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Protein

Polyadenylate-binding protein, cytoplasmic and nuclear

Gene

PAB1

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

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, interacts with the nuclear cleavage factor IA (CFIA), which is required for both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. Regulates PAN activity via interaction with the stimulator PAN3 or the inhibitor PBP1. In the cytoplasm, affects both translation and mRNA decay. Stimulates translation by interaction with translation initiation factor eIF4G, a subunit of the cap-binding complex eIF4F, bringing the 5'- and 3'-ends of the mRNA in proximity. The formation of this circular mRNP structure appears to be critical for the synergistic effects of the cap and the poly(A) tail in facilitating translation initiation, recycling of ribosomes, and mRNA stability. Also regulates translation termination by recruiting eukaryotic release factor 3 (eRF3). Interaction with eRF3 is also required for regulation of normal mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN. Loss of PAB1 from the mRNP after deadenylation triggers mRNA degradation. Inhibits the major cytoplasmic mRNA deadenylase CCR4-NOT complex. Is also associated peripherally with COPI vesicles through its interaction with ARF1, and this is required for correct localization of the asymmetrically distributed ASH1 mRNA.14 Publications

GO - Molecular functioni

  • nucleotide binding Source: InterPro
  • poly(A) binding Source: SGD
  • promoter-specific chromatin binding Source: SGD
  • ribonuclease inhibitor activity Source: SGD

GO - Biological processi

  • mRNA processing Source: UniProtKB-KW
  • mRNA transport Source: UniProtKB-KW
  • regulation of nuclear-transcribed mRNA poly(A) tail shortening Source: SGD
  • regulation of translational initiation Source: SGD
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA transport, Translation regulation, Transport

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-30326-MONOMER.
ReactomeiR-SCE-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-SCE-450408. AUF1 (hnRNP D0) binds and destabilizes mRNA.
R-SCE-450520. HuR (ELAVL1) binds and stabilizes mRNA.
R-SCE-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-SCE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Names & Taxonomyi

Protein namesi
Recommended name:
Polyadenylate-binding protein, cytoplasmic and nuclear
Short name:
PABP
Short name:
Poly(A)-binding protein
Alternative name(s):
ARS consensus-binding protein ACBP-67
Polyadenylate tail-binding protein
Gene namesi
Name:PAB1
Ordered Locus Names:YER165W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome V

Organism-specific databases

EuPathDBiFungiDB:YER165W.
SGDiS000000967. PAB1.

Subcellular locationi

  • Cytoplasm
  • Nucleus

  • Note: Predominantly cytoplasmic. Rapidly shuttles between the nucleus and the cytoplasm. Can be exported from the nucleus through at least 2 distinct pathways, the main being dependent on the exportin CRM1, and the second requiring MEX67 and ongoing mRNA export. Import is mediated by the importin SXM1.

