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Protein

Pumilio homology domain family member 4

Gene

PUF4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Is not essential for haploid growth, but may affect diploid formation.

GO - Molecular functioni

  • mRNA binding Source: SGD

GO - Biological processi

  • negative regulation of chromatin silencing involved in replicative cell aging Source: SGD
  • negative regulation of translation Source: SGD
  • nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: SGD
  • protein localization Source: SGD
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Enzyme and pathway databases

BioCyciYEAST:G3O-30535-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Pumilio homology domain family member 4
Gene namesi
Name:PUF4
Ordered Locus Names:YGL014W
ORF Names:YGL023
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VII

Organism-specific databases

EuPathDBiFungiDB:YGL014W.
SGDiS000002982. PUF4.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 888888Pumilio homology domain family member 4PRO_0000075925Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei205 – 2051PhosphothreonineCombined sources
Modified residuei212 – 2121PhosphothreonineCombined sources
Modified residuei252 – 2521PhosphothreonineCombined sources
Modified residuei256 – 2561PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP25339.
PeptideAtlasiP25339.

PTM databases

iPTMnetiP25339.

Interactioni

Protein-protein interaction databases

BioGridi33232. 101 interactions.
DIPiDIP-2638N.
IntActiP25339. 17 interactions.
MINTiMINT-425380.

Structurei

Secondary structure

1
888
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni555 – 5584Combined sources
Helixi561 – 5633Combined sources
Turni564 – 5663Combined sources
Helixi568 – 5714Combined sources
Beta strandi572 – 5743Combined sources
Helixi575 – 58713Combined sources
Helixi590 – 60011Combined sources
Helixi601 – 6033Combined sources
Helixi604 – 6085Combined sources
Helixi613 – 62311Combined sources
Helixi626 – 63611Combined sources
Helixi637 – 6393Combined sources
Helixi640 – 6456Combined sources
Helixi649 – 65911Combined sources
Helixi663 – 67311Combined sources
Helixi674 – 6763Combined sources
Helixi677 – 6815Combined sources
Helixi686 – 69611Combined sources
Helixi699 – 71113Combined sources
Helixi713 – 7175Combined sources
Helixi722 – 73211Combined sources
Helixi735 – 74612Combined sources
Helixi749 – 7535Combined sources
Helixi758 – 77215Combined sources
Helixi777 – 7859Combined sources
Helixi786 – 7883Combined sources
Helixi789 – 7935Combined sources
Helixi798 – 8069Combined sources
Helixi809 – 82113Combined sources
Helixi824 – 8329Combined sources
Helixi837 – 85115Combined sources
Helixi853 – 86311Combined sources
Helixi864 – 8663Combined sources
Helixi869 – 8735Combined sources
Helixi875 – 8817Combined sources
Beta strandi883 – 8853Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3BWTX-ray2.69A554-886[»]
3BX2X-ray2.84A/B554-888[»]
3BX3X-ray3.00A/B554-888[»]
4DZSX-ray3.14A/B536-888[»]
ProteinModelPortaliP25339.
SMRiP25339. Positions 554-886.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP25339.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini539 – 888350PUM-HDPROSITE-ProRule annotationAdd
BLAST
Repeati563 – 59836Pumilio 1Add
BLAST
Repeati599 – 63436Pumilio 2Add
BLAST
Repeati635 – 67137Pumilio 3Add
BLAST
Repeati672 – 70736Pumilio 4Add
BLAST
Repeati708 – 74336Pumilio 5Add
BLAST
Repeati744 – 78340Pumilio 6Add
BLAST
Repeati784 – 82138Pumilio 7Add
BLAST
Repeati823 – 86139Pumilio 8Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi8 – 3831Asp/Glu-rich (acidic)Add
BLAST
Compositional biasi471 – 54272Asn-richAdd
BLAST
Compositional biasi521 – 53515Poly-AsnAdd
BLAST

Sequence similaritiesi

Contains 1 PUM-HD domain.PROSITE-ProRule annotation
Contains 8 pumilio repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00730000112282.
HOGENOMiHOG000115799.
InParanoidiP25339.
OMAiFRRQTFH.
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. 8 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.

