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P31384

- CCR4_YEAST

UniProt

P31384 - CCR4_YEAST

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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

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. 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
Complete GO annotation...

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-KW
Complete GO annotation...

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. 283 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.
InParanoidiP31384.
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 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNDPSLLGYP NVGPQQQQQQ QQQQHAGLLG KGTPNALQQQ LHMNQLTGIP
60 70 80 90 100
PPGLMNNSDV HTSSNNNSRQ LLDQLANGNA NMLNMNMDNN NNNNNNNNNN
110 120 130 140 150
NNNGGGSGVM MNASTAAVNS IGMVPTVGTP VNINVNASNP LLHPHLDDPS
160 170 180 190 200
LLNNPIWKLQ LHLAAVSAQS LGQPNIYARQ NAMKKYLATQ QAQQAQQQAQ
210 220 230 240 250
QQAQQQVPGP FGPGPQAAPP ALQPTDFQQS HIAEASKSLV DCTKQALMEM
260 270 280 290 300
ADTLTDSKTA KKQQPTGDST PSGTATNSAV STPLTPKIEL FANGKDEANQ
310 320 330 340 350
ALLQHKKLSQ YSIDEDDDIE NRMVMPKDSK YDDQLWHALD LSNLQIFNIS
360 370 380 390 400
ANIFKYDFLT RLYLNGNSLT ELPAEIKNLS NLRVLDLSHN RLTSLPAELG
410 420 430 440 450
SCFQLKYFYF FDNMVTTLPW EFGNLCNLQF LGVEGNPLEK QFLKILTEKS
460 470 480 490 500
VTGLIFYLRD NRPEIPLPHE RRFIEINTDG EPQREYDSLQ QSTEHLATDL
510 520 530 540 550
AKRTFTVLSY NTLCQHYATP KMYRYTPSWA LSWDYRRNKL KEQILSYDSD
560 570 580 590 600
LLCLQEVESK TFEEYWVPLL DKHGYTGIFH AKARAKTMHS KDSKKVDGCC
610 620 630 640 650
IFFKRDQFKL ITKDAMDFSG AWMKHKKFQR TEDYLNRAMN KDNVALFLKL
660 670 680 690 700
QHIPSGDTIW AVTTHLHWDP KFNDVKTFQV GVLLDHLETL LKEETSHNFR
710 720 730 740 750
QDIKKFPVLI CGDFNSYINS AVYELINTGR VQIHQEGNGR DFGYMSEKNF
760 770 780 790 800
SHNLALKSSY NCIGELPFTN FTPSFTDVID YIWFSTHALR VRGLLGEVDP
810 820 830
EYVSKFIGFP NDKFPSDHIP LLARFEFMKT NTGSKKV
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. 283 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.
InParanoidi P31384.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 150 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