GO - Cellular componenti

  • cytoplasm Source: SGD
  • cytoplasmic stress granule Source: SGD
  • nucleus Source: SGD
  • ribosome Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi12L → A: Impairs nuclear export; when associated with A-15. 1 Publication1
Mutagenesisi15L → A: Impairs nuclear export; when associated with A-12. 1 Publication1
Mutagenesisi79L → A in PAB1-14; fails to bind poly(U), but not poly(A) RNA; when associated with Q-166; Q-259 and Q-362. 1 Publication1
Mutagenesisi83Y → V in PAB1-16; reduces affinity for oligo(A) about 100-fold, impairs poly(A)-dependent translation, but still interacts with eIF4G; when associated with V-170. In PAB1-15; fails to bind RNA; when associated with V-170; V-263 and V-366. 2 Publications1
Mutagenesisi134 – 136HPD → DKS in PAB1-134. 1 Publication3
Mutagenesisi148V → A in PAB1-148; greatly reduces poly(A)-dependent translation and moderately reduces stimulation of cap-dependent translation in vitro; when associated with N-151. 1 Publication1
Mutagenesisi151D → N in PAB1-148; greatly reduces poly(A)-dependent translation and moderately reduces stimulation of cap-dependent translation in vitro; when associated with A-148. 1 Publication1
Mutagenesisi157 – 159IAT → VVC in PAB1-157; greatly reduces poly(A)-dependent translation and stimulation of cap-dependent translation in vitro. 1 Publication3
Mutagenesisi166K → Q in PAB1-14; fails to bind poly(U), but not poly(A) RNA; when associated with A-79; Q-259 and Q-362. 1 Publication1
Mutagenesisi170F → V in PAB1-6; selectively reduces poly(A) RNA binding. In PAB1-16; reduces affinity for oligo(A) about 100-fold, impairs poly(A)-dependent translation, but still interacts with eIF4G; when associated with V-83. In PAB1-15; fails to bind RNA; when associated with V-83; V-263 and V-366. 2 Publications1
Mutagenesisi175 – 177EEG → TQE in PAB1-175; greatly reduces poly(A)-dependent translation and stimulation of cap-dependent translation in vitro. 1 Publication3
Mutagenesisi180 – 181KE → ER in PAB1-180; abolishes poly(A)-dependent translation and greatly reduces stimulation of cap-dependent translation in vitro. Impairs interaction with eIF4G. 1 Publication2
Mutagenesisi184 – 186DAL → EKM in PAB1-184; abolishes poly(A)-dependent translation and moderately reduces stimulation of cap-dependent translation in vitro. Impairs interaction with eIF4G. 1 Publication3
Mutagenesisi193 – 197GQEIY → DRKVF in PAB1-193; moderately reduces stimulation of cap-dependent translation in vitro. 1 Publication5
Mutagenesisi199 – 202APHL → GRFK in PAB1-199; moderately reduces poly(A)-dependent translation and stimulation of cap-dependent translation in vitro. 1 Publication4
Mutagenesisi259K → Q in PAB1-14; fails to bind poly(U), but not poly(A) RNA; when associated with A-79; Q-166 and Q-362. 1 Publication1
Mutagenesisi263F → V in PAB1-7. In PAB1-15; fails to bind RNA; when associated with V-83; V-170 and V-366. 1 Publication1
Mutagenesisi362K → Q in PAB1-14; fails to bind poly(U), but not poly(A) RNA; when associated with A-79; Q-166 and Q-259. 1 Publication1
Mutagenesisi366F → V in PAB1-8; selectively reduces poly(U) RNA binding. In PAB1-15; fails to bind RNA; when associated with V-83; V-170 and V-263. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000817202 – 577Polyadenylate-binding protein, cytoplasmic and nuclearAdd BLAST576

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanine1 Publication1
Cross-linki7Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei107Omega-N-methylarginine1 Publication1
Modified residuei249PhosphoserineCombined sources1
Modified residuei332PhosphoserineCombined sources1
Cross-linki337Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei405PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP04147.
PRIDEiP04147.

PTM databases

iPTMnetiP04147.

Interactioni

Subunit structurei

Binds to poly(A) mRNA to form a periodic structure with a packing density of one molecule per 25 adenylate residues. Interacts with the nuclear export factor CRM1 and with the importin SXM1. Interacts with RNA15, a component of the cleavage factor IA (CFIA) complex. Interacts with translation initiation factor eIF4G (TIF4631 or TIF4632) and release factor eRF3 (SUP35). Interacts with the PAB-dependent poly(A)-nuclease (PAN) complex regulatory subunit PAN3. Interacts with ARF1, DCP1, PBP1, the Hsp70 chaperone SSA1, and TPA1. Interacts with PAT1 in an RNA-dependent manner.18 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
PAN3P361025EBI-12823,EBI-12895
TIF4631P3993516EBI-12823,EBI-9002
TIF4632P399362EBI-12823,EBI-9006

Protein-protein interaction databases

BioGridi36918. 239 interactors.
DIPiDIP-2275N.
IntActiP04147. 176 interactors.
MINTiMINT-693056.

