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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
  • 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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi12 – 121L → A: Impairs nuclear export; when associated with A-15. 1 Publication
Mutagenesisi15 – 151L → A: Impairs nuclear export; when associated with A-12. 1 Publication
Mutagenesisi79 – 791L → 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 Publication
Mutagenesisi83 – 831Y → 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 Publications
Mutagenesisi134 – 1363HPD → DKS in PAB1-134. 1 Publication
Mutagenesisi148 – 1481V → 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 Publication
Mutagenesisi151 – 1511D → 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 Publication
Mutagenesisi157 – 1593IAT → VVC in PAB1-157; greatly reduces poly(A)-dependent translation and stimulation of cap-dependent translation in vitro. 1 Publication
Mutagenesisi166 – 1661K → 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 Publication
Mutagenesisi170 – 1701F → 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 Publications
Mutagenesisi175 – 1773EEG → TQE in PAB1-175; greatly reduces poly(A)-dependent translation and stimulation of cap-dependent translation in vitro. 1 Publication
Mutagenesisi180 – 1812KE → ER in PAB1-180; abolishes poly(A)-dependent translation and greatly reduces stimulation of cap-dependent translation in vitro. Impairs interaction with eIF4G. 1 Publication
Mutagenesisi184 – 1863DAL → EKM in PAB1-184; abolishes poly(A)-dependent translation and moderately reduces stimulation of cap-dependent translation in vitro. Impairs interaction with eIF4G. 1 Publication
Mutagenesisi193 – 1975GQEIY → DRKVF in PAB1-193; moderately reduces stimulation of cap-dependent translation in vitro. 1 Publication
Mutagenesisi199 – 2024APHL → GRFK in PAB1-199; moderately reduces poly(A)-dependent translation and stimulation of cap-dependent translation in vitro. 1 Publication
Mutagenesisi259 – 2591K → 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 Publication
Mutagenesisi263 – 2631F → V in PAB1-7. In PAB1-15; fails to bind RNA; when associated with V-83; V-170 and V-366. 1 Publication
Mutagenesisi362 – 3621K → 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 Publication
Mutagenesisi366 – 3661F → 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 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 577576Polyadenylate-binding protein, cytoplasmic and nuclearPRO_0000081720Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanine1 Publication
Cross-linki7 – 7Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei107 – 1071Omega-N-methylarginine1 Publication
Modified residuei249 – 2491PhosphoserineCombined sources
Modified residuei332 – 3321PhosphoserineCombined sources
Cross-linki337 – 337Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei405 – 4051PhosphoserineCombined sources

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP04147.

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 interactions.
DIPiDIP-2275N.
IntActiP04147. 176 interactions.
MINTiMINT-693056.

Structurei

Secondary structure

1
577
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi503 – 51715Combined sources
Helixi518 – 5203Combined sources
Helixi524 – 53411Combined sources
Helixi539 – 5468Combined sources
Helixi549 – 56820Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IFWNMR-A491-577[»]
ProteinModelPortaliP04147.
SMRiP04147. Positions 38-453, 489-577.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04147.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini38 – 11679RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini126 – 20378RRM 2PROSITE-ProRule annotationAdd
BLAST
Domaini219 – 29678RRM 3PROSITE-ProRule annotationAdd
BLAST
Domaini322 – 39978RRM 4PROSITE-ProRule annotationAdd
BLAST
Domaini489 – 56880PABCPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni9 – 6153Required and sufficient for nuclear exportSequence analysisAdd
BLAST
Regioni281 – 31737Required and sufficient for nuclear importSequence analysisAdd
BLAST
Regioni473 – 577105Interaction with SUP35Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi12 – 176Nuclear export signalSequence analysis

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi422 – 43110Poly-Ala

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti426 – 4261A → R in AAA34838 (PubMed:3518950).Curated

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
EntryMethodResolution (Å)ChainPositionsPDBsum
1IFWNMR-A491-577[»]
ProteinModelPortaliP04147.
SMRiP04147. Positions 38-453, 489-577.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

iPTMnetiP04147.

Proteomic databases

MaxQBiP04147.

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: September 7, 2016
This is version 196 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.