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P31384

- CCR4_YEAST

UniProt

P31384 - CCR4_YEAST

Protein

Glucose-repressible alcohol dehydrogenase transcriptional effector

Gene

CCR4

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 149 (01 Oct 2014)
      Sequence version 2 (05 Oct 2010)
      Previous versions | rss
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    Functioni

    Acts as 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. CCR4 has 3'-5' RNase activity with a strong preference for polyadenylated substrates and also low exonuclease activity towards single-stranded DNA. Discovered because of its role in the control of ADH2 gene expression. It is required for the expression of genes involved in non-fermentative growth and it mediates or is required for the action of the SPT6 and SPT10 genes.4 Publications

    Catalytic activityi

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

    Cofactori

    Magnesium.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi556 – 5561Magnesium

    GO - Molecular functioni

    1. 3'-5'-exoribonuclease activity Source: SGD
    2. metal ion binding Source: UniProtKB-KW
    3. poly(A)-specific ribonuclease activity Source: UniProtKB-EC
    4. protein binding Source: IntAct
    5. RNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. DNA replication Source: SGD
    2. DNA replication checkpoint Source: SGD
    3. nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: SGD
    4. nuclear-transcribed mRNA poly(A) tail shortening Source: SGD
    5. positive regulation of transcription elongation from RNA polymerase II promoter Source: SGD
    6. regulation of transcription from RNA polymerase II promoter Source: SGD
    7. replication fork protection Source: SGD
    8. RNA phosphodiester bond hydrolysis, exonucleolytic Source: GOC
    9. transcription elongation from RNA polymerase II promoter Source: SGD
    10. traversing start control point of mitotic cell cycle 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-28833-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glucose-repressible alcohol dehydrogenase transcriptional effector (EC:3.1.13.4)
    Alternative name(s):
    Carbon catabolite repressor protein 4
    Cytoplasmic deadenylase
    Gene namesi
    Name:CCR4
    Ordered Locus Names:YAL021C
    ORF Names:FUN27
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome I

    Organism-specific databases

    SGDiS000000019. CCR4.

    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
    Mutagenesisi556 – 5561E → A: Loss of activity. 1 Publication
    Mutagenesisi713 – 7131D → A: Strongly reduces activity. 1 Publication
    Mutagenesisi780 – 7801D → A: Reduces activity. 1 Publication
    Mutagenesisi818 – 8181H → A: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 837837Glucose-repressible alcohol dehydrogenase transcriptional effectorPRO_0000218577Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei33 – 331Phosphothreonine1 Publication
    Modified residuei278 – 2781Phosphoserine2 Publications
    Modified residuei285 – 2851Phosphothreonine2 Publications

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP31384.
    PaxDbiP31384.
    PeptideAtlasiP31384.

    Expressioni

    Gene expression databases

    GenevestigatoriP31384.

    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.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CAF40P538298EBI-4396,EBI-28306
    CDC39P256557EBI-4396,EBI-12139
    MOT2P349094EBI-4396,EBI-12174
    POP2P390089EBI-4396,EBI-13629

    Protein-protein interaction databases

    BioGridi31745. 282 interactions.
    DIPiDIP-2522N.
    IntActiP31384. 31 interactions.
    MINTiMINT-615079.
    STRINGi4932.YAL021C.

    Structurei

    Secondary structure

    1
    837
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni140 – 1423
    Helixi144 – 1463
    Helixi155 – 16915
    Helixi176 – 18611
    Helixi245 – 25814
    Beta strandi338 – 3403
    Helixi351 – 3555
    Helixi374 – 3796
    Beta strandi384 – 3863
    Helixi399 – 4024
    Beta strandi406 – 4094
    Helixi441 – 46020
    Helixi515 – 5173
    Turni520 – 5223
    Helixi528 – 5314
    Helixi533 – 54614
    Beta strandi550 – 5545
    Helixi559 – 5635
    Turni564 – 5663
    Beta strandi600 – 6023
    Helixi800 – 8034
    Beta strandi807 – 8115
    Beta strandi816 – 8183

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4B8CX-ray3.41D/J/K/L111-837[»]
    ProteinModelPortaliP31384.
    SMRiP31384. Positions 135-192, 295-827.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati334 – 35623LRR 1Add
    BLAST
    Repeati358 – 37922LRR 2Add
    BLAST
    Repeati381 – 40222LRR 3Add
    BLAST
    Repeati404 – 42623LRR 4Add
    BLAST
    Repeati427 – 44721LRR 5Add
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi15 – 2410Poly-Gln
    Compositional biasi77 – 10327Asn-richAdd
    BLAST
    Compositional biasi89 – 10315Poly-AsnAdd
    BLAST
    Compositional biasi190 – 20617Gln-richAdd
    BLAST

    Domaini

    The 169 C-terminal residues are important for deadenylase activity.

