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P38351

- PAF1_YEAST

UniProt

P38351 - PAF1_YEAST

Protein

RNA polymerase II-associated protein 1

Gene

PAF1

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 133 (01 Oct 2014)
      Sequence version 1 (01 Oct 1994)
      Previous versions | rss
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    Functioni

    The PAF1 complex is a multifunctional complex. Involved in transcription initiation via genetic interactions with TATA-binding proteins. Involved in elongation. It regulates 3'-end formation of snR47 by modulating the recruitment or stable association of NRD1 and NAB3 with RNA polymerase II. Also has a role in transcription-coupled histone modification. Required for activation of the RAD6/UBC2-BRE1 ubiquitin ligase complex, which ubiquitinates histone H2B to form H2BK123ub1. Also required for the methylation of histone H3 by the COMPASS complex to form H3K4me, by SET2 to form H3K36me, and by DOT1 to form H3K79me. RNA polymerase II associated protein important for transcription of a subset of genes. Required for both positive and negative regulation. Negatively regulates MAK16 expression. Also required for efficient CLN2 transcription in late G1 and may be involved in transcription of galactose-inducible genes.3 Publications

    GO - Molecular functioni

    1. chromatin binding Source: SGD
    2. protein binding Source: IntAct
    3. RNA polymerase II core binding Source: SGD
    4. RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity Source: SGD
    5. RNA polymerase II C-terminal domain phosphoserine binding Source: SGD
    6. RNA polymerase II transcription factor binding transcription factor activity Source: SGD
    7. TFIIF-class binding transcription factor activity Source: SGD

    GO - Biological processi

    1. chromatin silencing at rDNA Source: SGD
    2. DNA-templated transcription, termination Source: SGD
    3. global genome nucleotide-excision repair Source: SGD
    4. mRNA 3'-end processing Source: SGD
    5. negative regulation of DNA recombination Source: SGD
    6. negative regulation of transcription from RNA polymerase II promoter Source: SGD
    7. positive regulation of histone H3-K36 trimethylation Source: SGD
    8. positive regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues Source: SGD
    9. positive regulation of transcription elongation from RNA polymerase II promoter Source: SGD
    10. positive regulation of transcription elongation from RNA polymerase I promoter Source: SGD
    11. regulation of chromatin silencing at telomere Source: SGD
    12. regulation of histone H2B conserved C-terminal lysine ubiquitination Source: SGD
    13. regulation of histone H2B ubiquitination Source: SGD
    14. regulation of histone H3-K4 methylation Source: SGD
    15. regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues Source: SGD
    16. regulation of transcription by chromatin organization Source: SGD
    17. regulation of transcription-coupled nucleotide-excision repair Source: SGD
    18. regulation of transcription from RNA polymerase II promoter Source: SGD
    19. regulation of transcription involved in G1/S transition of mitotic cell cycle Source: SGD
    20. rRNA processing Source: SGD
    21. snoRNA 3'-end processing Source: SGD
    22. snoRNA transcription from an RNA polymerase II promoter Source: SGD
    23. transcription elongation from RNA polymerase II promoter Source: SGD
    24. transcription elongation from RNA polymerase I promoter Source: SGD
    25. transcription from RNA polymerase I promoter Source: SGD

    Keywords - Molecular functioni

    Activator, Repressor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29199-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    RNA polymerase II-associated protein 1
    Alternative name(s):
    Protein PAF1
    Gene namesi
    Name:PAF1
    Ordered Locus Names:YBR279W
    ORF Names:YBR2016
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome II

    Organism-specific databases

    CYGDiYBR279w.
    SGDiS000000483. PAF1.

    Subcellular locationi

    Nucleusnucleoplasm 1 Publication

    GO - Cellular componenti

    1. Cdc73/Paf1 complex Source: SGD
    2. nucleus Source: SGD
    3. transcriptionally active chromatin Source: SGD

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 445445RNA polymerase II-associated protein 1PRO_0000058174Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei147 – 1471Phosphoserine3 Publications
    Modified residuei422 – 4221Phosphothreonine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP38351.
    PaxDbiP38351.
    PeptideAtlasiP38351.
    PRIDEiP38351.

    Expressioni

    Gene expression databases

    GenevestigatoriP38351.

    Interactioni

    Subunit structurei

    Component of the PAF1 complex which consists of at least CDC73, CTR9, LEO1, PAF1 and RTF1. Interacts with FACT subunits POB3 and SPT16.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CDC73Q066978EBI-12855,EBI-29913
    CTR9P891056EBI-12855,EBI-5283
    LEO1P384395EBI-12855,EBI-10108
    RTF1P530649EBI-12855,EBI-16303
    SLT2Q007722EBI-12855,EBI-17372

    Protein-protein interaction databases

    BioGridi32973. 144 interactions.
    DIPiDIP-1149N.
    IntActiP38351. 10 interactions.
    MINTiMINT-600620.
    STRINGi4932.YBR279W.

    Structurei

    3D structure databases

    ProteinModelPortaliP38351.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi363 – 44583Asp/Glu-rich (acidic)Add
    BLAST

    Sequence similaritiesi

    Belongs to the PAF1 family.Curated

    Phylogenomic databases

    eggNOGiNOG276051.
    HOGENOMiHOG000000738.
    KOiK15174.
    OMAiDEWISMY.
    OrthoDBiEOG7F2534.

