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P39008

- POP2_YEAST

UniProt

P39008 - POP2_YEAST

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Protein

Poly(A) ribonuclease POP2

Gene
POP2, CAF1, YNR052C, N3470
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 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; catalytic Reviewed prediction
Metal bindingi190 – 1901Divalent metal cation; catalytic Reviewed prediction
Metal bindingi310 – 3101Divalent metal cation; catalytic Reviewed prediction
Metal bindingi394 – 3941Divalent metal cation; catalytic Reviewed prediction

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
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-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. 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
Complete GO annotation...

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.3 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.

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.

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

« Hide 'large scale' publications
  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: June 11, 2014
This is version 135 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.

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

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