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P29468

- PAP_YEAST

UniProt

P29468 - PAP_YEAST

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Protein

Poly(A) polymerase

Gene
PAP1, YKR002W
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Polymerase component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB.2 Publications

Catalytic activityi

ATP + RNA(n) = diphosphate + RNA(n+1).2 Publications

Cofactori

Binds 2 magnesium ions. Also active with manganese.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi100 – 1001Magnesium 1; catalytic
Metal bindingi100 – 1001Magnesium 2; catalytic
Metal bindingi102 – 1021Magnesium 1; catalytic
Metal bindingi102 – 1021Magnesium 2; catalytic
Sitei140 – 1401Interaction with RNA
Sitei145 – 1451Interaction with RNA
Metal bindingi154 – 1541Magnesium 2; catalytic
Binding sitei154 – 1541ATP
Binding sitei215 – 2151ATP
Binding sitei224 – 2241ATP
Sitei294 – 2941Interaction with RNA
Sitei314 – 3141Interaction with RNA
Sitei315 – 3151Interaction with RNA
Sitei387 – 3871Interaction with RNA
Sitei392 – 3921Interaction with RNA
Sitei487 – 4871Interaction with RNA

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi87 – 893ATP
Nucleotide bindingi99 – 1024ATP
Nucleotide bindingi100 – 1023ATP
Nucleotide bindingi233 – 2342ATP

GO - Molecular functioni

  1. ATP binding Source: UniProtKB
  2. magnesium ion binding Source: UniProtKB
  3. polynucleotide adenylyltransferase activity Source: UniProtKB
  4. protein binding Source: IntAct
  5. RNA binding Source: UniProtKB-KW

GO - Biological processi

  1. mRNA polyadenylation Source: SGD
  2. RNA polyadenylation Source: UniProtKB
  3. snoRNA polyadenylation Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-31980-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Poly(A) polymerase (EC:2.7.7.19)
Short name:
PAP
Alternative name(s):
Polynucleotide adenylyltransferase
Gene namesi
Name:PAP1
Ordered Locus Names:YKR002W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XI

Organism-specific databases

CYGDiYKR002w.
SGDiS000001710. PAP1.

Subcellular locationi

Nucleus 2 Publications

GO - Cellular componenti

  1. mRNA cleavage and polyadenylation specificity factor complex Source: SGD
  2. nucleoplasm Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi154 – 1541D → A: Loss of enzyme activity. 1 Publication
Mutagenesisi189 – 1891N → A: Slightly reduced rate of adenylyltransfer. 1 Publication
Mutagenesisi215 – 2151K → A: Reduces rate of adenylyltransfer about four-fold. 1 Publication
Mutagenesisi226 – 2261N → A: Reduces rate of adenylyltransfer by half. 1 Publication
Mutagenesisi485 – 4851C → R: Abolishes interaction with FIP1; when associated with Y-489. 1 Publication
Mutagenesisi489 – 4891V → Y: Abolishes interaction with FIP1; when associated with R-485. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 568568Poly(A) polymerasePRO_0000051621Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei452 – 4521Phosphoserine1 Publication
Modified residuei550 – 5501Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP29468.
PaxDbiP29468.
PeptideAtlasiP29468.

Expressioni

Gene expression databases

GenevestigatoriP29468.

Interactioni

Subunit structurei

Component of the cleavage and polyadenylation factor (CPF) complex, which is composed of PTI1, SYC1, SSU72, GLC7, MPE1, REF2, PFS2, PTA1, YSH1/BRR5, SWD2, CFT2/YDH1, YTH1, CFT1/YHH1, FIP1 and PAP1. Interacts with FIR1 and RRP6.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CFT1Q066327EBI-12917,EBI-32872
FIP1P4597611EBI-12917,EBI-6940
NAB6Q037352EBI-12917,EBI-27955
PTA1Q0132910EBI-12917,EBI-14145

Protein-protein interaction databases

BioGridi34134. 47 interactions.
DIPiDIP-2297N.
IntActiP29468. 28 interactions.
MINTiMINT-375429.
STRINGi4932.YKR002W.

Structurei

Secondary structure

1
568
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 73
Beta strandi8 – 103
Helixi20 – 3516
Helixi42 – 6928
Helixi74 – 796
Beta strandi83 – 875
Helixi88 – 925
Beta strandi101 – 1077
Helixi113 – 12513
Beta strandi130 – 1367
Beta strandi139 – 1413
Beta strandi143 – 1486
Beta strandi151 – 1599
Beta strandi161 – 1633
Helixi174 – 1774
Helixi182 – 20019
Helixi204 – 22017
Helixi226 – 2283
Helixi233 – 24614
Helixi252 – 26514
Beta strandi272 – 2754
Beta strandi281 – 2833
Turni289 – 2913
Helixi293 – 2964
Beta strandi305 – 3084
Turni312 – 3154
Helixi318 – 33922
Helixi345 – 3484
Helixi354 – 3574
Beta strandi359 – 37012
Helixi372 – 39423
Beta strandi399 – 4046
Beta strandi409 – 4146
Beta strandi417 – 4193
Helixi420 – 4278
Helixi431 – 4344
Helixi435 – 4384
Turni444 – 4463
Helixi451 – 4555
Beta strandi458 – 47013
Beta strandi475 – 4773
Helixi482 – 49413
Turni497 – 5004
Beta strandi502 – 51312
Helixi514 – 5163
Helixi519 – 5213