    Family and domain databases

    InterProiIPR007133. RNA_pol_II-assoc_Paf1.
    [Graphical view]
    PANTHERiPTHR23188. PTHR23188. 1 hit.
    PfamiPF03985. Paf1. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P38351-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKKQEYIAP IKYQNSLPVP QLPPKLLVYP ESPETNADSS QLINSLYIKT    50
    NVTNLIQQDE DLGMPVDLMK FPGLLNKLDS KLLYGFDNVK LDKDDRILLR 100
    DPRIDRLTKT DISKVTFLRR TEYVSNTIAA HDNTSLKRKR RLDDGDSDDE 150
    NLDVNHIISR VEGTFNKTDK WQHPVKKGVK MVKKWDLLPD TASMDQVYFI 200
    LKFMGSASLD TKEKKSLNTG IFRPVELEED EWISMYATDH KDSAILENEL 250
    EKGMDEMDDD SHEGKIYKFK RIRDYDMKQV AEKPMTELAI RLNDKDGIAY 300
    YKPLRSKIEL RRRRVNDIIK PLVKEHDIDQ LNVTLRNPST KEANIRDKLR 350
    MKFDPINFAT VDEEDDEDEE QPEDVKKESE GDSKTEGSEQ EGENEKDEEI 400
    KQEKENEQDE ENKQDENRAA DTPETSDAVH TEQKPEEEKE TLQEE 445
    Length:445
    Mass (Da):51,801
    Last modified:October 1, 1994 - v1
    Checksum:i46FB5AB37C3C1AAE
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X76053 Genomic DNA. Translation: CAA53642.1.
    Z36148 Genomic DNA. Translation: CAA85243.1.
    BK006936 Genomic DNA. Translation: DAA07394.1.
    PIRiS44541.
    RefSeqiNP_009838.1. NM_001178627.1.

    Genome annotation databases

    EnsemblFungiiYBR279W; YBR279W; YBR279W.
    GeneIDi852582.
    KEGGisce:YBR279W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X76053 Genomic DNA. Translation: CAA53642.1 .
    Z36148 Genomic DNA. Translation: CAA85243.1 .
    BK006936 Genomic DNA. Translation: DAA07394.1 .
    PIRi S44541.
    RefSeqi NP_009838.1. NM_001178627.1.

    3D structure databases

    ProteinModelPortali P38351.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32973. 144 interactions.
    DIPi DIP-1149N.
    IntActi P38351. 10 interactions.
    MINTi MINT-600620.
    STRINGi 4932.YBR279W.

    Proteomic databases

    MaxQBi P38351.
    PaxDbi P38351.
    PeptideAtlasi P38351.
    PRIDEi P38351.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YBR279W ; YBR279W ; YBR279W .
    GeneIDi 852582.
    KEGGi sce:YBR279W.

    Organism-specific databases

    CYGDi YBR279w.
    SGDi S000000483. PAF1.

    Phylogenomic databases

    eggNOGi NOG276051.
    HOGENOMi HOG000000738.
    KOi K15174.
    OMAi DEWISMY.
    OrthoDBi EOG7F2534.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-29199-MONOMER.

    Miscellaneous databases

    NextBioi 971727.
    PROi P38351.

    Gene expression databases

    Genevestigatori P38351.

    Family and domain databases

    InterProi IPR007133. RNA_pol_II-assoc_Paf1.
    [Graphical view ]
    PANTHERi PTHR23188. PTHR23188. 1 hit.
    Pfami PF03985. Paf1. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The sequence of a 32,420 bp segment located on the right arm of chromosome II from Saccharomyces cerevisiae."
      Holmstroem K., Brandt T., Kallesoe T.
      Yeast 10:S47-S62(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. "Complete DNA sequence of yeast chromosome II."
      Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C.
      , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
      EMBO J. 13:5795-5809(1994) [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. "A novel collection of accessory factors associated with yeast RNA polymerase II."
      Wade P.A., Werel W., Fentzke R.C., Thompson N.E., Leykam J.F., Burgess R.R., Jaehning J.A., Burton Z.F.
      Protein Expr. Purif. 8:85-90(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 5-11 AND 419-426.
    5. "Paf1p, an RNA polymerase II-associated factor in Saccharomyces cerevisiae, may have both positive and negative roles in transcription."
      Shi X., Finkelstein A., Wolf A.J., Wade P.A., Burton Z.F., Jaehning J.A.
      Mol. Cell. Biol. 16:669-676(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION, CHARACTERIZATION.
    6. "A role for Ctr9p and Paf1p in the regulation of G1 cyclin expression in yeast."
      Koch C., Wollmann P., Dahl M., Lottspeich F.
      Nucleic Acids Res. 27:2126-2134(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBUNIT.
    7. "Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex."
      Mueller C.L., Jaehning J.A.
      Mol. Cell. Biol. 22:1971-1980(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE PAF1 COMPLEX.
    8. "RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach."
      Krogan N.J., Kim M., Ahn S.H., Zhong G., Kobor M.S., Cagney G., Emili A., Shilatifard A., Buratowski S., Greenblatt J.F.
      Mol. Cell. Biol. 22:6979-6992(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH POB3 AND SPT16.
    9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    10. "Separation of the Saccharomyces cerevisiae Paf1 complex from RNA polymerase II results in changes in its subnuclear localization."
      Porter S.E., Penheiter K.L., Jaehning J.A.
      Eukaryot. Cell 4:209-220(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION.
    11. "A requirement for the Saccharomyces cerevisiae Paf1 complex in snoRNA 3' end formation."
      Sheldon K.E., Mauger D.M., Arndt K.M.
      Mol. Cell 20:225-236(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    12. "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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    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-147, 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-147 AND THR-422, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiPAF1_YEAST
    AccessioniPrimary (citable) accession number: P38351
    Secondary accession number(s): D6VQS4, Q9URC9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1994
    Last modified: October 1, 2014
    This is version 133 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 1040 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    3. Yeast chromosome II
      Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

    External Data

    Dasty 3