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Protein

Poly(A) RNA polymerase protein 2

Gene

PAP2

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

Catalytic subunit of the TRAMP complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates like cryptic transcripts generated by RNA polymerase II and III, or hypomethylated pre-tRNAi-Met. Polyadenylates RNA processing and degradation intermediates of snRNAs, snoRNAs and mRNAs that accumulate in strains lacking a functional exosome. TRF4 is also required for proper nuclear division in mitosis, DNA damage repair and sister chromatid cohesion. Involved in the regulation of histone mRNA levels. May mediate mitotic chromosome condensation.17 Publications

Catalytic activityi

ATP + RNA(n) = diphosphate + RNA(n+1).1 Publication

Cofactori

Mg2+By similarity, Mn2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi236Magnesium or manganese; catalyticBy similarity1
Metal bindingi238Magnesium or manganese; catalyticBy similarity1

GO - Molecular functioni

  • 5'-deoxyribose-5-phosphate lyase activity Source: SGD
  • metal ion binding Source: UniProtKB-KW
  • polynucleotide adenylyltransferase activity Source: UniProtKB

GO - Biological processi

  • base-excision repair Source: SGD
  • cell division Source: UniProtKB-KW
  • histone mRNA catabolic process Source: SGD
  • meiotic DNA double-strand break formation Source: SGD
  • mitotic nuclear division Source: UniProtKB-KW
  • ncRNA polyadenylation Source: UniProtKB
  • negative regulation of DNA recombination Source: SGD
  • nuclear mRNA surveillance of mRNA 3'-end processing Source: SGD
  • nuclear polyadenylation-dependent antisense transcript catabolic process Source: SGD
  • nuclear polyadenylation-dependent CUT catabolic process Source: SGD
  • nuclear polyadenylation-dependent mRNA catabolic process Source: SGD
  • nuclear polyadenylation-dependent rRNA catabolic process Source: SGD
  • nuclear polyadenylation-dependent snoRNA catabolic process Source: SGD
  • nuclear polyadenylation-dependent snRNA catabolic process Source: SGD
  • nuclear polyadenylation-dependent tRNA catabolic process Source: SGD
  • polyadenylation-dependent mRNA catabolic process Source: SGD
  • polyadenylation-dependent snoRNA 3'-end processing Source: SGD
  • snoRNA polyadenylation Source: SGD
  • tRNA modification Source: SGD
  • U4 snRNA 3'-end processing Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Cell cycle, Cell division, Mitosis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33512-MONOMER.
BRENDAi4.2.99.B1. 984.

Names & Taxonomyi

Protein namesi
Recommended name:
Poly(A) RNA polymerase protein 2 (EC:2.7.7.-)
Alternative name(s):
DNA polymerase kappa
DNA polymerase sigma
Topoisomerase 1-related protein TRF4
Gene namesi
Name:PAP2
Synonyms:TRF4
Ordered Locus Names:YOL115W
ORF Names:HRC584, O0716
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOL115W.
SGDiS000005475. PAP2.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
  • nucleolus Source: SGD
  • nucleus Source: SGD
  • TRAMP complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi131 – 133EDE → AAA in TRF4-131; slow growth. 1 Publication3
Mutagenesisi140 – 142ERE → AAA in TRF4-140; slow growth. 1 Publication3
Mutagenesisi182 – 185EIKD → AIAA in TRF4-182; lethal. 1 Publication4
Mutagenesisi194R → A in TRF4-194; lethal; when associated with A-195; A-196 and A-198. 1
Mutagenesisi195 – 198EEIE → AIAA in TRF4-194; lethal. 4
Mutagenesisi217 – 219DAD → AAA in TRF4-217; slow growth. 1 Publication3
Mutagenesisi224 – 225GS → AA in TRF4-224; lethal. 1 Publication2
Mutagenesisi236 – 238DID → AIA in TRF4-236; lethal. 3 Publications3
Mutagenesisi275 – 277KAR → AAA in TRF4-275; temperature sensitive. 1 Publication3
Mutagenesisi282K → A in TRF4-282; lethal; when associated with A-285. 1
Mutagenesisi285E → A in TRF4-282; lethal; when associated with A-282. 1
Mutagenesisi309 – 310RE → AA in TRF4-309; lethal. 1 Publication2
Mutagenesisi332 – 333RR → AA in TRF4-332; temperature sensitive. 1 Publication2
Mutagenesisi378E → A in TRF4-378; lethal; when associated with A-381. 1
Mutagenesisi381E → A in TRF4-378; lethal; when associated with A-378. 1
Mutagenesisi425D → A in TRF4-425; lethal; when associated with A-428 and A-429. 1
Mutagenesisi428 – 429DE → AA in TRF4-425; lethal; when associated with A-425. 2
Mutagenesisi444 – 445KK → AA in TRF4-444; lethal. 1 Publication2
Mutagenesisi467 – 469KDR → AAA in TRF4-467; temperature sensitive. 1 Publication3
Mutagenesisi486 – 487RD → AA in TRF4-486; lethal. 2
Mutagenesisi490 – 492DER → AAA in TRF4-486; lethal. 3
Mutagenesisi502E → A in TRF4-502; lethal; when associated with A-504. 1
Mutagenesisi504E → A in TRF4-502; lethal; when associated with A-502. 1
Mutagenesisi508 – 510KKR → AAA in TRF4-508; lethal. 1 Publication3
Mutagenesisi559 – 560KR → AA in TRF4-559; slow growth. 1 Publication2
Mutagenesisi560R → A in TRF4-559; slow growth; when associated with A-559. 1
Mutagenesisi572 – 574EDD → AAA in TRF4-572; slow growth. 1 Publication3