    Sequence similaritiesi

    Belongs to the CCR4/nocturin family.Curated
    Contains 5 LRR (leucine-rich) repeats.Curated

    Keywords - Domaini

    Leucine-rich repeat, Repeat

    Phylogenomic databases

    eggNOGiCOG4886.
    GeneTreeiENSGT00550000074364.
    HOGENOMiHOG000294222.
    KOiK12603.
    OMAiFEYNSVC.
    OrthoDBiEOG7KWSS5.

    Family and domain databases

    Gene3Di3.60.10.10. 1 hit.
    InterProiIPR005135. Endo/exonuclease/phosphatase.
    IPR001611. Leu-rich_rpt.
    IPR025875. Leu-rich_rpt_4.
    IPR003591. Leu-rich_rpt_typical-subtyp.
    [Graphical view]
    PfamiPF03372. Exo_endo_phos. 1 hit.
    PF12799. LRR_4. 1 hit.
    [Graphical view]
    SMARTiSM00369. LRR_TYP. 1 hit.
    [Graphical view]
    SUPFAMiSSF56219. SSF56219. 1 hit.
    PROSITEiPS51450. LRR. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P31384-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNDPSLLGYP NVGPQQQQQQ QQQQHAGLLG KGTPNALQQQ LHMNQLTGIP    50
    PPGLMNNSDV HTSSNNNSRQ LLDQLANGNA NMLNMNMDNN NNNNNNNNNN 100
    NNNGGGSGVM MNASTAAVNS IGMVPTVGTP VNINVNASNP LLHPHLDDPS 150
    LLNNPIWKLQ LHLAAVSAQS LGQPNIYARQ NAMKKYLATQ QAQQAQQQAQ 200
    QQAQQQVPGP FGPGPQAAPP ALQPTDFQQS HIAEASKSLV DCTKQALMEM 250
    ADTLTDSKTA KKQQPTGDST PSGTATNSAV STPLTPKIEL FANGKDEANQ 300
    ALLQHKKLSQ YSIDEDDDIE NRMVMPKDSK YDDQLWHALD LSNLQIFNIS 350
    ANIFKYDFLT RLYLNGNSLT ELPAEIKNLS NLRVLDLSHN RLTSLPAELG 400
    SCFQLKYFYF FDNMVTTLPW EFGNLCNLQF LGVEGNPLEK QFLKILTEKS 450
    VTGLIFYLRD NRPEIPLPHE RRFIEINTDG EPQREYDSLQ QSTEHLATDL 500
    AKRTFTVLSY NTLCQHYATP KMYRYTPSWA LSWDYRRNKL KEQILSYDSD 550
    LLCLQEVESK TFEEYWVPLL DKHGYTGIFH AKARAKTMHS KDSKKVDGCC 600
    IFFKRDQFKL ITKDAMDFSG AWMKHKKFQR TEDYLNRAMN KDNVALFLKL 650
    QHIPSGDTIW AVTTHLHWDP KFNDVKTFQV GVLLDHLETL LKEETSHNFR 700
    QDIKKFPVLI CGDFNSYINS AVYELINTGR VQIHQEGNGR DFGYMSEKNF 750
    SHNLALKSSY NCIGELPFTN FTPSFTDVID YIWFSTHALR VRGLLGEVDP 800
    EYVSKFIGFP NDKFPSDHIP LLARFEFMKT NTGSKKV 837
    Length:837
    Mass (Da):94,670
    Last modified:October 5, 2010 - v2
    Checksum:i5CDB2E8FEDDBEF6F
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti544 – 5441I → L in AAB24455. (PubMed:1459446)Curated
    Sequence conflicti803 – 8031V → E in AAB24455. (PubMed:1459446)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    S50459 Genomic DNA. Translation: AAB24455.1.
    L05146 Genomic DNA. Translation: AAC04936.1.
    BK006935 Genomic DNA. Translation: DAA06967.1.
    PIRiS36713.
    RefSeqiNP_009381.1. NM_001178166.1.

