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PUF3_YEAST
ID   PUF3_YEAST              Reviewed;         879 AA.
AC   Q07807; D6VXY9; Q02601;
DT   19-SEP-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   03-AUG-2022, entry version 170.
DE   RecName: Full=mRNA-binding protein PUF3;
DE   AltName: Full=Pumilio homology domain family member 3;
GN   Name=PUF3; OrderedLocusNames=YLL013C; ORFNames=L1325;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 90840 / EAY235 / FY23;
RX   PubMed=8810043;
RX   DOI=10.1002/(sici)1097-0061(19960615)12:7<693::aid-yea956>3.0.co;2-g;
RA   Miosga T., Zimmermann F.K.;
RT   "Sequence analysis of the CEN12 region of Saccharomyces cerevisiae on a
RT   43.7 kb fragment of chromosome XII including an open reading frame
RT   homologous to the human cystic fibrosis transmembrane conductance regulator
RT   protein CFTR.";
RL   Yeast 12:693-708(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169871;
RA   Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA   Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA   Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA   Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA   Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA   Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA   Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA   Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA   Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA   Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA   Zollner A., Hani J., Hoheisel J.D.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL   Nature 387:87-90(1997).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=24374639; DOI=10.1534/g3.113.008995;
RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 588-879.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9046100;
RX   DOI=10.1002/(sici)1097-0061(199702)13:2<183::aid-yea65>3.0.co;2-v;
RA   Purnelle B., Goffeau A.;
RT   "The sequence of 32kb on the left arm of yeast chromosome XII reveals six
RT   known genes, a new member of the seripauperins family and a new ABC
RT   transporter homologous to the human multidrug resistance protein.";
RL   Yeast 13:183-188(1997).
RN   [5]
RP   FUNCTION.
RX   PubMed=11101532; DOI=10.1093/emboj/19.23.6602;
RA   Olivas W.M., Parker R.;
RT   "The Puf3 protein is a transcript-specific regulator of mRNA degradation in
RT   yeast.";
RL   EMBO J. 19:6602-6611(2000).
RN   [6]
RP   SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX   PubMed=14562095; DOI=10.1038/nature02026;
RA   Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA   Weissman J.S., O'Shea E.K.;
RT   "Global analysis of protein localization in budding yeast.";
RL   Nature 425:686-691(2003).
RN   [7]
RP   LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX   PubMed=14562106; DOI=10.1038/nature02046;
RA   Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA   O'Shea E.K., Weissman J.S.;
RT   "Global analysis of protein expression in yeast.";
RL   Nature 425:737-741(2003).
RN   [8]
RP   SUBCELLULAR LOCATION.
RX   PubMed=12730603; DOI=10.1126/science.1082320;
RA   Sheth U., Parker R.;
RT   "Decapping and decay of messenger RNA occur in cytoplasmic processing
RT   bodies.";
RL   Science 300:805-808(2003).
RN   [9]
RP   RNA-BINDING, AND SUBCELLULAR LOCATION.
RX   PubMed=15024427; DOI=10.1371/journal.pbio.0020079;
RA   Gerber A.P., Herschlag D., Brown P.O.;
RT   "Extensive association of functionally and cytotopically related mRNAs with
RT   Puf family RNA-binding proteins in yeast.";
RL   PLoS Biol. 2:342-354(2004).
RN   [10]
RP   FUNCTION, AND RNA-BINDING.
RX   PubMed=15337848; DOI=10.1261/rna.7270204;
RA   Jackson J.S. Jr., Houshmandi S.S., Lopez Leban F., Olivas W.M.;
RT   "Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA
RT   decay in yeast.";
RL   RNA 10:1625-1636(2004).
RN   [11]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-83 AND SER-207, AND
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   STRAIN=YAL6B;
RX   PubMed=15665377; DOI=10.1074/mcp.m400219-mcp200;
RA   Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M.,
RA   Jensen O.N.;
RT   "Quantitative phosphoproteomics applied to the yeast pheromone signaling
RT   pathway.";
RL   Mol. Cell. Proteomics 4:310-327(2005).