Structurei

Secondary structure

1577
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi503 – 517Combined sources15
Helixi518 – 520Combined sources3
Helixi524 – 534Combined sources11
Helixi539 – 546Combined sources8
Helixi549 – 568Combined sources20

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IFWNMR-A491-577[»]
ProteinModelPortaliP04147.
SMRiP04147.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04147.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini38 – 116RRM 1PROSITE-ProRule annotationAdd BLAST79
Domaini126 – 203RRM 2PROSITE-ProRule annotationAdd BLAST78
Domaini219 – 296RRM 3PROSITE-ProRule annotationAdd BLAST78
Domaini322 – 399RRM 4PROSITE-ProRule annotationAdd BLAST78
Domaini489 – 568PABCPROSITE-ProRule annotationAdd BLAST80

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni9 – 61Required and sufficient for nuclear exportSequence analysisAdd BLAST53
Regioni281 – 317Required and sufficient for nuclear importSequence analysisAdd BLAST37
Regioni473 – 577Interaction with SUP35Add BLAST105

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi12 – 17Nuclear export signalSequence analysis6

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi422 – 431Poly-Ala10

Domaini

RNA recognition motifs (RRMs) 1 and 2 bind specifically to the poly(A) tail, whereas RRMs 3 and 4 bind non-specifically to polypyrimidine RNAs and may serve to bind to a different part of the messenger or to other RNAs. RRM 2 also mediates interaction with eIF-4G.1 Publication

Sequence similaritiesi

Contains 1 PABC domain.PROSITE-ProRule annotation
Contains 4 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00760000118913.
HOGENOMiHOG000217922.
InParanoidiP04147.
KOiK13126.
OMAiNHESAEA.
OrthoDBiEOG092C3SCB.

Family and domain databases

Gene3Di1.10.1900.10. 1 hit.
3.30.70.330. 4 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR006515. PABP_1234.
IPR002004. PABP_HYD.
IPR000504. RRM_dom.
IPR003954. RRM_dom_euk.
[Graphical view]
PfamiPF00658. PABP. 1 hit.
PF00076. RRM_1. 4 hits.
[Graphical view]
SMARTiSM00517. PolyA. 1 hit.
SM00360. RRM. 4 hits.
SM00361. RRM_1. 4 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
SSF63570. SSF63570. 1 hit.
TIGRFAMsiTIGR01628. PABP-1234. 1 hit.
PROSITEiPS51309. PABC. 1 hit.
PS50102. RRM. 4 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P04147-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADITDKTAE QLENLNIQDD QKQAATGSES QSVENSSASL YVGDLEPSVS
60 70 80 90 100
EAHLYDIFSP IGSVSSIRVC RDAITKTSLG YAYVNFNDHE AGRKAIEQLN
110 120 130 140 150
YTPIKGRLCR IMWSQRDPSL RKKGSGNIFI KNLHPDIDNK ALYDTFSVFG
160 170 180 190 200
DILSSKIATD ENGKSKGFGF VHFEEEGAAK EAIDALNGML LNGQEIYVAP
210 220 230 240 250
HLSRKERDSQ LEETKAHYTN LYVKNINSET TDEQFQELFA KFGPIVSASL
260 270 280 290 300
EKDADGKLKG FGFVNYEKHE DAVKAVEALN DSELNGEKLY VGRAQKKNER
310 320 330 340 350
MHVLKKQYEA YRLEKMAKYQ GVNLFVKNLD DSVDDEKLEE EFAPYGTITS
360 370 380 390 400
AKVMRTENGK SKGFGFVCFS TPEEATKAIT EKNQQIVAGK PLYVAIAQRK
410 420 430 440 450
DVRRSQLAQQ IQARNQMRYQ QATAAAAAAA AGMPGQFMPP MFYGVMPPRG
460 470 480 490 500
VPFNGPNPQQ MNPMGGMPKN GMPPQFRNGP VYGVPPQGGF PRNANDNNQF
510 520 530 540 550
YQQKQRQALG EQLYKKVSAK TSNEEAAGKI TGMILDLPPQ EVFPLLESDE
560 570
LFEQHYKEAS AAYESFKKEQ EQQTEQA
Length:577
Mass (Da):64,344
Last modified:January 23, 2007 - v4
Checksum:i4F97E494753E17C7
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti426A → R in AAA34838 (PubMed:3518950).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M12780 Genomic DNA. Translation: AAA34838.1.
M13371 Genomic DNA. Translation: AAA34787.1.
D00023 Genomic DNA. Translation: BAA00017.1.
U18922 Genomic DNA. Translation: AAB64692.1.
AY692854 Genomic DNA. Translation: AAT92873.1.
BK006939 Genomic DNA. Translation: DAA07827.1.
PIRiA25221. DNBYPA.
RefSeqiNP_011092.1. NM_001179055.1.

