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P29468

- PAP_YEAST

UniProt

P29468 - PAP_YEAST

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Protein

Poly(A) polymerase

Gene

PAP1

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

Mg2+1 Publication, Mn2+1 PublicationNote: 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 – 1541ATP1 Publication
Binding sitei215 – 2151ATP1 Publication
Binding sitei224 – 2241ATP1 Publication
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 – 893ATP1 Publication
Nucleotide bindingi99 – 1024ATP1 Publication
Nucleotide bindingi100 – 1023ATP1 Publication
Nucleotide bindingi233 – 2342ATP1 Publication

GO - Molecular functioni

  1. ATP binding Source: UniProtKB
  2. magnesium ion binding Source: UniProtKB
  3. polynucleotide adenylyltransferase activity Source: UniProtKB
  4. 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 RRP6.6 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 – 73Combined sources
Beta strandi8 – 103Combined sources
Helixi20 – 3516Combined sources
Helixi42 – 6928Combined sources
Helixi74 – 796Combined sources
Beta strandi83 – 875Combined sources
Helixi88 – 925Combined sources
Beta strandi101 – 1077Combined sources
Helixi113 – 12513Combined sources
Beta strandi130 – 1367Combined sources
Beta strandi139 – 1413Combined sources
Beta strandi143 – 1486Combined sources
Beta strandi151 – 1599Combined sources
Beta strandi161 – 1633Combined sources
Helixi174 – 1774Combined sources
Helixi182 – 20019Combined sources
Helixi204 – 22017Combined sources
Helixi226 – 2283Combined sources
Helixi233 – 24614Combined sources
Helixi252 – 26514Combined sources
Beta strandi272 – 2754Combined sources
Beta strandi281 – 2833Combined sources
Turni289 – 2913Combined sources
Helixi293 – 2964Combined sources
Beta strandi305 – 3084Combined sources
Turni312 – 3154Combined sources
Helixi318 – 33922Combined sources
Helixi345 – 3484Combined sources
Helixi354 – 3574Combined sources
Beta strandi359 – 37012Combined sources
Helixi372 – 39423Combined sources
Beta strandi399 – 4046Combined sources
Beta strandi409 – 4146Combined sources
Beta strandi417 – 4193Combined sources
Helixi420 – 4278Combined sources
Helixi431 – 4344Combined sources
Helixi435 – 4384Combined sources
Turni444 – 4463Combined sources
Helixi451 – 4555Combined sources
Beta strandi458 – 47013Combined sources
Beta strandi475 – 4773Combined sources
Helixi482 – 49413Combined sources
Turni497 – 5004Combined sources
Beta strandi502 – 51312Combined sources
Helixi514 – 5163Combined sources
Helixi519 – 5213Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP29468.

Family & Domainsi

Sequence similaritiesi

Belongs to the poly(A) polymerase family.Curated

Phylogenomic databases

eggNOGiCOG5186.
GeneTreeiENSGT00390000017928.
HOGENOMiHOG000204376.
InParanoidiP29468.
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

        10         20         30         40         50
MSSQKVFGIT GPVSTVGATA AENKLNDSLI QELKKEGSFE TEQETANRVQ
60 70 80 90 100
VLKILQELAQ RFVYEVSKKK NMSDGMARDA GGKIFTYGSY RLGVHGPGSD
110 120 130 140 150
IDTLVVVPKH VTREDFFTVF DSLLRERKEL DEIAPVPDAF VPIIKIKFSG
160 170 180 190 200
ISIDLICARL DQPQVPLSLT LSDKNLLRNL DEKDLRALNG TRVTDEILEL
210 220 230 240 250
VPKPNVFRIA LRAIKLWAQR RAVYANIFGF PGGVAWAMLV ARICQLYPNA
260 270 280 290 300
CSAVILNRFF IILSEWNWPQ PVILKPIEDG PLQVRVWNPK IYAQDRSHRM
310 320 330 340 350
PVITPAYPSM CATHNITEST KKVILQEFVR GVQITNDIFS NKKSWANLFE
360 370 380 390 400
KNDFFFRYKF YLEITAYTRG SDEQHLKWSG LVESKVRLLV MKLEVLAGIK
410 420 430 440 450
IAHPFTKPFE SSYCCPTEDD YEMIQDKYGS HKTETALNAL KLVTDENKEE
460 470 480 490 500
ESIKDAPKAY LSTMYIGLDF NIENKKEKVD IHIPCTEFVN LCRSFNEDYG
510 520 530 540 550
DHKVFNLALR FVKGYDLPDE VFDENEKRPS KKSKRKNLDA RHETVKRSKS
560
DAASGDNING TTAAVDVN
Length:568
Mass (Da):64,552
Last modified:April 1, 1993 - v1
Checksum:i759DE5210DC8D881
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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.
InParanoidi P29468.
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: November 26, 2014
This is version 142 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.1 Publication

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