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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)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

  • nuclear-transcribed mRNA poly(A) tail shortening Source: SGD
  • positive regulation of transcription elongation from RNA polymerase II promoter Source: SGD
  • regulation of transcription from RNA polymerase II promoter Source: SGD
  • 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
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNR052C.
SGDiS000005335. POP2.

Subcellular locationi

GO - Cellular componenti

  • CCR4-NOT core complex Source: SGD
  • cytoplasm Source: SGD
  • cytoplasmic mRNA processing body Source: SGD
  • nucleus Source: UniProtKB-SubCell
Complete GO annotation...

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.
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

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. 250 interactors.
DIPiDIP-1957N.
IntActiP39008. 36 interactors.
MINTiMINT-405477.

Structurei

Secondary structure

1433
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi155 – 158Combined sources4
Beta strandi161 – 163Combined sources3
Turni165 – 167Combined sources3
Helixi168 – 178Combined sources11
Turni179 – 181Combined sources3
Beta strandi184 – 192Combined sources9
Beta strandi197 – 200Combined sources4
Helixi205 – 217Combined sources13
Beta strandi221 – 230Combined sources10
Beta strandi238 – 240Combined sources3
Beta strandi242 – 248Combined sources7
Turni252 – 254Combined sources3
Helixi259 – 267Combined sources9
Helixi272 – 278Combined sources7
Helixi282 – 290Combined sources9
Beta strandi292 – 296Combined sources5
Beta strandi300 – 306Combined sources7
Helixi309 – 318Combined sources10
Helixi327 – 337Combined sources11
Beta strandi339 – 343Combined sources5
Helixi344 – 351Combined sources8
Helixi353 – 355Combined sources3
Helixi373 – 379Combined sources7
Helixi386 – 389Combined sources4
Helixi391 – 408Combined sources18
Turni409 – 411Combined sources3
Helixi419 – 422Combined sources4

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...

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.
OMAiGPSTWQF.
OrthoDBiEOG092C2LSI.

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)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.

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. 250 interactors.
DIPiDIP-1957N.
IntActiP39008. 36 interactors.
MINTiMINT-405477.

PTM databases

iPTMnetiP39008.

Proteomic databases

MaxQBiP39008.
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.
OMAiGPSTWQF.
OrthoDBiEOG092C2LSI.

Enzyme and pathway databases

BioCyciYEAST:G3O-33358-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP39008.
PROiP39008.

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...

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: November 2, 2016
This is version 157 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

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 one 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.