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P39008 (POP2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 135. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Poly(A) ribonuclease POP2

EC=3.1.13.4
Alternative name(s):
CCR4-associated factor 1
Gene names
Name:POP2
Synonyms:CAF1
Ordered Locus Names:YNR052C
ORF Names:N3470
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length433 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.7 Ref.9 Ref.11 Ref.15

Catalytic activity

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

Cofactor

Divalent metal cations. Mg2+ is the most probable.

Subunit structure

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. Ref.7 Ref.8 Ref.10

Subcellular location

Cytoplasm. Nucleus Ref.9.

Miscellaneous

Present with 1520 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the CAF1 family.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentCytoplasm
Nucleus
   LigandMagnesium
Metal-binding
RNA-binding
   Molecular functionActivator
Exonuclease
Hydrolase
Nuclease
Repressor
   PTMAcetylation
Phosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processRNA phosphodiester bond hydrolysis, exonucleolytic

Inferred from direct assay Ref.11. Source: GOC

nuclear-transcribed mRNA poly(A) tail shortening

Inferred from direct assay Ref.11PubMed 11889048. Source: SGD

positive regulation of transcription elongation from RNA polymerase II promoter

Inferred from direct assay PubMed 21406554. Source: SGD

regulation of transcription from RNA polymerase II promoter

Inferred from physical interaction Ref.8. Source: SGD

transcription elongation from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 11404327. Source: SGD

   Cellular_componentCCR4-NOT core complex

Inferred from physical interaction Ref.8. Source: SGD

cytoplasm

Inferred from direct assay PubMed 11889048. Source: SGD

cytoplasmic mRNA processing body

Inferred from direct assay PubMed 18611963. Source: SGD

nucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_function3'-5'-exoribonuclease activity

Inferred from direct assay Ref.11. Source: SGD

RNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

protein binding

Inferred from physical interaction Ref.10PubMed 11780629PubMed 11805826PubMed 16429126PubMed 18467557PubMed 18719252PubMed 21669201PubMed 9504907. Source: IntAct

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 433433Poly(A) ribonuclease POP2
PRO_0000212849

Regions

Compositional bias81 – 9010Poly-Gln
Compositional bias111 – 12515Poly-Gln
Compositional bias363 – 3697Poly-Gln

Sites

Metal binding1881Divalent metal cation; catalytic Potential
Metal binding1901Divalent metal cation; catalytic Potential
Metal binding3101Divalent metal cation; catalytic Potential
Metal binding3941Divalent metal cation; catalytic Potential

Amino acid modifications

Modified residue11N-acetylmethionine Ref.14
Modified residue971Phosphothreonine; by YAK1 Ref.12

Natural variations

Natural variant411K → Q in strain: A364A.
Natural variant911Q → QQQQQQQQQQQQQQQQQQ in strain: A364A.
Natural variant118 – 1225Missing in strain: A364A.
Natural variant2781L → S in strain: A364A.
Natural variant4121K → M.

Experimental info

Mutagenesis971T → A: No cell-cycle stop in response to glucose deprivation. Ref.12
Mutagenesis1881S → A: Abolishes poly(A) RNA degradation; when associated with A-190. Ref.15
Mutagenesis1901E → A: Abolishes poly(A) RNA degradation; when associated with A-188. Ref.15

Secondary structure

................................................... 433
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P39008 [UniParc].

Last modified October 1, 1996. Version 2.
Checksum: F3CAF97106A65933

FASTA43349,682
        10         20         30         40         50         60 
MQSMNVQPRV LAVGGEQFFS QRQASEQHQQ QNMGPQVYSP KVNRARMFPQ GMPVNTINGS 

        70         80         90        100        110        120 
VNQEMNNAYL LKQKNEPLLT QQQQQQQQQQ QPFNIGTPVS VASLPPGLNV LQQQQQQQQQ 

       130        140        150        160        170        180 
QQQQQQGVGL NRPLASQLPK HLTNQSMPPI FLPPPNYLFV RDVWKSNLYS EFAVIRQLVS 

       190        200        210        220        230        240 
QYNHVSISTE FVGTLARPIG TFRSKVDYHY QTMRANVDFL NPIQLGLSLS DANGNKPDNG 

       250        260        270        280        290        300 
PSTWQFNFEF DPKKEIMSTE SLELLRKSGI NFEKHENLGI DVFEFSQLLM DSGLMMDDSV 

       310        320        330        340        350        360 
TWITYHAAYD LGFLINILMN DSMPNNKEDF EWWVHQYMPN FYDLNLVYKI IQEFKNPQLQ 

       370        380        390        400        410        420 
QSSQQQQQQQ YSLTTLADEL GLPRFSIFTT TGGQSLLMLL SFCQLSKLSM HKFPNGTDFA 

       430 
KYQGVIYGID GDQ 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
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]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[14]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRS63383.
RefSeqNP_014450.3. NM_001183229.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1UOCX-ray2.30A/B147-433[»]
4B8AX-ray2.40B151-433[»]
4B8CX-ray3.41A/C/E/F146-433[»]
ProteinModelPortalP39008.
SMRP39008. Positions 149-428.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid35877. 246 interactions.
DIPDIP-1957N.
IntActP39008. 35 interactions.
MINTMINT-405477.
STRING4932.YNR052C.

Proteomic databases

MaxQBP39008.
PaxDbP39008.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYNR052C; YNR052C; YNR052C.
GeneID855788.
KEGGsce:YNR052C.

Organism-specific databases

CYGDYNR052c.
SGDS000005335. POP2.

Phylogenomic databases

eggNOGCOG5228.
GeneTreeENSGT00390000000080.
HOGENOMHOG000057134.
KOK12581.
OMASKADYHY.
OrthoDBEOG7BS4M9.

Enzyme and pathway databases

BioCycYEAST:G3O-33358-MONOMER.

Gene expression databases

GenevestigatorP39008.

Family and domain databases

Gene3D3.30.420.10. 1 hit.
InterProIPR006941. RNase_CAF1.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamPF04857. CAF1. 1 hit.
[Graphical view]
SUPFAMSSF53098. SSF53098. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP39008.
NextBio980271.
PROP39008.

Entry information

Entry namePOP2_YEAST
AccessionPrimary (citable) accession number: P39008
Secondary accession number(s): D6W1M7
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XIV

Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references