Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P39008

- POP2_YEAST

UniProt

P39008 - POP2_YEAST

Protein

Poly(A) ribonuclease POP2

Gene

POP2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 136 (01 Oct 2014)
      Sequence version 2 (01 Oct 1996)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    Functioni

    Acts as probably catalytic component of the CCR4-NOT core complex, which in the nucleus seems to be a general transcription factor, and in the cytoplasm the major mRNA deadenylase involved in mRNA turnover. In vitro, POP2 has 3'-exoribonuclease activity with a preference for poly(A) RNAs, but also degrades poly(U) and poly(C) RNAs. Is part of a glucose-sensing system involved in growth control in response to glucose availability.4 Publications

    Catalytic activityi

    Exonucleolytic cleavage of poly(A) to 5'-AMP.

    Cofactori

    Divalent metal cations. Mg2+ is the most probable.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi188 – 1881Divalent metal cation; catalyticSequence Analysis
    Metal bindingi190 – 1901Divalent metal cation; catalyticSequence Analysis
    Metal bindingi310 – 3101Divalent metal cation; catalyticSequence Analysis
    Metal bindingi394 – 3941Divalent metal cation; catalyticSequence Analysis

    GO - Molecular functioni

    1. 3'-5'-exoribonuclease activity Source: SGD
    2. metal ion binding Source: UniProtKB-KW
    3. protein binding Source: IntAct
    4. RNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. nuclear-transcribed mRNA poly(A) tail shortening Source: SGD
    2. positive regulation of transcription elongation from RNA polymerase II promoter Source: SGD
    3. regulation of transcription from RNA polymerase II promoter Source: SGD
    4. RNA phosphodiester bond hydrolysis, exonucleolytic Source: GOC
    5. transcription elongation from RNA polymerase II promoter Source: SGD

    Keywords - Molecular functioni

    Activator, Exonuclease, Hydrolase, Nuclease, Repressor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    Magnesium, Metal-binding, RNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-33358-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Poly(A) ribonuclease POP2 (EC:3.1.13.4)
    Alternative name(s):
    CCR4-associated factor 1
    Gene namesi
    Name:POP2
    Synonyms:CAF1
    Ordered Locus Names:YNR052C
    ORF Names:N3470
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XIV

    Organism-specific databases

    CYGDiYNR052c.
    SGDiS000005335. POP2.

    Subcellular locationi

    Cytoplasm 1 Publication. Nucleus 1 Publication

    GO - Cellular componenti

    1. CCR4-NOT core complex Source: SGD
    2. cytoplasm Source: SGD
    3. cytoplasmic mRNA processing body Source: SGD
    4. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi97 – 971T → A: No cell-cycle stop in response to glucose deprivation. 1 Publication
    Mutagenesisi188 – 1881S → A: Abolishes poly(A) RNA degradation; when associated with A-190. 1 Publication
    Mutagenesisi190 – 1901E → A: Abolishes poly(A) RNA degradation; when associated with A-188. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 433433Poly(A) ribonuclease POP2PRO_0000212849Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionine1 Publication
    Modified residuei97 – 971Phosphothreonine; by YAK11 Publication

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiP39008.
    PaxDbiP39008.

    Expressioni

    Gene expression databases

    GenevestigatoriP39008.

    Interactioni

    Subunit structurei

    Subunit of the 1.0 MDa CCR4-NOT core complex that contains CCR4, CAF1, NOT1, NOT2, NOT3, NOT4, NOT5, CAF40 and CAF130. In the complex interacts with NOT1. The core complex probably is part of a less characterized 1.9 MDa CCR4-NOT complex.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CAF40P538298EBI-13629,EBI-28306
    CCR4P313849EBI-13629,EBI-4396
    CDC39P256559EBI-13629,EBI-12139
    DHH1P395173EBI-13629,EBI-158
    MOT2P349093EBI-13629,EBI-12174

    Protein-protein interaction databases

    BioGridi35877. 246 interactions.
    DIPiDIP-1957N.
    IntActiP39008. 35 interactions.
    MINTiMINT-405477.
    STRINGi4932.YNR052C.