Genome annotation databases

EnsemblFungiiYER165W; YER165W; YER165W.
GeneIDi856912.
KEGGisce:YER165W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M12780 Genomic DNA. Translation: AAA34838.1.
M13371 Genomic DNA. Translation: AAA34787.1.
D00023 Genomic DNA. Translation: BAA00017.1.
U18922 Genomic DNA. Translation: AAB64692.1.
AY692854 Genomic DNA. Translation: AAT92873.1.
BK006939 Genomic DNA. Translation: DAA07827.1.
PIRiA25221. DNBYPA.
RefSeqiNP_011092.1. NM_001179055.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IFWNMR-A491-577[»]
ProteinModelPortaliP04147.
SMRiP04147.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36918. 239 interactors.
DIPiDIP-2275N.
IntActiP04147. 176 interactors.
MINTiMINT-693056.

PTM databases

iPTMnetiP04147.

Proteomic databases

MaxQBiP04147.
PRIDEiP04147.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYER165W; YER165W; YER165W.
GeneIDi856912.
KEGGisce:YER165W.

Organism-specific databases

EuPathDBiFungiDB:YER165W.
SGDiS000000967. PAB1.

Phylogenomic databases

GeneTreeiENSGT00760000118913.
HOGENOMiHOG000217922.
InParanoidiP04147.
KOiK13126.
OMAiNHESAEA.
OrthoDBiEOG092C3SCB.

Enzyme and pathway databases

BioCyciYEAST:G3O-30326-MONOMER.
ReactomeiR-SCE-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-SCE-450408. AUF1 (hnRNP D0) binds and destabilizes mRNA.
R-SCE-450520. HuR (ELAVL1) binds and stabilizes mRNA.
R-SCE-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-SCE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

EvolutionaryTraceiP04147.
PROiP04147.

Family and domain databases

Gene3Di1.10.1900.10. 1 hit.
3.30.70.330. 4 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR006515. PABP_1234.
IPR002004. PABP_HYD.
IPR000504. RRM_dom.
IPR003954. RRM_dom_euk.
[Graphical view]
PfamiPF00658. PABP. 1 hit.
PF00076. RRM_1. 4 hits.
[Graphical view]
SMARTiSM00517. PolyA. 1 hit.
SM00360. RRM. 4 hits.
SM00361. RRM_1. 4 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
SSF63570. SSF63570. 1 hit.
TIGRFAMsiTIGR01628. PABP-1234. 1 hit.
PROSITEiPS51309. PABC. 1 hit.
PS50102. RRM. 4 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPABP_YEAST
AccessioniPrimary (citable) accession number: P04147
Secondary accession number(s): D3DM73
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1986
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 198 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 198000 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 V
    Yeast (Saccharomyces cerevisiae) chromosome V: 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.