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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: -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

Miscellaneous

Present with 1520 molecules/cell in log phase SD medium.1 Publication

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)DescriptionActionsGraphical viewLength
Metal bindingi188Divalent metal cation; catalyticSequence analysis1
Metal bindingi190Divalent metal cation; catalyticSequence analysis1
Metal bindingi310Divalent metal cation; catalyticSequence analysis1
Metal bindingi394Divalent metal cation; catalyticSequence analysis1

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: SGD
  • metal ion binding Source: UniProtKB-KW
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

Keywordsi

Molecular functionActivator, Exonuclease, Hydrolase, Nuclease, Repressor, RNA-binding
Biological processTranscription, Transcription regulation
LigandMagnesium, Metal-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
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNR052C
SGDiS000005335 POP2

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi97T → A: No cell-cycle stop in response to glucose deprivation. 1 Publication1
Mutagenesisi188S → A: Abolishes poly(A) RNA degradation; when associated with A-190. 1 Publication1
Mutagenesisi190E → A: Abolishes poly(A) RNA degradation; when associated with A-188. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002128491 – 433Poly(A) ribonuclease POP2Add BLAST433

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1
Modified residuei97Phosphothreonine; by YAK11 Publication1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP39008
PaxDbiP39008
PRIDEiP39008

PTM databases

iPTMnetiP39008

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

Protein-protein interaction databases

BioGridi35877, 257 interactors
ComplexPortaliCPX-1800 Ccr4-Not complex
DIPiDIP-1957N
IntActiP39008, 40 interactors
MINTiP39008
STRINGi4932.YNR052C

Structurei

Secondary structure

1433
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP39008
SMRiP39008
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP39008

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi81 – 90Poly-Gln10
Compositional biasi111 – 125Poly-GlnAdd BLAST15
Compositional biasi363 – 369Poly-Gln7

Sequence similaritiesi

Belongs to the CAF1 family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000000080
HOGENOMiHOG000057134
InParanoidiP39008
KOiK12581
OMAiLSMECFK
OrthoDBiEOG092C2LSI

Family and domain databases

Gene3Di3.30.420.10, 1 hit
InterProiView protein in InterPro
IPR006941 RNase_CAF1
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf
PfamiView protein in Pfam
PF04857 CAF1, 1 hit
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)DescriptionActionsGraphical viewLength
Natural varianti41K → Q in strain: A364A. 1
Natural varianti91Q → QQQQQQQQQQQQQQQQQQ in strain: A364A. 1
Natural varianti118 – 122Missing in strain: A364A. 5
Natural varianti278L → S in strain: A364A. 1
Natural varianti412K → M. 1

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

Similar proteinsi

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UOCX-ray2.30A/B147-433[»]
4B8AX-ray2.40B151-433[»]
4B8CX-ray3.41A/C/E/F146-433[»]
ProteinModelPortaliP39008
SMRiP39008
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35877, 257 interactors
ComplexPortaliCPX-1800 Ccr4-Not complex
DIPiDIP-1957N
IntActiP39008, 40 interactors
MINTiP39008
STRINGi4932.YNR052C

PTM databases

iPTMnetiP39008

Proteomic databases

MaxQBiP39008
PaxDbiP39008
PRIDEiP39008

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNR052C; YNR052C; YNR052C
GeneIDi855788
KEGGisce:YNR052C

Organism-specific databases

EuPathDBiFungiDB:YNR052C
SGDiS000005335 POP2

Phylogenomic databases

GeneTreeiENSGT00390000000080
HOGENOMiHOG000057134
InParanoidiP39008
KOiK12581
OMAiLSMECFK
OrthoDBiEOG092C2LSI

Enzyme and pathway databases

BioCyciYEAST:G3O-33358-MONOMER

Miscellaneous databases

EvolutionaryTraceiP39008
PROiPR:P39008

Family and domain databases

Gene3Di3.30.420.10, 1 hit
InterProiView protein in InterPro
IPR006941 RNase_CAF1
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf
PfamiView protein in Pfam
PF04857 CAF1, 1 hit
SUPFAMiSSF53098 SSF53098, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPOP2_YEAST
AccessioniPrimary (citable) accession number: P39008
Secondary accession number(s): D6W1M7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: October 1, 1996
Last modified: September 12, 2018
This is version 171 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
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Main funding by: National Institutes of Health

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