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Q08685

- CLP1_YEAST

UniProt

Q08685 - CLP1_YEAST

Protein

mRNA cleavage and polyadenylation factor CLP1

Gene

CLP1

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 104 (01 Oct 2014)
      Sequence version 1 (01 Nov 1996)
      Previous versions | rss
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    Functioni

    Component of the cleavage factor IA (CF IA) complex, which is involved in the endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation. Associates with HRB1/CF IB to form the cleavage factor I (CF I) complex. CF I is required for correct positioning of a larger protein complex, the cleavage and polyadenylation factor (CPF) complex, which contains the catalytic subunits executing mRNA cleavage and polyadenylation. CLP1 mediates interactions between CF IA and CPF factors. CLP1 is also involved in maintaining the CF IA interaction with the C-terminal domain of RNA Pol II largest subunit via PCF11, which links pre-mRNA 3'-end processing to transcription termination.4 PublicationsUniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei33 – 331ATP1 PublicationUniRule annotation
    Binding sitei72 – 721ATP; via carbonyl oxygen1 PublicationUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi133 – 1386ATP1 PublicationUniRule annotation

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-HAMAP
    2. protein binding Source: IntAct

    GO - Biological processi

    1. mRNA 3'-end processing Source: SGD
    2. mRNA cleavage Source: SGD
    3. mRNA polyadenylation Source: SGD

    Keywords - Biological processi

    mRNA processing

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-33742-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    mRNA cleavage and polyadenylation factor CLP1UniRule annotation
    Gene namesi
    Name:CLP1UniRule annotation
    Ordered Locus Names:YOR250C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XV

    Organism-specific databases

    CYGDiYOR250c.
    SGDiS000005776. CLP1.

    Subcellular locationi

    Nucleus UniRule annotation

    GO - Cellular componenti

    1. mRNA cleavage factor complex Source: SGD

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Disruption phenotypei

    Causes defective 3'-end formation and transcriptional read-through.1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi136 – 1361K → A: Completely abolishes interaction with PCF11. No effect on growth; when associated with A-137. 1 Publication
    Mutagenesisi137 – 1371T → A: Completely abolishes interaction with PCF11. No effect on growth; when associated with A-136. 1 Publication
    Mutagenesisi161 – 1611D → A: Compromises interaction with PCF11. No effect on growth. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 445445mRNA cleavage and polyadenylation factor CLP1PRO_0000076211Add
    BLAST

    Proteomic databases

    MaxQBiQ08685.
    PaxDbiQ08685.
    PeptideAtlasiQ08685.

    Expressioni

    Gene expression databases

    GenevestigatoriQ08685.

    Interactioni

    Subunit structurei

    Component of the cleavage factor IA (CF IA) complex, which is a heterohexameric complex with 2:2:1:1 stoichiometry of RNA14, RNA15, PCF11 and CLP1. It contains 2 copies of an RNA14-RNA15 dimer and 1 copy of CLP1-PCF11. The complex interacts with the cleavage factor HRB1/CF IB to form the cleavage factor I (CF I) complex, and binds to RNA. Interacts directly with PCF11. Interacts with the CPF components CFT1, PTA1, PFS2, YSH1 and SSU72.5 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    PCF11P3908113EBI-29732,EBI-12980

    Protein-protein interaction databases

    BioGridi34640. 35 interactions.
    DIPiDIP-1487N.
    IntActiQ08685. 9 interactions.
    MINTiMINT-394953.
    STRINGi4932.YOR250C.

    Structurei

    Secondary structure

    1
    445
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi24 – 285
    Beta strandi32 – 376
    Beta strandi43 – 519
    Beta strandi53 – 553
    Beta strandi65 – 706
    Beta strandi72 – 798
    Beta strandi81 – 866
    Turni92 – 943
    Beta strandi96 – 994
    Helixi103 – 11917
    Beta strandi120 – 1223
    Beta strandi125 – 1317
    Helixi136 – 14712
    Helixi148 – 1514
    Beta strandi156 – 1594
    Beta strandi166 – 1683
    Beta strandi172 – 1776
    Beta strandi194 – 1963
    Beta strandi206 – 2094
    Beta strandi212 – 2143
    Helixi215 – 2173
    Helixi219 – 23921
    Helixi241 – 2466
    Beta strandi248 – 2514
    Helixi255 – 2573
    Helixi263 – 2719
    Beta strandi276 – 2816
    Helixi286 – 29914
    Helixi301 – 3033
    Beta strandi304 – 3074
    Helixi318 – 33417
    Turni337 – 3393
    Beta strandi344 – 3496
    Helixi350 – 3523
    Beta strandi355 – 3584
    Helixi361 – 3644
    Beta strandi371 – 3733
    Helixi378 – 3814
    Beta strandi384 – 3929
    Helixi397 – 4026
    Beta strandi405 – 41511
    Turni416 – 4194
    Beta strandi420 – 43011
    Beta strandi434 – 4429

