P39008 (POP2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	433 AA.
Sequence status	Complete.
Protein existence	Evidence 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 process	Transcription Transcription regulation
Cellular component	Cytoplasm Nucleus
Ligand	Magnesium Metal-binding RNA-binding
Molecular function	Activator Exonuclease Hydrolase Nuclease Repressor
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	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 transcription elongation from RNA polymerase II promoter Inferred from mutant phenotype PubMed 11404327. Source: SGD
Cellular_component	CCR4-NOT core complex Inferred from physical interaction Ref.8. Source: SGD cytoplasmic mRNA processing body Inferred from direct assay PubMed 18611963. Source: SGD mating projection tip Inferred from direct assay PubMed 19053807. Source: SGD nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	3'-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
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CAF40	P53829	8	EBI-13629,EBI-28306
CCR4	P31384	9	EBI-13629,EBI-4396
CDC39	P25655	8	EBI-13629,EBI-12139
DHH1	P39517	3	EBI-13629,EBI-158
MOT2	P34909	3	EBI-13629,EBI-12174

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 433

433

Poly(A) ribonuclease POP2

PRO_0000212849

Regions

Compositional bias

81 – 90

10

Poly-Gln

Compositional bias

111 – 125

15

Poly-Gln

Compositional bias

363 – 369

7

Poly-Gln

Sites

Metal binding

188

1

Divalent metal cation; catalytic Potential

Metal binding

190

1

Divalent metal cation; catalytic Potential

Metal binding

310

1

Divalent metal cation; catalytic Potential

Metal binding

394

1

Divalent metal cation; catalytic Potential

Amino acid modifications

Modified residue

39

1

Phosphoserine Ref.14

Modified residue

97

1

Phosphothreonine; by YAK1 Ref.12

Natural variations

Natural variant

41

1

K → Q in strain: A364A.

Natural variant

91

1

Q → QQQQQQQQQQQQQQQQQQ in strain: A364A.

Natural variant

118 – 122

5

Missing in strain: A364A.

Natural variant

278

1

L → S in strain: A364A.

Natural variant

412

1

K → M.

Experimental info

Mutagenesis

97

1

T → A: No cell-cycle stop in response to glucose deprivation. Ref.12

Mutagenesis

188

1

S → A: Abolishes poly(A) RNA degradation; when associated with A-190. Ref.15

Mutagenesis

190

1

E → A: Abolishes poly(A) RNA degradation; when associated with A-188. Ref.15

Secondary structure

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433

Helix Strand Turn

Details...

Helix

155 – 158

4

Beta strand

161 – 163

3

Turn

165 – 167

3

Helix

168 – 178

11

Turn

179 – 181

3

Beta strand

184 – 192

9

Beta strand

197 – 200

4

Helix

205 – 217

13

Beta strand

221 – 230

10

Beta strand

238 – 240

3

Beta strand

242 – 248

7

Turn

252 – 254

3

Helix

259 – 267

9

Helix

272 – 278

7

Helix

282 – 290

9

Beta strand

292 – 296

5

Beta strand

300 – 306

7

Helix

309 – 318

10

Helix

327 – 337

11

Beta strand

339 – 343

5

Helix

344 – 351

8

Helix

353 – 355

3

Helix

373 – 379

7

Helix

386 – 389

4

Helix

391 – 408

18

Turn

409 – 411

3

Helix

419 – 422

4

Sequences

	Sequence		Length	Mass (Da)
	P39008 [UniParc]. Last modified October 1, 1996. Version 2. Checksum: F3CAF97106A65933	FASTA	433	49,682
	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

References

	« Hide 'large scale' referencesShow '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. , 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]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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. , 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]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-39, MASS SPECTROMETRY.
[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.

PIR

S63383.

RefSeq

NP_014450.3. NM_001183229.3.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P39008.

SMR

P39008. Positions 149-428.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1957N.

IntAct

P39008. 34 interactions.

MINT

MINT-405477.

STRING

4932.YNR052C.

Proteomic databases

PaxDb

P39008.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YNR052C; YNR052C; YNR052C.

GeneID

855788.

KEGG

sce:YNR052C.

Organism-specific databases

CYGD

YNR052c.

SGD

S000005335. POP2.

Phylogenomic databases

eggNOG

COG5228.

GeneTree

ENSGT00390000000080.

HOGENOM

HOG000057134.

KO

K12581.

OMA

PRFSIFT.

OrthoDB

EOG4MGWHH.

Enzyme and pathway databases

BioCyc

YEAST:G3O-33358-MONOMER.

Gene expression databases

Genevestigator

P39008.

GermOnline

YNR052C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR006941. RNase_CAF1.
IPR012337. RNaseH-like_dom.
[Graphical view]

Pfam

PF04857. CAF1. 1 hit.
[Graphical view]

SUPFAM

SSF53098. RNaseH_fold. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P39008.

NextBio

980271.

Entry information

Entry name

POP2_YEAST

Accession

Primary (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:	May 29, 2013
This is version 127 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program