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FA0X-ray2.60A/B1-537[»]
2HHPX-ray1.80A1-530[»]
2O1PX-ray2.70A/B1-538[»]
2Q66X-ray1.80A5-529[»]
3C66X-ray2.60A/B1-526[»]
ProteinModelPortaliP29468.
SMRiP29468. Positions 3-531.

Miscellaneous databases

EvolutionaryTraceiP29468.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG5186.
GeneTreeiENSGT00390000017928.
HOGENOMiHOG000204376.
KOiK14376.
OMAiMSDGMAR.
OrthoDBiEOG7M6DHG.

Family and domain databases

Gene3Di3.30.70.590. 1 hit.
InterProiIPR002934. Nucleotidyltransferase.
IPR011068. NuclTrfase_I_C.
IPR007012. PolA_pol_cen_dom.
IPR007010. PolA_pol_RNA-bd_dom.
IPR014492. PolyA_polymerase.
[Graphical view]
PfamiPF01909. NTP_transf_2. 1 hit.
PF04928. PAP_central. 1 hit.
PF04926. PAP_RNA-bind. 1 hit.
[Graphical view]
PIRSFiPIRSF018425. PolyA_polymerase. 1 hit.
SUPFAMiSSF55003. SSF55003. 1 hit.

Sequencei

Sequence statusi: Complete.

P29468-1 [UniParc]FASTAAdd to Basket

« Hide

MSSQKVFGIT GPVSTVGATA AENKLNDSLI QELKKEGSFE TEQETANRVQ    50
VLKILQELAQ RFVYEVSKKK NMSDGMARDA GGKIFTYGSY RLGVHGPGSD 100
IDTLVVVPKH VTREDFFTVF DSLLRERKEL DEIAPVPDAF VPIIKIKFSG 150
ISIDLICARL DQPQVPLSLT LSDKNLLRNL DEKDLRALNG TRVTDEILEL 200
VPKPNVFRIA LRAIKLWAQR RAVYANIFGF PGGVAWAMLV ARICQLYPNA 250
CSAVILNRFF IILSEWNWPQ PVILKPIEDG PLQVRVWNPK IYAQDRSHRM 300
PVITPAYPSM CATHNITEST KKVILQEFVR GVQITNDIFS NKKSWANLFE 350
KNDFFFRYKF YLEITAYTRG SDEQHLKWSG LVESKVRLLV MKLEVLAGIK 400
IAHPFTKPFE SSYCCPTEDD YEMIQDKYGS HKTETALNAL KLVTDENKEE 450
ESIKDAPKAY LSTMYIGLDF NIENKKEKVD IHIPCTEFVN LCRSFNEDYG 500
DHKVFNLALR FVKGYDLPDE VFDENEKRPS KKSKRKNLDA RHETVKRSKS 550
DAASGDNING TTAAVDVN 568
Length:568
Mass (Da):64,552
Last modified:April 1, 1993 - v1
Checksum:i759DE5210DC8D881
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X60307 Genomic DNA. Translation: CAA42852.1.
X65124 Genomic DNA. Translation: CAA46250.1.
Z28227 Genomic DNA. Translation: CAA82072.1.
BK006944 Genomic DNA. Translation: DAA09158.1.
PIRiS19031.
RefSeqiNP_012927.3. NM_001179792.3.

Genome annotation databases

EnsemblFungiiYKR002W; YKR002W; YKR002W.
GeneIDi853871.
KEGGisce:YKR002W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X60307 Genomic DNA. Translation: CAA42852.1 .
X65124 Genomic DNA. Translation: CAA46250.1 .
Z28227 Genomic DNA. Translation: CAA82072.1 .
BK006944 Genomic DNA. Translation: DAA09158.1 .
PIRi S19031.
RefSeqi NP_012927.3. NM_001179792.3.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1FA0 X-ray 2.60 A/B 1-537 [» ]
2HHP X-ray 1.80 A 1-530 [» ]
2O1P X-ray 2.70 A/B 1-538 [» ]
2Q66 X-ray 1.80 A 5-529 [» ]
3C66 X-ray 2.60 A/B 1-526 [» ]
ProteinModelPortali P29468.
SMRi P29468. Positions 3-531.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 34134. 47 interactions.
DIPi DIP-2297N.
IntActi P29468. 28 interactions.
MINTi MINT-375429.
STRINGi 4932.YKR002W.

