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P39081

- PCF11_YEAST

UniProt

P39081 - PCF11_YEAST

Protein

Protein PCF11

Gene

PCF11

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 121 (01 Oct 2014)
      Sequence version 2 (15 Jul 1998)
      Previous versions | rss
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    Functioni

    Component of the cleavage factor IA (CFIA) complex, which is involved in the endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factor NAB4/CFIB and the cleavage and polyadenylation factor (CPF) complex. Independently involved in RNA polymerase II transcript termination. Binds RNA. Seems to bridge RNA polymerase II and the native transcript and may be involved in dismantling the RNA polymerase II elongation complex.2 Publications

    GO - Molecular functioni

    1. mRNA binding Source: SGD
    2. protein binding Source: IntAct
    3. RNA polymerase II core binding Source: SGD

    GO - Biological processi

    1. mRNA cleavage Source: SGD
    2. mRNA polyadenylation Source: SGD
    3. regulation of transcription, DNA-templated Source: UniProtKB-KW
    4. termination of RNA polymerase II transcription Source: SGD

    Keywords - Biological processi

    mRNA processing, Transcription, Transcription regulation, Transcription termination

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29807-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protein PCF11
    Alternative name(s):
    protein 1 of CF I
    Gene namesi
    Name:PCF11
    Ordered Locus Names:YDR228C
    ORF Names:YD9934.13C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    CYGDiYDR228c.
    SGDiS000002636. PCF11.

    Subcellular locationi

    Nucleus Curated

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi66 – 661A → D: Loss of interaction with RBP1 CTD. 1 Publication
    Mutagenesisi68 – 703DSI → AAA: Loss of interaction with RBP1 CTD.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 626626Protein PCF11PRO_0000058247Add
    BLAST

    Proteomic databases

    MaxQBiP39081.
    PaxDbiP39081.
    PeptideAtlasiP39081.

    Expressioni

    Gene expression databases

    GenevestigatoriP39081.

    Interactioni

    Subunit structurei

    Component of the CFIA complex, which is composed of RNA14, RNA15, PCF11 and CLP1. Interacts with RNA14, RNA15 and RTT103. Interacts directly with the phosphorylated CTD domain of RPB1/RNA polymerase II.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CLP1Q0868513EBI-12980,EBI-29732
    RNA14P2529812EBI-12980,EBI-15632
    RNA15P252999EBI-12980,EBI-15640
    SHO1P400732EBI-12980,EBI-18140

    Protein-protein interaction databases

    BioGridi32280. 85 interactions.
    DIPiDIP-944N.
    IntActiP39081. 78 interactions.
    MINTiMINT-389878.
    STRINGi4932.YDR228C.

    Structurei

    Secondary structure

    1
    626
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1614
    Helixi24 – 3613
    Helixi38 – 403
    Helixi41 – 5414
    Helixi57 – 7317
    Helixi78 – 836
    Helixi86 – 9510
    Helixi99 – 11214
    Helixi115 – 1173
    Helixi125 – 13713
    Helixi486 – 4905
    Helixi495 – 4984

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1SZ9X-ray2.10A/B/C1-140[»]
    1SZAX-ray2.20A/B/C1-140[»]
    2BF0X-ray2.30X1-138[»]
    2NPIX-ray2.95C/D454-563[»]
    4C0BX-ray2.77C/D454-563[»]
    4C0HX-ray2.70C/D454-563[»]
    4OI4X-ray2.40B/D/U454-563[»]
    ProteinModelPortaliP39081.
    SMRiP39081. Positions 2-140, 473-499.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39081.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini4 – 139136CIDPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 130130Interaction with RBP1 CTD (CID)Add
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi234 – 25320Poly-GlnAdd
    BLAST
    Compositional biasi470 – 4734Poly-Thr

    Sequence similaritiesi

    Contains 1 CID domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiNOG268273.
    GeneTreeiENSGT00440000034259.
    HOGENOMiHOG000115468.
    KOiK14400.
    OMAiHADENDE.
    OrthoDBiEOG76QFSS.

    Family and domain databases

    Gene3Di1.25.40.90. 1 hit.
    InterProiIPR021605. CFIA_Pcf11.
    IPR006569. CID_dom.
    IPR008942. ENTH_VHS.
    [Graphical view]
    PfamiPF11526. CFIA_Pcf11. 1 hit.
    [Graphical view]
    SMARTiSM00582. RPR. 1 hit.
    [Graphical view]
    SUPFAMiSSF48464. SSF48464. 1 hit.
    PROSITEiPS51391. CID. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P39081-1 [UniParc]FASTAAdd to Basket

