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
