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Protein

mRNA-binding protein PUF3

Gene

PUF3

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

RNA-binding protein involved in post-transcriptional regulation. Negatively regulates expression of COX17 by binding to the 3'-UTR of COX17 mRNA. Promotes decay of COX17 mRNA by enhancing its rate of deadenylation and subsequent turnover. Predominantly binds to mRNAs encoding mitochondrial proteins and localizes them to the vicinity of mitochondria for translation. Regulates mitochondrial biogenesis, motility and morphology.7 Publications

GO - Molecular functioni

  • mRNA binding Source: SGD

GO - Biological processi

  • aerobic respiration Source: SGD
  • intracellular mRNA localization Source: SGD
  • mitochondrion localization Source: SGD
  • mitochondrion organization Source: SGD
  • nuclear-transcribed mRNA catabolic process Source: SGD
  • nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: SGD
Complete GO annotation...

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-32118-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
mRNA-binding protein PUF3
Alternative name(s):
Pumilio homology domain family member 3
Gene namesi
Name:PUF3
Ordered Locus Names:YLL013C
ORF Names:L1325
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLL013C.
SGDiS000003936. PUF3.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • cytoplasmic side of mitochondrial outer membrane Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Membrane, Mitochondrion, Mitochondrion outer membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi553 – 5531S → C: Prevents binding to COX17 mRNA and its rapid decay and increases affinity to HO mRNA, a PUF5 target. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 879879mRNA-binding protein PUF3PRO_0000075924Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei83 – 831PhosphothreonineCombined sources
Modified residuei207 – 2071PhosphoserineCombined sources
Modified residuei210 – 2101PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ07807.
PeptideAtlasiQ07807.

PTM databases

iPTMnetiQ07807.

Interactioni

Protein-protein interaction databases

BioGridi31238. 1793 interactions.
DIPiDIP-4449N.
IntActiQ07807. 25 interactions.
MINTiMINT-552454.

Structurei

Secondary structure

1
879
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi516 – 5227Combined sources
Helixi536 – 5394Combined sources
Helixi543 – 5475Combined sources
Helixi550 – 56011Combined sources
Helixi565 – 57511Combined sources
Helixi576 – 5783Combined sources
Helixi579 – 5846Combined sources
Turni586 – 5883Combined sources
Helixi589 – 59810Combined sources
Helixi601 – 61111Combined sources
Helixi615 – 6206Combined sources
Helixi624 – 63411Combined sources
Helixi637 – 6448Combined sources
Helixi645 – 6473Combined sources
Helixi651 – 6566Combined sources
Helixi660 – 67011Combined sources
Helixi673 – 6753Combined sources
Turni677 – 6793Combined sources
Helixi680 – 6834Combined sources
Turni684 – 6863Combined sources
Helixi687 – 6915Combined sources
Helixi696 – 70611Combined sources
Helixi709 – 7179Combined sources
Turni718 – 7214Combined sources
Helixi723 – 7286Combined sources
Helixi732 – 7409Combined sources
Helixi748 – 76215Combined sources
Helixi765 – 7695Combined sources
Helixi774 – 78411Combined sources
Helixi787 – 7948Combined sources
Turni795 – 7973Combined sources
Helixi802 – 8065Combined sources
Helixi813 – 8186Combined sources
Helixi823 – 83311Combined sources
Helixi836 – 85520Combined sources
Helixi865 – 87410Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3K49X-ray2.50A/C/E511-879[»]
3K4EX-ray3.20A/C/E511-879[»]
ProteinModelPortaliQ07807.
SMRiQ07807. Positions 515-875.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ07807.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini513 – 871359PUM-HDPROSITE-ProRule annotationAdd
BLAST
Repeati538 – 57336Pumilio 1Add
BLAST
Repeati574 – 60936Pumilio 2Add
BLAST
Repeati610 – 64536Pumilio 3Add
BLAST
Repeati646 – 68136Pumilio 4Add
BLAST
Repeati682 – 71736Pumilio 5Add
BLAST
Repeati718 – 75942Pumilio 6Add
BLAST
Repeati760 – 79536Pumilio 7Add
BLAST
Repeati807 – 84438Pumilio 8Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi398 – 40912Poly-GlnAdd
BLAST
Compositional biasi412 – 4187Poly-Gln

Sequence similaritiesi

Belongs to the PUF3 family.Curated
Contains 1 PUM-HD domain.PROSITE-ProRule annotation
Contains 8 pumilio repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00390000017241.
InParanoidiQ07807.
KOiK17944.
OMAiLQMYACR.
OrthoDBiEOG7K0ZN7.