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001203141 – 584Poly(A) RNA polymerase protein 2Add BLAST584

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei570PhosphoserineBy similarity1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP53632.
PRIDEiP53632.

PTM databases

iPTMnetiP53632.

Interactioni

Subunit structurei

Component of the TRAMP complex (also called TRF4 complex) composed of at least HUL4, MTR4, PAP2/TRF4 and either AIR1 or AIR2. Interacts with NOP53 and POL2. Interacts directly with AIR2.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
AIR1P405075EBI-19517,EBI-25083
AIR2Q1247612EBI-19517,EBI-31475
MTR4P4704710EBI-19517,EBI-11592

Protein-protein interaction databases

BioGridi34285. 401 interactors.
DIPiDIP-4214N.
IntActiP53632. 11 interactors.
MINTiMINT-500696.

Structurei

Secondary structure

1584
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi122 – 125Combined sources4
Helixi162 – 164Combined sources3
Helixi175 – 189Combined sources15
Helixi194 – 212Combined sources19
Beta strandi220 – 224Combined sources5
Turni225 – 229Combined sources5
Beta strandi237 – 241Combined sources5
Helixi247 – 249Combined sources3
Helixi250 – 263Combined sources14
Beta strandi271 – 277Combined sources7
Beta strandi279 – 285Combined sources7
Turni286 – 289Combined sources4
Beta strandi290 – 297Combined sources8
Helixi303 – 313Combined sources11
Helixi318 – 331Combined sources14
Helixi337 – 339Combined sources3
Helixi344 – 356Combined sources13
Helixi359 – 362Combined sources4
Helixi368 – 370Combined sources3
Helixi372 – 385Combined sources14
Turni389 – 391Combined sources3
Beta strandi392 – 399Combined sources8
Beta strandi401 – 405Combined sources5
Helixi406 – 408Combined sources3
Helixi410 – 412Combined sources3
Beta strandi418 – 420Combined sources3
Beta strandi423 – 425Combined sources3
Beta strandi428 – 432Combined sources5
Turni433 – 436Combined sources4
Helixi440 – 462Combined sources23
Helixi466 – 469Combined sources4
Turni476 – 478Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2MOWNMR-B573-584[»]
3NYBX-ray2.70A161-481[»]
4U4CX-ray2.40B111-160[»]
ProteinModelPortaliP53632.
SMRiP53632.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP53632.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini371 – 431PAP-associatedAdd BLAST61

Sequence similaritiesi

Belongs to the DNA polymerase type-B-like family.Curated
Contains 1 PAP-associated domain.Curated

Phylogenomic databases

GeneTreeiENSGT00400000022055.
HOGENOMiHOG000246586.
InParanoidiP53632.
KOiK03514.
OMAiTNNISRG.
OrthoDBiEOG092C144L.

