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P29468 (PAP_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 136. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Poly(A) polymerase

Short name=PAP
EC=2.7.7.19
Alternative name(s):
Polynucleotide adenylyltransferase
Gene names
Name:PAP1
Ordered Locus Names:YKR002W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length568 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.14 Ref.15

Catalytic activity

ATP + RNA(n) = diphosphate + RNA(n+1). Ref.14 Ref.15

Cofactor

Binds 2 magnesium ions. Also active with manganese. Ref.14

Subunit structure

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. Ref.5 Ref.6 Ref.7 Ref.15

Subcellular location

Nucleus Ref.7 Ref.8.

Miscellaneous

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

Sequence similarities

Belongs to the poly(A) polymerase family.

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 568568Poly(A) polymerase
PRO_0000051621

Regions

Nucleotide binding87 – 893ATP
Nucleotide binding99 – 1024ATP
Nucleotide binding100 – 1023ATP
Nucleotide binding233 – 2342ATP

Sites

Metal binding1001Magnesium 1; catalytic
Metal binding1001Magnesium 2; catalytic
Metal binding1021Magnesium 1; catalytic
Metal binding1021Magnesium 2; catalytic
Metal binding1541Magnesium 2; catalytic
Binding site1541ATP
Binding site2151ATP
Binding site2241ATP
Site1401Interaction with RNA
Site1451Interaction with RNA
Site2941Interaction with RNA
Site3141Interaction with RNA
Site3151Interaction with RNA
Site3871Interaction with RNA
Site3921Interaction with RNA
Site4871Interaction with RNA

Amino acid modifications

Modified residue4521Phosphoserine Ref.10
Modified residue5501Phosphoserine Ref.11

Experimental info

Mutagenesis1541D → A: Loss of enzyme activity. Ref.14
Mutagenesis1891N → A: Slightly reduced rate of adenylyltransfer. Ref.14
Mutagenesis2151K → A: Reduces rate of adenylyltransfer about four-fold. Ref.14
Mutagenesis2261N → A: Reduces rate of adenylyltransfer by half. Ref.14
Mutagenesis4851C → R: Abolishes interaction with FIP1; when associated with Y-489. Ref.15
Mutagenesis4891V → Y: Abolishes interaction with FIP1; when associated with R-485. Ref.15

Secondary structure

........................................................................................ 568
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P29468 [UniParc].

Last modified April 1, 1993. Version 1.
Checksum: 759DE5210DC8D881

FASTA56864,552
        10         20         30         40         50         60 
MSSQKVFGIT GPVSTVGATA AENKLNDSLI QELKKEGSFE TEQETANRVQ VLKILQELAQ 

        70         80         90        100        110        120 
RFVYEVSKKK NMSDGMARDA GGKIFTYGSY RLGVHGPGSD IDTLVVVPKH VTREDFFTVF 

       130        140        150        160        170        180 
DSLLRERKEL DEIAPVPDAF VPIIKIKFSG ISIDLICARL DQPQVPLSLT LSDKNLLRNL 

       190        200        210        220        230        240 
DEKDLRALNG TRVTDEILEL VPKPNVFRIA LRAIKLWAQR RAVYANIFGF PGGVAWAMLV 

       250        260        270        280        290        300 
ARICQLYPNA CSAVILNRFF IILSEWNWPQ PVILKPIEDG PLQVRVWNPK IYAQDRSHRM 

       310        320        330        340        350        360 
PVITPAYPSM CATHNITEST KKVILQEFVR GVQITNDIFS NKKSWANLFE KNDFFFRYKF 

       370        380        390        400        410        420 
YLEITAYTRG SDEQHLKWSG LVESKVRLLV MKLEVLAGIK IAHPFTKPFE SSYCCPTEDD 

       430        440        450        460        470        480 
YEMIQDKYGS HKTETALNAL KLVTDENKEE ESIKDAPKAY LSTMYIGLDF NIENKKEKVD 

       490        500        510        520        530        540 
IHIPCTEFVN LCRSFNEDYG DHKVFNLALR FVKGYDLPDE VFDENEKRPS KKSKRKNLDA 

       550        560 
RHETVKRSKS DAASGDNING TTAAVDVN 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
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]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[9]"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].
[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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X60307 Genomic DNA. Translation: CAA42852.1.
X65124 Genomic DNA. Translation: CAA46250.1.
Z28227 Genomic DNA. Translation: CAA82072.1.
BK006944 Genomic DNA. Translation: DAA09158.1.
PIRS19031.
RefSeqNP_012927.3. NM_001179792.3.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1FA0X-ray2.60A/B1-537[»]
2HHPX-ray1.80A1-530[»]
2O1PX-ray2.70A/B1-538[»]
2Q66X-ray1.80A5-529[»]
3C66X-ray2.60A/B1-537[»]
ProteinModelPortalP29468.
SMRP29468. Positions 3-531.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34134. 47 interactions.
DIPDIP-2297N.
IntActP29468. 28 interactions.
MINTMINT-375429.
STRING4932.YKR002W.

Proteomic databases

PaxDbP29468.
PeptideAtlasP29468.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYKR002W; YKR002W; YKR002W.
GeneID853871.
KEGGsce:YKR002W.

Organism-specific databases

CYGDYKR002w.
SGDS000001710. PAP1.

Phylogenomic databases

eggNOGCOG5186.
GeneTreeENSGT00390000017928.
HOGENOMHOG000204376.
KOK14376.
OMAMSDGMAR.
OrthoDBEOG7M6DHG.

Enzyme and pathway databases

BioCycYEAST:G3O-31980-MONOMER.

Gene expression databases

GenevestigatorP29468.

Family and domain databases

Gene3D3.30.70.590. 1 hit.
InterProIPR002934. Nucleotidyltransferase.
IPR011068. NuclTrfase_I_C.
IPR007012. PolA_pol_cen_dom.
IPR007010. PolA_pol_RNA-bd_dom.
IPR014492. PolyA_polymerase.
[Graphical view]
PfamPF01909. NTP_transf_2. 1 hit.
PF04928. PAP_central. 1 hit.
PF04926. PAP_RNA-bind. 1 hit.
[Graphical view]
PIRSFPIRSF018425. PolyA_polymerase. 1 hit.
SUPFAMSSF55003. SSF55003. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP29468.
NextBio975142.
PROP29468.

Entry information

Entry namePAP_YEAST
AccessionPrimary (citable) accession number: P29468
Secondary accession number(s): D6VXT8
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: April 1, 1993
Last modified: April 16, 2014
This is version 136 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XI

Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references