Family and domain databases

Gene3Di1.25.10.10. 1 hit.
InterProiIPR011989. ARM-like.
IPR016024. ARM-type_fold.
IPR033133. PUM-HD.
IPR001313. Pumilio_RNA-bd_rpt.
[Graphical view]
PfamiPF00806. PUF. 6 hits.
[Graphical view]
SMARTiSM00025. Pumilio. 8 hits.
[Graphical view]
SUPFAMiSSF48371. SSF48371. 1 hit.
PROSITEiPS50302. PUM. 8 hits.
PS50303. PUM_HD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q07807-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEMNMDMDMD MELASIVSSL SALSHSNNNG GQAAAAGIVN GGAAGSQQIG
60 70 80 90 100
GFRRSSFTTA NEVDSEILLL HGSSESSPIF KKTALSVGTA PPFSTNSKKF
110 120 130 140 150
FGNGGNYYQY RSTDTASLSS ASYNNYHTHH TAANLGKNNK VNHLLGQYSA
160 170 180 190 200
SIAGPVYYNG NDNNNSGGEG FFEKFGKSLI DGTRELESQD RPDAVNTQSQ
210 220 230 240 250
FISKSVSNAS LDTQNTFEQN VESDKNFNKL NRNTTNSGSL YHSSSNSGSS
260 270 280 290 300
ASLESENAHY PKRNIWNVAN TPVFRPSNNP AAVGATNVAL PNQQDGPANN
310 320 330 340 350
NFPPYMNGFP PNQFHQGPHY QNFPNYLIGS PSNFISQMIS VQIPANEDTE
360 370 380 390 400
DSNGKKKKKA NRPSSVSSPS SPPNNSPFPF AYPNPMMFMP PPPLSAPQQQ
410 420 430 440 450
QQQQQQQQQE DQQQQQQQEN PYIYYPTPNP IPVKMPKDEK TFKKRNNKNH
460 470 480 490 500
PANNSNNANK QANPYLENSI PTKNTSKKNA SSKSNESTAN NHKSHSHSHP
510 520 530 540 550
HSQSLQQQQQ TYHRSPLLEQ LRNSSSDKNS NSNMSLKDIF GHSLEFCKDQ
560 570 580 590 600
HGSRFIQREL ATSPASEKEV IFNEIRDDAI ELSNDVFGNY VIQKFFEFGS
610 620 630 640 650
KIQKNTLVDQ FKGNMKQLSL QMYACRVIQK ALEYIDSNQR IELVLELSDS
660 670 680 690 700
VLQMIKDQNG NHVIQKAIET IPIEKLPFIL SSLTGHIYHL STHSYGCRVI
710 720 730 740 750
QRLLEFGSSE DQESILNELK DFIPYLIQDQ YGNYVIQYVL QQDQFTNKEM
760 770 780 790 800
VDIKQEIIET VANNVVEYSK HKFASNVVEK SILYGSKNQK DLIISKILPR
810 820 830 840 850
DKNHALNLED DSPMILMIKD QFANYVIQKL VNVSEGEGKK LIVIAIRAYL
860 870
DKLNKSNSLG NRHLASVEKL AALVENAEV
Length:879
Mass (Da):98,068
Last modified:November 1, 1996 - v1
Checksum:i13F6D2D829CBCBF6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X97560 Genomic DNA. Translation: CAA66165.1.
X91488 Genomic DNA. Translation: CAA62779.1.
Z73117 Genomic DNA. Translation: CAA97457.1.
Z73118 Genomic DNA. Translation: CAA97458.1.
BK006945 Genomic DNA. Translation: DAA09305.1.
PIRiS64755.
RefSeqiNP_013088.1. NM_001181833.1.

Genome annotation databases

EnsemblFungiiYLL013C; YLL013C; YLL013C.
GeneIDi850647.
KEGGisce:YLL013C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X97560 Genomic DNA. Translation: CAA66165.1.
X91488 Genomic DNA. Translation: CAA62779.1.
Z73117 Genomic DNA. Translation: CAA97457.1.
Z73118 Genomic DNA. Translation: CAA97458.1.
BK006945 Genomic DNA. Translation: DAA09305.1.
PIRiS64755.
RefSeqiNP_013088.1. NM_001181833.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3K49X-ray2.50A/C/E511-879[»]
3K4EX-ray3.20A/C/E511-879[»]
ProteinModelPortaliQ07807.
SMRiQ07807. Positions 515-875.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31238. 1793 interactions.
DIPiDIP-4449N.
IntActiQ07807. 25 interactions.
MINTiMINT-552454.