Proteomic databases

MaxQBi P29468.
PaxDbi P29468.
PeptideAtlasi P29468.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YKR002W ; YKR002W ; YKR002W .
GeneIDi 853871.
KEGGi sce:YKR002W.

Organism-specific databases

CYGDi YKR002w.
SGDi S000001710. PAP1.

Phylogenomic databases

eggNOGi COG5186.
GeneTreei ENSGT00390000017928.
HOGENOMi HOG000204376.
KOi K14376.
OMAi MSDGMAR.
OrthoDBi EOG7M6DHG.

Enzyme and pathway databases

BioCyci YEAST:G3O-31980-MONOMER.

Miscellaneous databases

EvolutionaryTracei P29468.
NextBioi 975142.
PROi P29468.

Gene expression databases

Genevestigatori P29468.

Family and domain databases

Gene3Di 3.30.70.590. 1 hit.
InterProi IPR002934. Nucleotidyltransferase.
IPR011068. NuclTrfase_I_C.
IPR007012. PolA_pol_cen_dom.
IPR007010. PolA_pol_RNA-bd_dom.
IPR014492. PolyA_polymerase.
[Graphical view ]
Pfami PF01909. NTP_transf_2. 1 hit.
PF04928. PAP_central. 1 hit.
PF04926. PAP_RNA-bind. 1 hit.
[Graphical view ]
PIRSFi PIRSF018425. PolyA_polymerase. 1 hit.
SUPFAMi SSF55003. SSF55003. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and expression of the essential gene for poly(A) polymerase from S. cerevisiae."
    Lingner J., Kellermann J., Keller W.
    Nature 354:496-498(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
    Strain: ATCC 204510 / AB320.
  2. "DNA sequencing and analysis of a 24.7 kb segment encompassing centromere CEN11 of Saccharomyces cerevisiae reveals nine previously unknown open reading frames."
    Duesterhoeft A., Philippsen P.
    Yeast 8:749-759(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. "Complete DNA sequence of yeast chromosome XI."
    Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C.
    , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W.
    Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "The Uba2 and Ufd1 proteins of Saccharomyces cerevisiae interact with poly(A) polymerase and affect the polyadenylation activity of cell extracts."
    del Olmo M., Mizrahi N., Gross S., Moore C.L.
    Mol. Gen. Genet. 255:209-218(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH FIR1.
  6. "A nuclear 3'-5' exonuclease involved in mRNA degradation interacts with Poly(A) polymerase and the hnRNA protein Npl3p."
    Burkard K.T.D., Butler J.S.
    Mol. Cell. Biol. 20:604-616(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RRP6.
  7. "Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3'-ends."
    Nedea E., He X., Kim M., Pootoolal J., Zhong G., Canadien V., Hughes T., Buratowski S., Moore C.L., Greenblatt J.
    J. Biol. Chem. 278:33000-33010(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE CPF COMPLEX, SUBCELLULAR LOCATION, IDENTIFICATION BY MASS SPECTROMETRY.
  8. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  10. "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-452, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-550, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "Structure of yeast poly(A) polymerase alone and in complex with 3'-dATP."
    Bard J., Zhelkovsky A.M., Helmling S., Earnest T.N., Moore C.L., Bohm A.
    Science 289:1346-1349(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 1-537 IN COMPLEX WITH ATP ANALOG AND MANGANESE IONS.
  13. "X-ray crystallographic and steady state fluorescence characterization of the protein dynamics of yeast polyadenylate polymerase."
    Balbo P.B., Toth J., Bohm A.
    J. Mol. Biol. 366:1401-1415(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 1-530.
  14. "Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis."
    Balbo P.B., Bohm A.
    Structure 15:1117-1131(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 5-529 OF MUTANT ALA-154 IN COMPLEX WITH ATP; MAGNESIUM IONS AND OLIGONUCLEOTIDE, CATALYTIC ACTIVITY, FUNCTION, COFACTOR, MUTAGENESIS OF ASP-154; ASN-189; LYS-215 AND ASN-226.
  15. "Structure of yeast poly(A) polymerase in complex with a peptide from Fip1, an intrinsically disordered protein."
    Meinke G., Ezeokonkwo C., Balbo P., Stafford W., Moore C., Bohm A.
    Biochemistry 47:6859-6869(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 1-537 IN COMPLEX WITH FIP1, FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH FIP1, MUTAGENESIS OF CYS-485 AND VAL-489.

Entry informationi

Entry nameiPAP_YEAST
AccessioniPrimary (citable) accession number: P29468
Secondary accession number(s): D6VXT8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: April 1, 1993
Last modified: July 9, 2014
This is version 139 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 17100 molecules/cell in log phase SD medium.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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 XI
    Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

External Data

Dasty 3

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