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2NPIX-ray2.95A/B2-445[»]
    4C0BX-ray2.77A/B1-445[»]
    4C0HX-ray2.70A/B1-445[»]
    4OI4X-ray2.40A/C1-445[»]
    ProteinModelPortaliQ08685.
    SMRiQ08685. Positions 19-445.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ08685.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the Clp1 family. Clp1 subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG5623.
    GeneTreeiENSGT00390000000344.
    HOGENOMiHOG000231935.
    KOiK14399.
    OMAiWHGCELE.
    OrthoDBiEOG789CM7.

    Family and domain databases

    HAMAPiMF_03035. Clp1.
    InterProiIPR028606. Clp1.
    IPR029007. MobB-typ_P-loop.
    IPR027417. P-loop_NTPase.
    IPR010655. Pre-mRNA_cleavage_cplxII_Clp1.
    [Graphical view]
    PfamiPF06807. Clp1. 1 hit.
    PF03205. MobB. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 2 hits.

    Sequencei

    Sequence statusi: Complete.

    Q08685-1 [UniParc]FASTAAdd to Basket

    « Hide

    MASLPGIDEH TTSEELITGD NEWHKLVIPK GSDWQIDLKA EGKLIVKVNS    50
    GIVEIFGTEL AVDDEYTFQN WKFPIYAVEE TELLWKCPDL TTNTITVKPN 100
    HTMKYIYNLH FMLEKIRMSN FEGPRVVIVG GSQTGKTSLS RTLCSYALKF 150
    NAYQPLYINL DPQQPIFTVP GCISATPISD ILDAQLPTWG QSLTSGATLL 200
    HNKQPMVKNF GLERINENKD LYLECISQLG QVVGQRLHLD PQVRRSGCIV 250
    DTPSISQLDE NLAELHHIIE KLNVNIMLVL CSETDPLWEK VKKTFGPELG 300
    NNNIFFIPKL DGVSAVDDVY KRSLQRTSIR EYFYGSLDTA LSPYAIGVDY 350
    EDLTIWKPSN VFDNEVGRVE LFPVTITPSN LQHAIIAITF AERRADQATV 400
    IKSPILGFAL ITEVNEKRRK LRVLLPVPGR LPSKAMILTS YRYLE 445
    Length:445
    Mass (Da):50,226
    Last modified:November 1, 1996 - v1
    Checksum:iB00F7659E83090DA
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z75158 Genomic DNA. Translation: CAA99472.1.
    AY558048 Genomic DNA. Translation: AAS56374.1.
    BK006948 Genomic DNA. Translation: DAA11017.1.
    PIRiS67147.
    RefSeqiNP_014893.1. NM_001183669.1.

    Genome annotation databases

    EnsemblFungiiYOR250C; YOR250C; YOR250C.
    GeneIDi854424.
    KEGGisce:YOR250C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z75158 Genomic DNA. Translation: CAA99472.1 .
    AY558048 Genomic DNA. Translation: AAS56374.1 .
    BK006948 Genomic DNA. Translation: DAA11017.1 .
    PIRi S67147.
    RefSeqi NP_014893.1. NM_001183669.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2NPI X-ray 2.95 A/B 2-445 [» ]
    4C0B X-ray 2.77 A/B 1-445 [» ]
    4C0H X-ray 2.70 A/B 1-445 [» ]
    4OI4 X-ray 2.40 A/C 1-445 [» ]
    ProteinModelPortali Q08685.
    SMRi Q08685. Positions 19-445.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 34640. 35 interactions.
    DIPi DIP-1487N.
    IntActi Q08685. 9 interactions.
    MINTi MINT-394953.
    STRINGi 4932.YOR250C.

    Proteomic databases

    MaxQBi Q08685.
    PaxDbi Q08685.
    PeptideAtlasi Q08685.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YOR250C ; YOR250C ; YOR250C .
    GeneIDi 854424.
    KEGGi sce:YOR250C.