PTM databases

iPTMnetiQ07807.

Proteomic databases

MaxQBiQ07807.
PeptideAtlasiQ07807.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLL013C; YLL013C; YLL013C.
GeneIDi850647.
KEGGisce:YLL013C.

Organism-specific databases

EuPathDBiFungiDB:YLL013C.
SGDiS000003936. PUF3.

Phylogenomic databases

GeneTreeiENSGT00390000017241.
InParanoidiQ07807.
KOiK17944.
OMAiLQMYACR.
OrthoDBiEOG7K0ZN7.

Enzyme and pathway databases

BioCyciYEAST:G3O-32118-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ07807.
NextBioi966590.
PROiQ07807.

Family and domain databases

Gene3Di1.25.10.10. 1 hit.
InterProiIPR011989. ARM-like.
IPR016024. ARM-type_fold.
IPR033133. PUM-HD.
IPR001313. Pumilio_RNA-bd_rpt.
[Graphical view]
PfamiPF00806. PUF. 6 hits.
[Graphical view]
SMARTiSM00025. Pumilio. 8 hits.
[Graphical view]
SUPFAMiSSF48371. SSF48371. 1 hit.
PROSITEiPS50302. PUM. 8 hits.
PS50303. PUM_HD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence analysis of the CEN12 region of Saccharomyces cerevisiae on a 43.7 kb fragment of chromosome XII including an open reading frame homologous to the human cystic fibrosis transmembrane conductance regulator protein CFTR."
    Miosga T., Zimmermann F.K.
    Yeast 12:693-708(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 90840 / EAY235 / FY23.
  2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
    Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H.
    , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
    Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "The sequence of 32kb on the left arm of yeast chromosome XII reveals six known genes, a new member of the seripauperins family and a new ABC transporter homologous to the human multidrug resistance protein."
    Purnelle B., Goffeau A.
    Yeast 13:183-188(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 588-879.
    Strain: ATCC 204508 / S288c.
  5. "The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast."
    Olivas W.M., Parker R.
    EMBO J. 19:6602-6611(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  8. "Decapping and decay of messenger RNA occur in cytoplasmic processing bodies."
    Sheth U., Parker R.
    Science 300:805-808(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  9. "Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast."
    Gerber A.P., Herschlag D., Brown P.O.
    PLoS Biol. 2:342-354(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: RNA-BINDING, SUBCELLULAR LOCATION.
  10. "Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast."
    Jackson J.S. Jr., Houshmandi S.S., Lopez Leban F., Olivas W.M.
    RNA 10:1625-1636(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, RNA-BINDING.
  11. "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway."
    Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N.
    Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-83 AND SER-207, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: YAL6B.
  12. "Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast."
    Ringner M., Krogh M.
    PLoS Comput. Biol. 1:585-592(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  13. "Yeast Puf3 mutants reveal the complexity of Puf-RNA binding and identify a loop required for regulation of mRNA decay."
    Houshmandi S.S., Olivas W.M.
    RNA 11:1655-1666(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, RNA-BINDING, MUTAGENESIS OF SER-553.
  14. "Puf3p, a Pumilio family RNA binding protein, localizes to mitochondria and regulates mitochondrial biogenesis and motility in budding yeast."
    Garcia-Rodriguez L.J., Gay A.C., Pon L.A.
    J. Cell Biol. 176:197-207(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH MDM12.
  15. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  16. "Yeast mitochondrial biogenesis: a role for the PUF RNA-binding protein Puf3p in mRNA localization."
    Saint-Georges Y., Garcia M., Delaveau T., Jourdren L., Le Crom S., Lemoine S., Tanty V., Devaux F., Jacq C.
    PLoS ONE 3:1-12(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  17. "Puf1p acts in combination with other yeast Puf proteins to control mRNA stability."
    Ulbricht R.J., Olivas W.M.
    RNA 14:246-262(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  18. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-210, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiPUF3_YEAST
AccessioniPrimary (citable) accession number: Q07807
Secondary accession number(s): D6VXY9, Q02601
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2003
Last sequence update: November 1, 1996
Last modified: May 11, 2016
This is version 132 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 846 molecules/cell in log phase SD medium.1 Publication

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 XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: 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.