RN   [12]
RP   FUNCTION.
RX   PubMed=16355254; DOI=10.1371/journal.pcbi.0010072;
RA   Ringner M., Krogh M.;
RT   "Folding free energies of 5'-UTRs impact post-transcriptional regulation on
RT   a genomic scale in yeast.";
RL   PLoS Comput. Biol. 1:585-592(2005).
RN   [13]
RP   FUNCTION, RNA-BINDING, AND MUTAGENESIS OF SER-553.
RX   PubMed=16244132; DOI=10.1261/rna.2168505;
RA   Houshmandi S.S., Olivas W.M.;
RT   "Yeast Puf3 mutants reveal the complexity of Puf-RNA binding and identify a
RT   loop required for regulation of mRNA decay.";
RL   RNA 11:1655-1666(2005).
RN   [14]
RP   FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH MDM12.
RX   PubMed=17210948; DOI=10.1083/jcb.200606054;
RA   Garcia-Rodriguez L.J., Gay A.C., Pon L.A.;
RT   "Puf3p, a Pumilio family RNA binding protein, localizes to mitochondria and
RT   regulates mitochondrial biogenesis and motility in budding yeast.";
RL   J. Cell Biol. 176:197-207(2007).
RN   [15]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA   Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT   "A multidimensional chromatography technology for in-depth phosphoproteome
RT   analysis.";
RL   Mol. Cell. Proteomics 7:1389-1396(2008).
RN   [16]
RP   FUNCTION.
RX   PubMed=18523582; DOI=10.1371/journal.pone.0002293;
RA   Saint-Georges Y., Garcia M., Delaveau T., Jourdren L., Le Crom S.,
RA   Lemoine S., Tanty V., Devaux F., Jacq C.;
RT   "Yeast mitochondrial biogenesis: a role for the PUF RNA-binding protein
RT   Puf3p in mRNA localization.";
RL   PLoS ONE 3:1-12(2008).
RN   [17]
RP   FUNCTION.
RX   PubMed=18094119; DOI=10.1261/rna.847408;
RA   Ulbricht R.J., Olivas W.M.;
RT   "Puf1p acts in combination with other yeast Puf proteins to control mRNA
RT   stability.";
RL   RNA 14:246-262(2008).
RN   [18]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-210, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=19779198; DOI=10.1126/science.1172867;
RA   Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT   "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT   into evolution.";
RL   Science 325:1682-1686(2009).
CC   -!- FUNCTION: RNA-binding protein involved in post-transcriptional
CC       regulation. Negatively regulates expression of COX17 by binding to the
CC       3'-UTR of COX17 mRNA. Promotes decay of COX17 mRNA by enhancing its
CC       rate of deadenylation and subsequent turnover. Predominantly binds to
CC       mRNAs encoding mitochondrial proteins and localizes them to the
CC       vicinity of mitochondria for translation. Regulates mitochondrial
CC       biogenesis, motility and morphology. {ECO:0000269|PubMed:11101532,
CC       ECO:0000269|PubMed:15337848, ECO:0000269|PubMed:16244132,
CC       ECO:0000269|PubMed:16355254, ECO:0000269|PubMed:17210948,
CC       ECO:0000269|PubMed:18094119, ECO:0000269|PubMed:18523582}.
CC   -!- SUBCELLULAR LOCATION: Mitochondrion outer membrane; Peripheral membrane
CC       protein; Cytoplasmic side. Cytoplasm. Note=Localizes to multiple
CC       discrete foci in the cytoplasm.
CC   -!- MISCELLANEOUS: Present with 846 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the PUF3 family. {ECO:0000305}.
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DR   EMBL; X97560; CAA66165.1; -; Genomic_DNA.
DR   EMBL; X91488; CAA62779.1; -; Genomic_DNA.
DR   EMBL; Z73117; CAA97457.1; -; Genomic_DNA.
DR   EMBL; Z73118; CAA97458.1; -; Genomic_DNA.
DR   EMBL; BK006945; DAA09305.1; -; Genomic_DNA.
