protein 2PRO_0000097239Add
    BLAST

    Proteomic databases

    MaxQBiP42073.
    PaxDbiP42073.

    Expressioni

    Gene expression databases

    GenevestigatoriP42073.

    Interactioni

    Subunit structurei

    Interacts with FIR1. Component of the cleavage and polyadenylation factor (CPF) complex, which is composed of PTI1, SYC1, SSU72, GLC7, MPE1, REF2, PFS2, PTA1, YSH1/BRR5, SWD2, CFT2/YDH1, YTH1, CFT1/YHH1, FIP1 and PAP1. Component of the APT complex, which is a subcomplex of CPF, and is composed of PTI1, SYC1, SSU72, GLC7, REF2, PTA1 and SWD2.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    GLC7P325987EBI-14915,EBI-13715

    Protein-protein interaction databases

    BioGridi32247. 60 interactions.
    DIPiDIP-871N.
    IntActiP42073. 31 interactions.
    MINTiMINT-394246.
    STRINGi4932.YDR195W.

    Structurei

    3D structure databases

    ProteinModelPortaliP42073.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi321 – 33111Ser/Thr-richAdd
    BLAST

    Phylogenomic databases

    eggNOGiNOG46408.
    KOiK15543.
    OMAiINIAHAM.
    OrthoDBiEOG754HZP.

    Sequencei

    Sequence statusi: Complete.

    P42073-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSAPVPQLVN ISHALQASTI QQIRLDMVDF NKDCKLSSIQ LARIDKYIDS    50
    LQAALNQFTK DNLHIERKEK NVTEADIQLY SGLKSMYLDY LNQLIKLKHE 100
    KQHHSTPPIA NDVSLDFFVN QLPKFSPEER KNYIDNLILN KNSHNRLSKM 150
    DGLVDAVINL CVLDTSVAEN VRSYMKLLDT LGFQKGSNST GTKANLKKKL 200
    ASSKAKIKDS EKEKEKEKDK SKVKMKTKLK PSPLLNNDDK NSSPSPTAST 250
    SSMKKLKSGL FNKNEAKSTE SLPTSSKKKL SFSKYLNKDD ADMTKLGTKR 300
    SIDVDFKVNP EASTVASNII SSSTSGSSTT TVATPASSEE PLKKKTKISV 350
    QDSNVQSILR NGKPKKARIS SIKFLDDSQL IKVYGDDLPN QGLQVSPTQL 400
    KKILKPFKEG EPKEIILFED MSIKLKPLDL MFLKNTNSDD YMDISETKGG 450
    PIHCETRTPL IYRKNFNHFN PDLNKRPPRE PIEFDLNGNT NSTPTIAKAF 500
    GKNSLLLRKD RGGLPYKHVP IVKRNKYPPR PVH 533
    Length:533
    Mass (Da):59,819
    Last modified:February 1, 1996 - v2
    Checksum:i36B0982B005697C4
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U20261 Genomic DNA. Translation: AAA85866.1.
    Z48784 Genomic DNA. Translation: CAA88708.1.
    BK006938 Genomic DNA. Translation: DAA12038.1.
    PIRiS52702.
    RefSeqiNP_010481.3. NM_001180503.3.

    Genome annotation databases

    EnsemblFungiiYDR195W; YDR195W; YDR195W.
    GeneIDi851776.
    KEGGisce:YDR195W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U20261 Genomic DNA. Translation: AAA85866.1 .
    Z48784 Genomic DNA. Translation: CAA88708.1 .
    BK006938 Genomic DNA. Translation: DAA12038.1 .
    PIRi S52702.
    RefSeqi NP_010481.3. NM_001180503.3.

    3D structure databases

    ProteinModelPortali P42073.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32247. 60 interactions.
    DIPi DIP-871N.
    IntActi P42073. 31 interactions.
    MINTi MINT-394246.
    STRINGi 4932.YDR195W.

    Proteomic databases

    MaxQBi P42073.
    PaxDbi P42073.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDR195W ; YDR195W ; YDR195W .
    GeneIDi 851776.
    KEGGi sce:YDR195W.

    Organism-specific databases

    CYGDi YDR195w.
    SGDi S000002603. REF2.

    Phylogenomic databases

    eggNOGi NOG46408.
    KOi K15543.
    OMAi INIAHAM.
    OrthoDBi EOG754HZP.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-29782-MONOMER.

    Miscellaneous databases

    NextBioi 969576.

    Gene expression databases

    Genevestigatori P42073.

    Family and domain databases

    ProtoNeti Search...

    Publicationsi

    1. Russnak R.
      Submitted (JAN-1995) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
      Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
      , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
      Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "REF2 encodes an RNA-binding protein directly involved in yeast mRNA 3'-end formation."
      Russnak R., Nehrke K.W., Platt T.
      Mol. Cell. Biol. 15:1689-1697(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: PRELIMINARY NUCLEOTIDE SEQUENCE OF 1-429, FUNCTION.
    5. "RNA binding analysis of yeast REF2 and its two-hybrid interaction with a new gene product, FIR1."
      Russnak R., Pereira S., Platt T.
      Gene Expr. 6:241-258(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH FIR1.
    6. "Pti1p and Ref2p found in association with the mRNA 3' end formation complex direct snoRNA maturation."
      Dheur S., Vo le T.A., Voisinet-Hakil F., Minet M., Schmitter J.-M., Lacroute F., Wyers F., Minvielle-Sebastia L.
      EMBO J. 22:2831-2840(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN SNORNA 3-END FORMATION.
    7. "Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3'-ends."
      Nedea E., He X., Kim M., Pootoolal J., Zhong G., Canadien V., Hughes T., Buratowski S., Moore C.L., Greenblatt J.
      J. Biol. Chem. 278:33000-33010(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE CPF COMPLEX, COMPOSITION OF THE APT COMPLEX, SUBCELLULAR LOCATION, IDENTIFICATION BY MASS SPECTROMETRY.
    8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    9. "Identification of factors regulating poly(A) tail synthesis and maturation."
      Mangus D.A., Smith M.M., McSweeney J.M., Jacobson A.
      Mol. Cell. Biol. 24:4196-4206(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    10. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
      Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
      J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    11. "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].

    Entry informationi

    Entry nameiREF2_YEAST
    AccessioniPrimary (citable) accession number: P42073
    Secondary accession number(s): D6VSH8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: February 1, 1996
    Last modified: October 1, 2014
    This is version 116 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 7450 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    2. Yeast chromosome IV
      Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

    External Data

    Dasty 3