Family and domain databases

InterProiIPR002058. PAP_assoc.
IPR002934. Polymerase_NTP_transf_dom.
[Graphical view]
PfamiPF01909. NTP_transf_2. 1 hit.
PF03828. PAP_assoc. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P53632-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGAKSVTASS SKKIKNRHNG KVKKSKKIKK VRKPQKSISL NDENEVEILP
60 70 80 90 100
SRNEQETNKL PKDHVTADGI LVLEHKSDDD EGFDVYDGHF DNPTDIPSTT
110 120 130 140 150
EESKTPSLAV HGDEKDLANN DDFISLSASS EDEQAEQEEE REKQELEIKK
160 170 180 190 200
EKQKEILNTD YPWILNHDHS KQKEISDWLT FEIKDFVAYI SPSREEIEIR
210 220 230 240 250
NQTISTIREA VKQLWPDADL HVFGSYSTDL YLPGSDIDCV VTSELGGKES
260 270 280 290 300
RNNLYSLASH LKKKNLATEV EVVAKARVPI IKFVEPHSGI HIDVSFERTN
310 320 330 340 350
GIEAAKLIRE WLDDTPGLRE LVLIVKQFLH ARRLNNVHTG GLGGFSIICL
360 370 380 390 400
VFSFLHMHPR IITNEIDPKD NLGVLLIEFF ELYGKNFGYD DVALGSSDGY
410 420 430 440 450
PVYFPKSTWS AIQPIKNPFS LAIQDPGDES NNISRGSFNI RDIKKAFAGA
460 470 480 490 500
FDLLTNRCFE LHSATFKDRL GKSILGNVIK YRGKARDFKD ERGLVLNKAI
510 520 530 540 550
IENENYHKKR SRIIHDEDFA EDTVTSTATA TTTDDDYEIT NPPAKKAKIE
560 570 580
EKPESEPAKR NSGETYITVS SEDDDEDGYN PYTL
Length:584
Mass (Da):66,031
Last modified:October 1, 1996 - v1
Checksum:i8A58B29E4BFDC022
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U31355 Genomic DNA. Translation: AAC49091.1.
Z48149 Genomic DNA. Translation: CAA88145.1.
Z74857 Genomic DNA. Translation: CAA99134.1.
AY723865 Genomic DNA. Translation: AAU09782.1.
BK006948 Genomic DNA. Translation: DAA10668.1.
PIRiS51882.
RefSeqiNP_014526.1. NM_001183369.1.

Genome annotation databases

EnsemblFungiiYOL115W; YOL115W; YOL115W.
GeneIDi854034.
KEGGisce:YOL115W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U31355 Genomic DNA. Translation: AAC49091.1.
Z48149 Genomic DNA. Translation: CAA88145.1.
Z74857 Genomic DNA. Translation: CAA99134.1.
AY723865 Genomic DNA. Translation: AAU09782.1.
BK006948 Genomic DNA. Translation: DAA10668.1.
PIRiS51882.
RefSeqiNP_014526.1. NM_001183369.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2MOWNMR-B573-584[»]
3NYBX-ray2.70A161-481[»]
4U4CX-ray2.40B111-160[»]
ProteinModelPortaliP53632.
SMRiP53632.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34285. 401 interactors.
DIPiDIP-4214N.
IntActiP53632. 11 interactors.
MINTiMINT-500696.

PTM databases

iPTMnetiP53632.

Proteomic databases

MaxQBiP53632.
PRIDEiP53632.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOL115W; YOL115W; YOL115W.
GeneIDi854034.
KEGGisce:YOL115W.

Organism-specific databases

EuPathDBiFungiDB:YOL115W.
SGDiS000005475. PAP2.

Phylogenomic databases

GeneTreeiENSGT00400000022055.
HOGENOMiHOG000246586.
InParanoidiP53632.
KOiK03514.
OMAiTNNISRG.
OrthoDBiEOG092C144L.

Enzyme and pathway databases

BioCyciYEAST:G3O-33512-MONOMER.
BRENDAi4.2.99.B1. 984.

Miscellaneous databases

EvolutionaryTraceiP53632.
PROiP53632.

Family and domain databases

InterProiIPR002058. PAP_assoc.
IPR002934. Polymerase_NTP_transf_dom.
[Graphical view]
PfamiPF01909. NTP_transf_2. 1 hit.
PF03828. PAP_assoc. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPAP2_YEAST
AccessioniPrimary (citable) accession number: P53632
Secondary accession number(s): D6W1V2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: November 2, 2016
This is version 144 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 7550 molecules/cell in log phase SD medium.1 Publication

Caution

Was originally thought to have DNA polymerase activity.Curated

Keywords - Technical termi

3D-structure, Complete proteome, 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 XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: 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.