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Protein

Poly(A) ribonuclease POP2

Gene

POP2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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

Mg2+Note: 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. 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 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
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.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. 247 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 – 1584Combined sources
Beta strandi161 – 1633Combined sources
Turni165 – 1673Combined sources
Helixi168 – 17811Combined sources
Turni179 – 1813Combined sources
Beta strandi184 – 1929Combined sources
Beta strandi197 – 2004Combined sources
Helixi205 – 21713Combined sources
Beta strandi221 – 23010Combined sources
Beta strandi238 – 2403Combined sources
Beta strandi242 – 2487Combined sources
Turni252 – 2543Combined sources
Helixi259 – 2679Combined sources
Helixi272 – 2787Combined sources
Helixi282 – 2909Combined sources
Beta strandi292 – 2965Combined sources
Beta strandi300 – 3067Combined sources
Helixi309 – 31810Combined sources
Helixi327 – 33711Combined sources
Beta strandi339 – 3435Combined sources
Helixi344 – 3518Combined sources
Helixi353 – 3553Combined sources
Helixi373 – 3797Combined sources
Helixi386 – 3894Combined sources
Helixi391 – 40818Combined sources
Turni409 – 4113Combined sources
Helixi419 – 4224Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidiP39008.
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

        10         20         30         40         50
MQSMNVQPRV LAVGGEQFFS QRQASEQHQQ QNMGPQVYSP KVNRARMFPQ
60 70 80 90 100
GMPVNTINGS VNQEMNNAYL LKQKNEPLLT QQQQQQQQQQ QPFNIGTPVS
110 120 130 140 150
VASLPPGLNV LQQQQQQQQQ QQQQQQGVGL NRPLASQLPK HLTNQSMPPI
160 170 180 190 200
FLPPPNYLFV RDVWKSNLYS EFAVIRQLVS QYNHVSISTE FVGTLARPIG
210 220 230 240 250
TFRSKVDYHY QTMRANVDFL NPIQLGLSLS DANGNKPDNG PSTWQFNFEF
260 270 280 290 300
DPKKEIMSTE SLELLRKSGI NFEKHENLGI DVFEFSQLLM DSGLMMDDSV
310 320 330 340 350
TWITYHAAYD LGFLINILMN DSMPNNKEDF EWWVHQYMPN FYDLNLVYKI
360 370 380 390 400
IQEFKNPQLQ QSSQQQQQQQ YSLTTLADEL GLPRFSIFTT TGGQSLLMLL
410 420 430
SFCQLSKLSM HKFPNGTDFA KYQGVIYGID GDQ
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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...

Protein-protein interaction databases

BioGridi35877. 247 interactions.
DIPiDIP-1957N.
IntActiP39008. 35 interactions.
MINTiMINT-405477.
STRINGi4932.YNR052C.

Proteomic databases

MaxQBiP39008.
PaxDbiP39008.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CYGDiYNR052c.
SGDiS000005335. POP2.

Phylogenomic databases

eggNOGiCOG5228.
GeneTreeiENSGT00390000000080.
HOGENOMiHOG000057134.
InParanoidiP39008.
KOiK12581.
OMAiSKADYHY.
OrthoDBiEOG7BS4M9.

Enzyme and pathway databases

BioCyciYEAST:G3O-33358-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP39008.
NextBioi980271.
PROiP39008.

Gene expression databases

GenevestigatoriP39008.

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.
ProtoNetiSearch...

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: January 7, 2015
This is version 139 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.