    Genome annotation databases

    EnsemblFungiiYAL021C; YAL021C; YAL021C.
    GeneIDi851212.
    KEGGisce:YAL021C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    S50459 Genomic DNA. Translation: AAB24455.1 .
    L05146 Genomic DNA. Translation: AAC04936.1 .
    BK006935 Genomic DNA. Translation: DAA06967.1 .
    PIRi S36713.
    RefSeqi NP_009381.1. NM_001178166.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4B8C X-ray 3.41 D/J/K/L 111-837 [» ]
    ProteinModelPortali P31384.
    SMRi P31384. Positions 135-192, 295-827.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31745. 282 interactions.
    DIPi DIP-2522N.
    IntActi P31384. 31 interactions.
    MINTi MINT-615079.
    STRINGi 4932.YAL021C.

    Proteomic databases

    MaxQBi P31384.
    PaxDbi P31384.
    PeptideAtlasi P31384.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YAL021C ; YAL021C ; YAL021C .
    GeneIDi 851212.
    KEGGi sce:YAL021C.

    Organism-specific databases

    SGDi S000000019. CCR4.

    Phylogenomic databases

    eggNOGi COG4886.
    GeneTreei ENSGT00550000074364.
    HOGENOMi HOG000294222.
    KOi K12603.
    OMAi FEYNSVC.
    OrthoDBi EOG7KWSS5.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-28833-MONOMER.

    Miscellaneous databases

    NextBioi 968091.
    PROi P31384.

    Gene expression databases

    Genevestigatori P31384.

    Family and domain databases

    Gene3Di 3.60.10.10. 1 hit.
    InterProi IPR005135. Endo/exonuclease/phosphatase.
    IPR001611. Leu-rich_rpt.
    IPR025875. Leu-rich_rpt_4.
    IPR003591. Leu-rich_rpt_typical-subtyp.
    [Graphical view ]
    Pfami PF03372. Exo_endo_phos. 1 hit.
    PF12799. LRR_4. 1 hit.
    [Graphical view ]
    SMARTi SM00369. LRR_TYP. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56219. SSF56219. 1 hit.
    PROSITEi PS51450. LRR. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The CCR4 protein from Saccharomyces cerevisiae contains a leucine-rich repeat region which is required for its control of ADH2 gene expression."
      Malvar T., Biron R.W., Kaback D.B., Denis C.L.
      Genetics 132:951-962(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Sequencing of chromosome I from Saccharomyces cerevisiae: analysis of a 32 kb region between the LTE1 and SPO7 genes."
      Ouellette B.F.F., Clark M.W., Keng T., Storms R.K., Zhong W.-W., Zeng B., Fortin N., Delaney S., Barton A.B., Kaback D.B., Bussey H.
      Genome 36:32-42(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204511 / S288c / AB972.
    3. "Molecular cloning of chromosome I DNA from Saccharomyces cerevisiae: analysis of the genes in the FUN38-MAK16-SPO7 region."
      Barton A.B., Kaback D.B.
      J. Bacteriol. 176:1872-1880(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204511 / S288c / AB972.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    6. "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.
    7. "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.
    8. "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.
    9. "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.
    10. "CCR4, a 3'-5' poly(A) RNA and ssDNA exonuclease, is the catalytic component of the cytoplasmic deadenylase."
      Chen J., Chiang Y.-C., Denis C.L.
      EMBO J. 21:1414-1426(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN MRNA DEADENYLATION, MUTAGENESIS OF GLU-556; ASP-713; ASP-780 AND HIS-818.
    11. "Ccr4p is the catalytic subunit of a Ccr4p/Pop2p/Notp mRNA deadenylase complex in Saccharomyces cerevisiae."
      Tucker M., Staples R.R., Valencia-Sanchez M.A., Muhlrad D., Parker R.
      EMBO J. 21:1427-1436(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN MRNA DEADENYLATION.
    12. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    13. "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 THR-285, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    14. "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-278, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. "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 THR-33; SER-278 AND THR-285, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiCCR4_YEAST
    AccessioniPrimary (citable) accession number: P31384
    Secondary accession number(s): D6VPJ7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 1, 1993
    Last sequence update: October 5, 2010
    Last modified: October 1, 2014
    This is version 149 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 2780 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 I
      Yeast (Saccharomyces cerevisiae) chromosome I: entries and gene names

    External Data

    Dasty 3