P25339-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTKGLKEEI DDVPSVDPVV SETVNSALEQ LQLDDPEENA TSNAFANKVS
60 70 80 90 100
QDSQFANGPP SQMFPHPQMM GGMGFMPYSQ MMQVPHNPCP FFPPPDFNDP
110 120 130 140 150
TAPLSSSPLN AGGPPMLFKN DSLPFQMLSS GAAVATQGGQ NLNPLINDNS
160 170 180 190 200
MKVLPIASAD PLWTHSNVPG SASVAIEETT ATLQESLPSK GRESNNKASS
210 220 230 240 250
FRRQTFHALS PTDLINAANN VTLSKDFQSD MQNFSKAKKP SVGANNTAKT
260 270 280 290 300
RTQSISFDNT PSSTSFIPPT NSVSEKLSDF KIETSKEDLI NKTAPAKKES
310 320 330 340 350
PTTYGAAYPY GGPLLQPNPI MPGHPHNISS PIYGIRSPFP NSYEMGAQFQ
360 370 380 390 400
PFSPILNPTS HSLNANSPIP LTQSPIHLAP VLNPSSNSVA FSDMKNDGGK
410 420 430 440 450
PTTDNDKAGP NVRMDLINPN LGPSMQPFHI LPPQQNTPPP PWLYSTPPPF
460 470 480 490 500
NAMVPPHLLA QNHMPLMNSA NNKHHGRNNN SMSSHNDNDN IGNSNYNNKD
510 520 530 540 550
TGRSNVGKMK NMKNSYHGYY NNNNNNNNNN NNNNNSNATN SNSAEKQRKI
560 570 580 590 600
EESSRFADAV LDQYIGSIHS LCKDQHGCRF LQKQLDILGS KAADAIFEET
610 620 630 640 650
KDYTVELMTD SFGNYLIQKL LEEVTTEQRI VLTKISSPHF VEISLNPHGT
660 670 680 690 700
RALQKLIECI KTDEEAQIVV DSLRPYTVQL SKDLNGNHVI QKCLQRLKPE
710 720 730 740 750
NFQFIFDAIS DSCIDIATHR HGCCVLQRCL DHGTTEQCDN LCDKLLALVD
760 770 780 790 800
KLTLDPFGNY VVQYIITKEA EKNKYDYTHK IVHLLKPRAI ELSIHKFGSN
810 820 830 840 850
VIEKILKTAI VSEPMILEIL NNGGETGIQS LLNDSYGNYV LQTALDISHK
860 870 880
QNDYLYKRLS EIVAPLLVGP IRNTPHGKRI IGMLHLDS
Length:888
Mass (Da):97,798
Last modified:October 1, 1996 - v2
Checksum:i659BA1062439F642
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti595 – 5951A → R (PubMed:1909073).Curated
Sequence conflicti595 – 5951A → R (PubMed:1882553).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S57889 Genomic DNA. Translation: AAB19616.1.
S58126 Genomic DNA. Translation: AAD13898.1.
Z72536 Genomic DNA. Translation: CAA96714.1.
BK006941 Genomic DNA. Translation: DAA08084.1.
PIRiS64016.
RefSeqiNP_011501.1. NM_001180879.1.

Genome annotation databases

EnsemblFungiiYGL014W; YGL014W; YGL014W.
GeneIDi852870.
KEGGisce:YGL014W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S57889 Genomic DNA. Translation: AAB19616.1.
S58126 Genomic DNA. Translation: AAD13898.1.
Z72536 Genomic DNA. Translation: CAA96714.1.
BK006941 Genomic DNA. Translation: DAA08084.1.
PIRiS64016.
RefSeqiNP_011501.1. NM_001180879.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3BWTX-ray2.69A554-886[»]
3BX2X-ray2.84A/B554-888[»]
3BX3X-ray3.00A/B554-888[»]
4DZSX-ray3.14A/B536-888[»]
ProteinModelPortaliP25339.
SMRiP25339. Positions 554-886.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33232. 101 interactions.
DIPiDIP-2638N.
IntActiP25339. 17 interactions.
MINTiMINT-425380.

PTM databases

iPTMnetiP25339.

Proteomic databases

MaxQBiP25339.
PeptideAtlasiP25339.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYGL014W; YGL014W; YGL014W.
GeneIDi852870.
KEGGisce:YGL014W.

Organism-specific databases

EuPathDBiFungiDB:YGL014W.
SGDiS000002982. PUF4.

Phylogenomic databases

GeneTreeiENSGT00730000112282.
HOGENOMiHOG000115799.
InParanoidiP25339.
OMAiFRRQTFH.
OrthoDBiEOG7K0ZN7.

Enzyme and pathway databases

BioCyciYEAST:G3O-30535-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP25339.
NextBioi972496.
PROiP25339.

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. 8 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. "The YGL023 gene encodes a putative regulatory protein."
    Chen W., Balzi E., Capieaux E., Goffeau A.
    Yeast 7:309-312(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 46191 / IL125-2B.
  2. "The DNA sequencing of the 17 kb HindIII fragment spanning the LEU1 and ATE1 loci on chromosome VII from Saccharomyces cerevisiae reveals the PDR6 gene, a new member of the genetic network controlling pleiotropic drug resistance."
    Chen W., Balzi E., Capieaux E., Choder M., Goffeau A.
    Yeast 7:287-299(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 46191 / IL125-2B.
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
    Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
    , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
    Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  6. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-205 AND THR-212, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  7. "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].
  8. "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 THR-205; THR-252 AND SER-256, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiPUF4_YEAST
AccessioniPrimary (citable) accession number: P25339
Secondary accession number(s): D6VUC3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: October 1, 1996
Last modified: May 11, 2016
This is version 152 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 721 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 VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: 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.