    Structurei

    Secondary structure

    1
    433
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi155 – 1584
    Beta strandi161 – 1633
    Turni165 – 1673
    Helixi168 – 17811
    Turni179 – 1813
    Beta strandi184 – 1929
    Beta strandi197 – 2004
    Helixi205 – 21713
    Beta strandi221 – 23010
    Beta strandi238 – 2403
    Beta strandi242 – 2487
    Turni252 – 2543
    Helixi259 – 2679
    Helixi272 – 2787
    Helixi282 – 2909
    Beta strandi292 – 2965
    Beta strandi300 – 3067
    Helixi309 – 31810
    Helixi327 – 33711
    Beta strandi339 – 3435
    Helixi344 – 3518
    Helixi353 – 3553
    Helixi373 – 3797
    Helixi386 – 3894
    Helixi391 – 40818
    Turni409 – 4113
    Helixi419 – 4224

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1UOCX-ray2.30A/B147-433[»]
    4B8AX-ray2.40B151-433[»]
    4B8CX-ray3.41A/C/E/F146-433[»]
    ProteinModelPortaliP39008.
    SMRiP39008. Positions 149-428.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39008.

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi81 – 9010Poly-Gln
    Compositional biasi111 – 12515Poly-GlnAdd
    BLAST
    Compositional biasi363 – 3697Poly-Gln

    Sequence similaritiesi

    Belongs to the CAF1 family.Curated

    Phylogenomic databases

    eggNOGiCOG5228.
    GeneTreeiENSGT00390000000080.
    HOGENOMiHOG000057134.
    KOiK12581.
    OMAiSKADYHY.
    OrthoDBiEOG7BS4M9.

    Family and domain databases

    Gene3Di3.30.420.10. 1 hit.
    InterProiIPR006941. RNase_CAF1.
    IPR012337. RNaseH-like_dom.
    [Graphical view]
    PfamiPF04857. CAF1. 1 hit.
    [Graphical view]
    SUPFAMiSSF53098. SSF53098. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P39008-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQSMNVQPRV LAVGGEQFFS QRQASEQHQQ QNMGPQVYSP KVNRARMFPQ    50
    GMPVNTINGS VNQEMNNAYL LKQKNEPLLT QQQQQQQQQQ QPFNIGTPVS 100
    VASLPPGLNV LQQQQQQQQQ QQQQQQGVGL NRPLASQLPK HLTNQSMPPI 150
    FLPPPNYLFV RDVWKSNLYS EFAVIRQLVS QYNHVSISTE FVGTLARPIG 200
    TFRSKVDYHY QTMRANVDFL NPIQLGLSLS DANGNKPDNG PSTWQFNFEF 250
    DPKKEIMSTE SLELLRKSGI NFEKHENLGI DVFEFSQLLM DSGLMMDDSV 300
    TWITYHAAYD LGFLINILMN DSMPNNKEDF EWWVHQYMPN FYDLNLVYKI 350
    IQEFKNPQLQ QSSQQQQQQQ YSLTTLADEL GLPRFSIFTT TGGQSLLMLL 400
    SFCQLSKLSM HKFPNGTDFA KYQGVIYGID GDQ 433
    Length:433
    Mass (Da):49,682
    Last modified:October 1, 1996 - v2
    Checksum:iF3CAF97106A65933
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti41 – 411K → Q in strain: A364A.
    Natural varianti91 – 911Q → QQQQQQQQQQQQQQQQQQ in strain: A364A.
    Natural varianti118 – 1225Missing in strain: A364A.
    Natural varianti278 – 2781L → S in strain: A364A.
    Natural varianti412 – 4121K → M.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D12807 Genomic DNA. Translation: BAA02246.1.
    D12808 Genomic DNA. Translation: BAA02247.1.
    Z71667 Genomic DNA. Translation: CAA96333.1.
    AY692792 Genomic DNA. Translation: AAT92811.1.
    M88607 Genomic DNA. Translation: AAA34832.1.
    BK006947 Genomic DNA. Translation: DAA10593.1.
    PIRiS63383.
    RefSeqiNP_014450.3. NM_001183229.3.

    Genome annotation databases

    EnsemblFungiiYNR052C; YNR052C; YNR052C.
    GeneIDi855788.
    KEGGisce:YNR052C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D12807 Genomic DNA. Translation: BAA02246.1 .
    D12808 Genomic DNA. Translation: BAA02247.1 .
    Z71667 Genomic DNA. Translation: CAA96333.1 .
    AY692792 Genomic DNA. Translation: AAT92811.1 .
    M88607 Genomic DNA. Translation: AAA34832.1 .
    BK006947 Genomic DNA. Translation: DAA10593.1 .
    PIRi S63383.
    RefSeqi NP_014450.3. NM_001183229.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1UOC X-ray 2.30 A/B 147-433 [» ]
    4B8A X-ray 2.40 B 151-433 [» ]
    4B8C X-ray 3.41 A/C/E/F 146-433 [» ]
    ProteinModelPortali P39008.
    SMRi P39008. Positions 149-428.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 35877. 246 interactions.
    DIPi DIP-1957N.
    IntActi P39008. 35 interactions.
    MINTi MINT-405477.
    STRINGi 4932.YNR052C.