DR   PIR; S64755; S64755.
DR   RefSeq; NP_013088.1; NM_001181833.1.
DR   PDB; 3K49; X-ray; 2.50 A; A/C/E=511-879.
DR   PDB; 3K4E; X-ray; 3.20 A; A/C/E=511-879.
DR   PDBsum; 3K49; -.
DR   PDBsum; 3K4E; -.
DR   AlphaFoldDB; Q07807; -.
DR   SMR; Q07807; -.
DR   BioGRID; 31238; 1976.
DR   DIP; DIP-4449N; -.
DR   IntAct; Q07807; 27.
DR   MINT; Q07807; -.
DR   STRING; 4932.YLL013C; -.
DR   iPTMnet; Q07807; -.
DR   MaxQB; Q07807; -.
DR   PaxDb; Q07807; -.
DR   PRIDE; Q07807; -.
DR   EnsemblFungi; YLL013C_mRNA; YLL013C; YLL013C.
DR   GeneID; 850647; -.
DR   KEGG; sce:YLL013C; -.
DR   SGD; S000003936; PUF3.
DR   VEuPathDB; FungiDB:YLL013C; -.
DR   eggNOG; KOG1488; Eukaryota.
DR   GeneTree; ENSGT00940000169170; -.
DR   HOGENOM; CLU_004017_6_1_1; -.
DR   InParanoid; Q07807; -.
DR   OMA; APLILMM; -.
DR   BioCyc; YEAST:G3O-32118-MON; -.
DR   EvolutionaryTrace; Q07807; -.
DR   PRO; PR:Q07807; -.
DR   Proteomes; UP000002311; Chromosome XII.
DR   RNAct; Q07807; protein.
DR   GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR   GO; GO:0032473; C:cytoplasmic side of mitochondrial outer membrane; IDA:SGD.
DR   GO; GO:0003730; F:mRNA 3'-UTR binding; IBA:GO_Central.
DR   GO; GO:0003729; F:mRNA binding; IDA:SGD.
DR   GO; GO:0009060; P:aerobic respiration; IMP:SGD.
DR   GO; GO:0008298; P:intracellular mRNA localization; IMP:SGD.
DR   GO; GO:0051646; P:mitochondrion localization; IMP:SGD.
DR   GO; GO:0007005; P:mitochondrion organization; IMP:SGD.
DR   GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; IDA:SGD.
DR   GO; GO:0000288; P:nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay; IMP:SGD.
DR   GO; GO:0045727; P:positive regulation of translation; IMP:SGD.
DR   GO; GO:0010608; P:post-transcriptional regulation of gene expression; IBA:GO_Central.
DR   GO; GO:0010795; P:regulation of ubiquinone biosynthetic process; IMP:SGD.
DR   CDD; cd07920; Pumilio; 1.
DR   Gene3D; 1.25.10.10; -; 1.
DR   InterPro; IPR011989; ARM-like.
DR   InterPro; IPR016024; ARM-type_fold.
DR   InterPro; IPR033133; PUM-HD.
DR   InterPro; IPR033712; Pumilio_RNA-bd.
DR   InterPro; IPR001313; Pumilio_RNA-bd_rpt.
DR   Pfam; PF00806; PUF; 8.
DR   SMART; SM00025; Pumilio; 8.
DR   SUPFAM; SSF48371; SSF48371; 1.
DR   PROSITE; PS50302; PUM; 8.
DR   PROSITE; PS50303; PUM_HD; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Membrane; Mitochondrion;
KW   Mitochondrion outer membrane; Phosphoprotein; Reference proteome; Repeat;
KW   RNA-binding.