    Organism-specific databases

    CYGDi YOR250c.
    SGDi S000005776. CLP1.

    Phylogenomic databases

    eggNOGi COG5623.
    GeneTreei ENSGT00390000000344.
    HOGENOMi HOG000231935.
    KOi K14399.
    OMAi WHGCELE.
    OrthoDBi EOG789CM7.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-33742-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q08685.
    NextBioi 976637.
    PROi Q08685.

    Gene expression databases

    Genevestigatori Q08685.

    Family and domain databases

    HAMAPi MF_03035. Clp1.
    InterProi IPR028606. Clp1.
    IPR029007. MobB-typ_P-loop.
    IPR027417. P-loop_NTPase.
    IPR010655. Pre-mRNA_cleavage_cplxII_Clp1.
    [Graphical view ]
    Pfami PF06807. Clp1. 1 hit.
    PF03205. MobB. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52540. SSF52540. 2 hits.
    ProtoNeti Search...

    Publicationsi

    1. "Sequencing analysis of a 36.8 kb fragment of yeast chromosome XV reveals 26 open reading frames including SEC63, CDC31, SUG2, GCD1, RBL2, PNT1, PAC1 and VPH1."
      Poirey R., Jauniaux J.-C.
      Yeast 13:483-487(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "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.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. "Purification of the Saccharomyces cerevisiae cleavage/polyadenylation factor I. Separation into two components that are required for both cleavage and polyadenylation of mRNA 3' ends."
      Kessler M.M., Zhao J., Moore C.L.
      J. Biol. Chem. 271:27167-27175(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: COMPOSITION OF THE CFIA COMPLEX.
    6. "The major yeast poly(A)-binding protein is associated with cleavage factor IA and functions in premessenger RNA 3'-end formation."
      Minvielle-Sebastia L., Preker P.J., Wiederkehr T., Strahm Y., Keller W.
      Proc. Natl. Acad. Sci. U.S.A. 94:7897-7902(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE CFIA COMPLEX.
    7. "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.
    8. "Human RNA 5'-kinase (hClp1) can function as a tRNA splicing enzyme in vivo."
      Ramirez A., Shuman S., Schwer B.
      RNA 14:1737-1745(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: LACK OF POLYNUCLEOTIDE KINASE ACTIVITY, MUTAGENESIS OF 136-LYS-THR-137 AND ASP-161.
    9. "Reconstitution of CF IA from overexpressed subunits reveals stoichiometry and provides insights into molecular topology."
      Gordon J.M., Shikov S., Kuehner J.N., Liriano M., Lee E., Stafford W., Poulsen M.B., Harrison C., Moore C., Bohm A.
      Biochemistry 50:10203-10214(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.
    10. "The P-loop domain of yeast Clp1 mediates interactions between CF IA and CPF factors in pre-mRNA 3' end formation."
      Holbein S., Scola S., Loll B., Dichtl B.S., Hubner W., Meinhart A., Dichtl B.
      PLoS ONE 6:E29139-E29139(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBUNIT, DISRUPTION PHENOTYPE, MUTAGENESIS OF LYS-136; THR-137 AND ASP-161.
    11. "The interaction of Pcf11 and Clp1 is needed for mRNA 3'-end formation and is modulated by amino acids in the ATP-binding site."
      Ghazy M.A., Gordon J.M., Lee S.D., Singh B.N., Bohm A., Hampsey M., Moore C.
      Nucleic Acids Res. 40:1214-1225(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH PCF11.
    12. "An essential role for Clp1 in assembly of polyadenylation complex CF IA and Pol II transcription termination."
      Haddad R., Maurice F., Viphakone N., Voisinet-Hakil F., Fribourg S., Minvielle-Sebastia L.
      Nucleic Acids Res. 40:1226-1239(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    13. "Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor."
      Noble C.G., Beuth B., Taylor I.A.
      Nucleic Acids Res. 35:87-99(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) OF 2-445 IN COMPLEX WITH ATP AND PCF11.

    Entry informationi

    Entry nameiCLP1_YEAST
    AccessioniPrimary (citable) accession number: Q08685
    Secondary accession number(s): D6W2V1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 24, 2006
    Last sequence update: November 1, 1996
    Last modified: October 1, 2014
    This is version 104 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Caution

    May lack the polyribonucleotide 5'-hydroxyl-kinase and polynucleotide 5'-hydroxyl-kinase activities that are characteristic of the human ortholog.Curated

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

    External Data

    Dasty 3