    « Hide

    MDHDTEVIVK DFNSILEELT FNSRPIITTL TKLAEENISC AQYFVDAIES    50
    RIEKCMPKQK LYAFYALDSI CKNVGSPYTI YFSRNLFNLY KRTYLLVDNT 100
    TRTKLINMFK LWLNPNDTGL PLFEGSALEK IEQFLIKASA LHQKNLQAML 150
    PTPTVPLLLR DIDKLTCLTS ERLKNQPNDE KLKMKLLVLS QLKQELKREK 200
    LTLNALKQVQ MQLRQVFSQD QQVLQERMRY HELQQQQQQQ QQQQQQQQQQ 250
    QQQYHETKDM VGSYTQNSNS AIPLFGNNSD TTNQQNSLSS SLFGNISGVE 300
    SFQEIEKKKS LNKINNLYAS LKAEGLIYTP PKESIVTLYK KLNGHSNYSL 350
    DSHEKQLMKN LPKIPLLNDI LSDCKAYFAT VNIDVLNNPS LQLSEQTLLQ 400
    ENPIVQNNLI HLLYRSKPNK CSVCGKRFGN SESEKLLQNE HLDWHFRINT 450
    RIKGSQNTAN TGISNSNLNT TTTRKNIQSR NWYLSDSQWA AFKDDEITST 500
    KHKNDYTDPH ANKNIDKSAL NIHADENDEG SVDNTLGSDR SNELEIRGKY 550
    VVVPETSQDM AFKCPICKET VTGVYDEESG EWVWKNTIEV NGKYFHSTCY 600
    HETSQNSSKS NSGKVGLDDL KKLVTK 626
    Length:626
    Mass (Da):71,898
    Last modified:July 15, 1998 - v2
    Checksum:i66F91BA9577E82F1
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti286 – 2883NSL → ILS in AAC33145. (PubMed:7885847)Curated
    Sequence conflicti515 – 5151I → V in AAC33145. (PubMed:7885847)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z48612 Genomic DNA. Translation: CAA88508.1.
    U13239 Genomic DNA. Translation: AAC33145.1.
    BK006938 Genomic DNA. Translation: DAA12070.1.
    PIRiS59435.
    RefSeqiNP_010514.3. NM_001180536.3.

    Genome annotation databases

    EnsemblFungiiYDR228C; YDR228C; YDR228C.
    GeneIDi851814.
    KEGGisce:YDR228C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z48612 Genomic DNA. Translation: CAA88508.1 .
    U13239 Genomic DNA. Translation: AAC33145.1 .
    BK006938 Genomic DNA. Translation: DAA12070.1 .
    PIRi S59435.
    RefSeqi NP_010514.3. NM_001180536.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1SZ9 X-ray 2.10 A/B/C 1-140 [» ]
    1SZA X-ray 2.20 A/B/C 1-140 [» ]
    2BF0 X-ray 2.30 X 1-138 [» ]
    2NPI X-ray 2.95 C/D 454-563 [» ]
    4C0B X-ray 2.77 C/D 454-563 [» ]
    4C0H X-ray 2.70 C/D 454-563 [» ]
    4OI4 X-ray 2.40 B/D/U 454-563 [» ]
    ProteinModelPortali P39081.
    SMRi P39081. Positions 2-140, 473-499.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32280. 85 interactions.
    DIPi DIP-944N.
    IntActi P39081. 78 interactions.
    MINTi MINT-389878.
    STRINGi 4932.YDR228C.

    Proteomic databases

    MaxQBi P39081.
    PaxDbi P39081.
    PeptideAtlasi P39081.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDR228C ; YDR228C ; YDR228C .
    GeneIDi 851814.
    KEGGi sce:YDR228C.

    Organism-specific databases

    CYGDi YDR228c.
    SGDi S000002636. PCF11.

    Phylogenomic databases

    eggNOGi NOG268273.
    GeneTreei ENSGT00440000034259.
    HOGENOMi HOG000115468.
    KOi K14400.
    OMAi HADENDE.
    OrthoDBi EOG76QFSS.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-29807-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P39081.
    NextBioi 969674.
    PROi P39081.

    Gene expression databases

    Genevestigatori P39081.

    Family and domain databases

    Gene3Di 1.25.40.90. 1 hit.
    InterProi IPR021605. CFIA_Pcf11.
    IPR006569. CID_dom.
    IPR008942. ENTH_VHS.
    [Graphical view ]
    Pfami PF11526. CFIA_Pcf11. 1 hit.
    [Graphical view ]
    SMARTi SM00582. RPR. 1 hit.
    [Graphical view ]
    SUPFAMi SSF48464. SSF48464. 1 hit.
    PROSITEi PS51391. CID. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "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.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. "Insertion site specificity of the transposon Tn3."
      Davies C.J., Hutchison C.A. III
      Nucleic Acids Res. 23:507-514(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 286-626.
    4. "PCF11 encodes a third protein component of yeast cleavage and polyadenylation factor I."
      Amrani N., Minet M., Wyers F., Dufour M.-E., Aggerbeck L.P., Lacroute F.
      Mol. Cell. Biol. 17:1102-1109(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE CFIA COMPLEX, INTERACTION WITH RNA14 AND RNA15.
    5. "Five subunits are required for reconstitution of the cleavage and polyadenylation activities of Saccharomyces cerevisiae cleavage factor I."
      Gross S., Moore C.
      Proc. Natl. Acad. Sci. U.S.A. 98:6080-6085(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF THE CFIA COMPLEX.
    6. "Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae."
      Barilla D., Lee B.A., Proudfoot N.J.
      Proc. Natl. Acad. Sci. U.S.A. 98:445-450(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH RBP1.
    7. "Independent functions of yeast Pcf11p in pre-mRNA 3' end processing and in transcription termination."
      Sadowski M., Dichtl B., Huebner W., Keller W.
      EMBO J. 22:2167-2177(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH RBP1, MUTAGENESIS OF ALA-66 AND 68-ASP--ILE-70.
    8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    9. "The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II."
      Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E., Greenblatt J.F., Buratowski S.
      Nature 432:517-522(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH RTT103.
    10. "CTD-dependent dismantling of the RNA polymerase II elongation complex by the pre-mRNA 3'-end processing factor, Pcf11."
      Zhang Z., Fu J., Gilmour D.S.
      Genes Dev. 19:1572-1580(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, RNA-BINDING.
    11. "Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors."
      Meinhart A., Cramer P.
      Nature 430:223-226(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 1-140.
    12. Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-138.

    Entry informationi

    Entry nameiPCF11_YEAST
    AccessioniPrimary (citable) accession number: P39081
    Secondary accession number(s): D6VSL0, Q04932
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: July 15, 1998
    Last modified: October 1, 2014
    This is version 121 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 2800 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

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

    External Data

    Dasty 3