    Proteomic databases

    MaxQBi P39008.
    PaxDbi P39008.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YNR052C ; YNR052C ; YNR052C .
    GeneIDi 855788.
    KEGGi sce:YNR052C.

    Organism-specific databases

    CYGDi YNR052c.
    SGDi S000005335. POP2.

    Phylogenomic databases

    eggNOGi COG5228.
    GeneTreei ENSGT00390000000080.
    HOGENOMi HOG000057134.
    KOi K12581.
    OMAi SKADYHY.
    OrthoDBi EOG7BS4M9.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-33358-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P39008.
    NextBioi 980271.
    PROi P39008.

    Gene expression databases

    Genevestigatori P39008.

    Family and domain databases

    Gene3Di 3.30.420.10. 1 hit.
    InterProi IPR006941. RNase_CAF1.
    IPR012337. RNaseH-like_dom.
    [Graphical view ]
    Pfami PF04857. CAF1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53098. SSF53098. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Molecular analysis of POP2 gene, a gene required for glucose-derepression of gene expression in Saccharomyces cerevisiae."
      Sakai A., Chibazakura T., Shimizu Y., Hishinuma F.
      Nucleic Acids Res. 20:6227-6233(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c and ATCC 204626 / S288c / A364A.
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
      Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J.
      , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
      Nature 387:93-98(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. Cusick M.E.
      Submitted (MAR-1992) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 213-433.
    6. "Identification of a mouse protein whose homolog in Saccharomyces cerevisiae is a component of the CCR4 transcriptional regulatory complex."
      Draper M.P., Salvadore C., Denis C.L.
      Mol. Cell. Biol. 15:3487-3495(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    7. "The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively."
      Liu H.Y., Badarinarayana V., Audino D.C., Rappsilber J., Mann M., Denis C.L.
      EMBO J. 17:1096-1106(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE CCR4-NOT CORE COMPLEX, FUNCTION OF THE CCR4-NOT CORE COMPLEX IN TRANSCRIPTIONAL REGULATION.
    8. "The CCR4 and CAF1 proteins of the CCR4-NOT complex are physically and functionally separated from NOT2, NOT4, and NOT5."
      Bai Y., Salvadore C., Chiang Y.C., Collart M.A., Liu H.Y., Denis C.L.
      Mol. Cell. Biol. 19:6642-6651(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH NOT1.
    9. "The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae."
      Tucker M., Valencia-Sanchez M.A., Staples R.R., Chen J., Denis C.L., Parker R.
      Cell 104:377-386(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN MRNA DEADENYLATION, SUBCELLULAR LOCATION.
    10. "Purification and characterization of the 1.0 MDa CCR4-NOT complex identifies two novel components of the complex."
      Chen J., Rappsilber J., Chiang Y.C., Russell P., Mann M., Denis C.L.
      J. Mol. Biol. 314:683-694(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE CCR4-NOT CORE COMPLEX.
    11. "The yeast POP2 gene encodes a nuclease involved in mRNA deadenylation."
      Daugeron M.-C., Mauxion F., Seraphin B.
      Nucleic Acids Res. 29:2448-2455(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN MRNA DEADENYLATION.
    12. "Yak1p, a DYRK family kinase, translocates to the nucleus and phosphorylates yeast Pop2p in response to a glucose signal."
      Moriya H., Shimizu-Yoshida Y., Omori A., Iwashita S., Katoh M., Sakai A.
      Genes Dev. 15:1217-1228(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION AT THR-97, MUTAGENESIS OF THR-97.
    13. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    14. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. "X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex."
      Thore S., Mauxion F., Seraphin B., Suck D.
      EMBO Rep. 4:1150-1155(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 147-433 IN COMPLEX WITH METAL IONS, FUNCTION IN MRNA DEADENYLATION, MUTAGENESIS OF SER-188 AND GLU-190.

    Entry informationi

    Entry nameiPOP2_YEAST
    AccessioniPrimary (citable) accession number: P39008
    Secondary accession number(s): D6W1M7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: October 1, 1996
    Last modified: October 1, 2014
    This is version 136 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 1520 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 XIV
      Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

    External Data

    Dasty 3