P29468 (PAP_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	568 AA.
Sequence status	Complete.
Protein existence	Evidence 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.13 Ref.14
Catalytic activity	ATP + RNA(n) = diphosphate + RNA(n+1). Ref.13 Ref.14
Cofactor	Binds 2 magnesium ions. Also active with manganese. Ref.13
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.14
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.

Ontologies

Keywords
Biological process	mRNA processing
Cellular component	Nucleus
Ligand	ATP-binding Magnesium Manganese Metal-binding Nucleotide-binding RNA-binding
Molecular function	Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	mRNA polyadenylation Inferred from direct assay Ref.1. Source: SGD snoRNA polyadenylation Inferred from genetic interaction PubMed 18951092. Source: SGD
Cellular_component	mRNA cleavage and polyadenylation specificity factor complex Inferred from direct assay Ref.7. Source: SGD
Molecular_function	ATP binding Inferred from direct assay Ref.13. Source: UniProtKB RNA binding Inferred from electronic annotation. Source: UniProtKB-KW magnesium ion binding Inferred from direct assay Ref.13. Source: UniProtKB polynucleotide adenylyltransferase activity Inferred from direct assay Ref.13. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 568

568

Poly(A) polymerase

PRO_0000051621

Regions

Nucleotide binding

87 – 89

3

ATP

Nucleotide binding

99 – 102

4

ATP

Nucleotide binding

100 – 102

3

ATP

Nucleotide binding

233 – 234

2

ATP

Sites

Metal binding

100

1

Magnesium 1; catalytic

Metal binding

100

1

Magnesium 2; catalytic

Metal binding

102

1

Magnesium 1; catalytic

Metal binding

102

1

Magnesium 2; catalytic

Metal binding

154

1

Magnesium 2; catalytic

Binding site

154

1

ATP

Binding site

215

1

ATP

Binding site

224

1

ATP

Site

140

1

Interaction with RNA

Site

145

1

Interaction with RNA

Site

294

1

Interaction with RNA

Site

314

1

Interaction with RNA

Site

315

1

Interaction with RNA

Site

387

1

Interaction with RNA

Site

392

1

Interaction with RNA

Site

487

1

Interaction with RNA

Amino acid modifications

Modified residue

452

1

Phosphoserine Ref.10

Modified residue

548

1

Phosphoserine Ref.10

Experimental info

Mutagenesis

154

1

D → A: Loss of enzyme activity. Ref.13

Mutagenesis

189

1

N → A: Slightly reduced rate of adenylyltransfer. Ref.13

Mutagenesis

215

1

K → A: Reduces rate of adenylyltransfer about four-fold. Ref.13

Mutagenesis

226

1

N → A: Reduces rate of adenylyltransfer by half. Ref.13

Mutagenesis

485

1

C → R: Abolishes interaction with FIP1; when associated with Y-489. Ref.14

Mutagenesis

489

1

V → Y: Abolishes interaction with FIP1; when associated with R-485. Ref.14

Secondary structure

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568

Helix Strand Turn

Details...

Helix

5 – 7

3

Beta strand

8 – 10

3

Helix

20 – 35

16

Helix

42 – 69

28

Helix

74 – 79

6

Beta strand

83 – 87

5

Helix

88 – 92

5

Beta strand

101 – 107

7

Helix

113 – 125

13

Beta strand

130 – 136

7

Beta strand

139 – 141

3

Beta strand

143 – 148

6

Beta strand

151 – 159

9

Beta strand

161 – 163

3

Helix

174 – 177

4

Helix

182 – 200

19

Helix

204 – 220

17

Helix

226 – 228

3

Helix

233 – 246

14

Helix

252 – 265

14

Beta strand

272 – 275

4

Beta strand

281 – 283

3

Turn

289 – 291

3

Helix

293 – 296

4

Beta strand

305 – 308

4

Turn

312 – 315

4

Helix

318 – 339

22

Helix

345 – 348

4

Helix

354 – 357

4

Beta strand

359 – 370

12

Helix

372 – 394

23

Beta strand

399 – 404

6

Beta strand

409 – 414

6

Beta strand

417 – 419

3

Helix

420 – 427

8

Helix

431 – 434

4

Helix

435 – 438

4

Turn

444 – 446

3

Helix

451 – 455

5

Beta strand

458 – 470

13

Beta strand

475 – 477

3

Helix

482 – 494

13

Turn

497 – 500

4

Beta strand

502 – 513

12

Helix

514 – 516

3

Helix

519 – 521

3

Sequences

	Sequence		Length	Mass (Da)
	P29468 [UniParc]. Last modified April 1, 1993. Version 1. Checksum: 759DE5210DC8D881	FASTA	568	64,552
	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

References

	« Hide 'large scale' referencesShow '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. , 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 AND SER-548, MASS SPECTROMETRY.
[11]	"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.
[12]	"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.
[13]	"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.
[14]	"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.

PIR

S19031.

RefSeq

NP_012927.3. NM_001179792.3.

3D structure databases

PDBe
RCSB PDB
PDBj

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	1-537	[»]

ProteinModelPortal

P29468.

SMR

P29468. Positions 3-531.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2297N.

IntAct

P29468. 27 interactions.

MINT

MINT-375429.

STRING

4932.YKR002W.

Proteomic databases

PaxDb

P29468.

PeptideAtlas

P29468.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YKR002W; YKR002W; YKR002W.

GeneID

853871.

KEGG

sce:YKR002W.

Organism-specific databases

CYGD

YKR002w.

SGD

S000001710. PAP1.

Phylogenomic databases

eggNOG

COG5186.

GeneTree

ENSGT00390000017928.

HOGENOM

HOG000204376.

KO

K14376.

OMA

FPGGVAW.

OrthoDB

EOG4SR150.

Enzyme and pathway databases

BioCyc

YEAST:G3O-31980-MONOMER.

Gene expression databases

Genevestigator

P29468.

GermOnline

YKR002W. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.30.70.590. 1 hit.

InterPro

IPR002934. Nucleotidyltransferase.
IPR011068. NuclTrfase_I_C.
IPR007012. PolA_pol_cen_dom.
IPR007010. PolA_pol_RNA-bd_dom.
IPR014492. PolyA_polymerase.
[Graphical view]

Pfam

PF01909. NTP_transf_2. 1 hit.
PF04928. PAP_central. 1 hit.
PF04926. PAP_RNA-bind. 1 hit.
[Graphical view]

PIRSF

PIRSF018425. PolyA_polymerase. 1 hit.

SUPFAM

SSF55003. PAP_C. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P29468.

NextBio

975142.

Entry information

Entry name

PAP_YEAST

Accession

Primary (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:	May 29, 2013
This is version 130 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program