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Protein

Poly(A) polymerase

Gene

PAP1

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

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)DescriptionActionsGraphical viewLength
Metal bindingi100Magnesium 1; catalytic1
Metal bindingi100Magnesium 2; catalytic1
Metal bindingi102Magnesium 1; catalytic1
Metal bindingi102Magnesium 2; catalytic1
Metal bindingi154Magnesium 2; catalytic1
Binding sitei154ATP1 Publication1
Binding sitei215ATP1 Publication1
Binding sitei224ATP1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi87 – 89ATP1 Publication3
Nucleotide bindingi99 – 102ATP1 Publication4
Nucleotide bindingi100 – 102ATP1 Publication3
Nucleotide bindingi233 – 234ATP1 Publication2

GO - Molecular functioni

  • ATP binding Source: UniProtKB
  • magnesium ion binding Source: UniProtKB
  • polynucleotide adenylyltransferase activity Source: UniProtKB
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

  • mRNA polyadenylation Source: SGD
  • RNA polyadenylation Source: UniProtKB
  • 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.
BRENDAi2.7.7.19. 984.

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
Proteomesi
  • UP000002311 Componenti: Chromosome XI

Organism-specific databases

EuPathDBiFungiDB:YKR002W.
SGDiS000001710. PAP1.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi154D → A: Loss of enzyme activity. 1 Publication1
Mutagenesisi189N → A: Slightly reduced rate of adenylyltransfer. 1 Publication1
Mutagenesisi215K → A: Reduces rate of adenylyltransfer about four-fold. 1 Publication1
Mutagenesisi226N → A: Reduces rate of adenylyltransfer by half. 1 Publication1
Mutagenesisi485C → R: Abolishes interaction with FIP1; when associated with Y-489. 1 Publication1
Mutagenesisi489V → Y: Abolishes interaction with FIP1; when associated with R-485. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000516211 – 568Poly(A) polymeraseAdd BLAST568

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei452PhosphoserineCombined sources1
Modified residuei550PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP29468.
PRIDEiP29468.

PTM databases

iPTMnetiP29468.

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei140Interaction with RNA1
Sitei145Interaction with RNA1
Sitei294Interaction with RNA1
Sitei314Interaction with RNA1
Sitei315Interaction with RNA1
Sitei387Interaction with RNA1
Sitei392Interaction with RNA1
Sitei487Interaction with RNA1

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. 49 interactors.
DIPiDIP-2297N.
IntActiP29468. 29 interactors.
MINTiMINT-375429.

Structurei

Secondary structure

1568
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 7Combined sources3
Beta strandi8 – 10Combined sources3
Helixi20 – 35Combined sources16
Helixi42 – 69Combined sources28
Helixi74 – 79Combined sources6
Beta strandi83 – 87Combined sources5
Helixi88 – 92Combined sources5
Beta strandi101 – 107Combined sources7
Helixi113 – 125Combined sources13
Beta strandi130 – 136Combined sources7
Beta strandi139 – 141Combined sources3
Beta strandi143 – 148Combined sources6
Beta strandi151 – 159Combined sources9
Beta strandi161 – 163Combined sources3
Helixi174 – 177Combined sources4
Helixi182 – 200Combined sources19
Helixi204 – 220Combined sources17
Helixi226 – 228Combined sources3
Helixi233 – 246Combined sources14
Helixi252 – 265Combined sources14
Beta strandi272 – 275Combined sources4
Beta strandi281 – 283Combined sources3
Turni289 – 291Combined sources3
Helixi293 – 296Combined sources4
Beta strandi305 – 308Combined sources4
Turni312 – 315Combined sources4
Helixi318 – 339Combined sources22
Helixi345 – 348Combined sources4
Helixi354 – 357Combined sources4
Beta strandi359 – 370Combined sources12
Helixi372 – 394Combined sources23
Beta strandi399 – 404Combined sources6
Beta strandi409 – 414Combined sources6
Beta strandi417 – 419Combined sources3
Helixi420 – 427Combined sources8
Beta strandi428 – 430Combined sources3
Helixi431 – 434Combined sources4
Helixi435 – 439Combined sources5
Turni444 – 446Combined sources3
Helixi451 – 455Combined sources5
Beta strandi458 – 470Combined sources13
Beta strandi475 – 477Combined sources3
Helixi482 – 494Combined sources13
Turni497 – 500Combined sources4
Beta strandi502 – 513Combined sources12
Helixi514 – 516Combined sources3
Helixi519 – 521Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP29468.

Family & Domainsi

Sequence similaritiesi

Belongs to the poly(A) polymerase family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000017928.
HOGENOMiHOG000204376.
InParanoidiP29468.
KOiK14376.
OMAiAYDAEPH.
OrthoDBiEOG092C1VMQ.

Family and domain databases

Gene3Di3.30.70.590. 1 hit.
InterProiIPR011068. NuclTrfase_I_C.
IPR007012. PolA_pol_cen_dom.
IPR007010. PolA_pol_RNA-bd_dom.
IPR014492. PolyA_polymerase.
IPR002934. Polymerase_NTP_transf_dom.
[Graphical view]
PANTHERiPTHR10682. PTHR10682. 2 hits.
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.
PIRiS19031.
RefSeqiNP_012927.3. NM_001179792.3.

3D structure databases

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

Protein-protein interaction databases

BioGridi34134. 49 interactors.
DIPiDIP-2297N.
IntActiP29468. 29 interactors.
MINTiMINT-375429.

PTM databases

iPTMnetiP29468.

Proteomic databases

MaxQBiP29468.
PRIDEiP29468.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YKR002W.
SGDiS000001710. PAP1.

Phylogenomic databases

GeneTreeiENSGT00390000017928.
HOGENOMiHOG000204376.
InParanoidiP29468.
KOiK14376.
OMAiAYDAEPH.
OrthoDBiEOG092C1VMQ.

Enzyme and pathway databases

BioCyciYEAST:G3O-31980-MONOMER.
BRENDAi2.7.7.19. 984.

Miscellaneous databases

EvolutionaryTraceiP29468.
PROiP29468.

Family and domain databases

Gene3Di3.30.70.590. 1 hit.
InterProiIPR011068. NuclTrfase_I_C.
IPR007012. PolA_pol_cen_dom.
IPR007010. PolA_pol_RNA-bd_dom.
IPR014492. PolyA_polymerase.
IPR002934. Polymerase_NTP_transf_dom.
[Graphical view]
PANTHERiPTHR10682. PTHR10682. 2 hits.
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.
ProtoNetiSearch...

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 2, 2016
This is version 160 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

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.