FT   CHAIN           1..879
FT                   /note="mRNA-binding protein PUF3"
FT                   /id="PRO_0000075924"
FT   DOMAIN          513..871
FT                   /note="PUM-HD"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00318"
FT   REPEAT          538..573
FT                   /note="Pumilio 1"
FT   REPEAT          574..609
FT                   /note="Pumilio 2"
FT   REPEAT          610..645
FT                   /note="Pumilio 3"
FT   REPEAT          646..681
FT                   /note="Pumilio 4"
FT   REPEAT          682..717
FT                   /note="Pumilio 5"
FT   REPEAT          718..759
FT                   /note="Pumilio 6"
FT   REPEAT          760..795
FT                   /note="Pumilio 7"
FT   REPEAT          807..844
FT                   /note="Pumilio 8"
FT   REGION          222..256
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          344..417
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          443..512
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        370..397
FT                   /note="Pro residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        398..417
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        448..491
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOD_RES         83
FT                   /note="Phosphothreonine"
FT                   /evidence="ECO:0007744|PubMed:15665377"
FT   MOD_RES         207
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:15665377"
FT   MOD_RES         210
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MUTAGEN         553
FT                   /note="S->C: Prevents binding to COX17 mRNA and its rapid
FT                   decay and increases affinity to HO mRNA, a PUF5 target."
FT                   /evidence="ECO:0000269|PubMed:16244132"
FT   HELIX           516..522
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           536..539
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           543..547
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           550..560
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           565..575
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           576..578
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           579..584
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   TURN            586..588
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           589..598
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           601..611
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           615..620
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           624..634
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           637..644
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           645..647
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           651..656
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           660..670
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           673..675
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   TURN            677..679
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           680..683
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   TURN            684..686
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           687..691
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           696..706
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           709..717
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   TURN            718..721
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           723..728
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           732..740
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           748..762
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           765..769
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           774..784
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           787..794
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   TURN            795..797
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           802..806
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           813..818
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           823..833
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           836..855
FT                   /evidence="ECO:0007829|PDB:3K49"
FT   HELIX           865..874
FT                   /evidence="ECO:0007829|PDB:3K49"
SQ   SEQUENCE   879 AA;  98068 MW;  13F6D2D829CBCBF6 CRC64;
     MEMNMDMDMD MELASIVSSL SALSHSNNNG GQAAAAGIVN GGAAGSQQIG GFRRSSFTTA
     NEVDSEILLL HGSSESSPIF KKTALSVGTA PPFSTNSKKF FGNGGNYYQY RSTDTASLSS
     ASYNNYHTHH TAANLGKNNK VNHLLGQYSA SIAGPVYYNG NDNNNSGGEG FFEKFGKSLI
     DGTRELESQD RPDAVNTQSQ FISKSVSNAS LDTQNTFEQN VESDKNFNKL NRNTTNSGSL
     YHSSSNSGSS ASLESENAHY PKRNIWNVAN TPVFRPSNNP AAVGATNVAL PNQQDGPANN
     NFPPYMNGFP PNQFHQGPHY QNFPNYLIGS PSNFISQMIS VQIPANEDTE DSNGKKKKKA
     NRPSSVSSPS SPPNNSPFPF AYPNPMMFMP PPPLSAPQQQ QQQQQQQQQE DQQQQQQQEN
     PYIYYPTPNP IPVKMPKDEK TFKKRNNKNH PANNSNNANK QANPYLENSI PTKNTSKKNA
     SSKSNESTAN NHKSHSHSHP HSQSLQQQQQ TYHRSPLLEQ LRNSSSDKNS NSNMSLKDIF
     GHSLEFCKDQ HGSRFIQREL ATSPASEKEV IFNEIRDDAI ELSNDVFGNY VIQKFFEFGS
     KIQKNTLVDQ FKGNMKQLSL QMYACRVIQK ALEYIDSNQR IELVLELSDS VLQMIKDQNG
     NHVIQKAIET IPIEKLPFIL SSLTGHIYHL STHSYGCRVI QRLLEFGSSE DQESILNELK
     DFIPYLIQDQ YGNYVIQYVL QQDQFTNKEM VDIKQEIIET VANNVVEYSK HKFASNVVEK
     SILYGSKNQK DLIISKILPR DKNHALNLED DSPMILMIKD QFANYVIQKL VNVSEGEGKK
     LIVIAIRAYL DKLNKSNSLG NRHLASVEKL AALVENAEV
 
 
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