PUM3_DANRE
ID PUM3_DANRE Reviewed; 629 AA.
AC X1WGX5;
DT 20-JAN-2016, integrated into UniProtKB/Swiss-Prot.
DT 20-JAN-2016, sequence version 2.
DT 03-AUG-2022, entry version 49.
DE RecName: Full=Pumilio homolog 3 {ECO:0000305};
GN Name=pum3; Synonyms=puf-a {ECO:0000303|PubMed:19319195};
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955 {ECO:0000312|Proteomes:UP000000437};
RN [1] {ECO:0000305}
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL
RP STAGE, AND DISRUPTION PHENOTYPE.
RX PubMed=19319195; DOI=10.1371/journal.pone.0004980;
RA Kuo M.W., Wang S.H., Chang J.C., Chang C.H., Huang L.J., Lin H.H., Yu A.L.,
RA Li W.H., Yu J.;
RT "A novel puf-A gene predicted from evolutionary analysis is involved in the
RT development of eyes and primordial germ-cells.";
RL PLoS ONE 4:E4980-E4980(2009).
RN [2] {ECO:0000312|Proteomes:UP000000437}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen {ECO:0000312|Proteomes:UP000000437};
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
CC -!- FUNCTION: Inhibits the poly(ADP-ribosyl)ation activity of PARP1 and the
CC degradation of PARP1 by CASP3 following genotoxic stress (By
CC similarity). Binds to double-stranded RNA or DNA without sequence
CC specificity (By similarity). Involved in development of the eye and of
CC primordial germ cells (PubMed:19319195). {ECO:0000250|UniProtKB:Q15397,
CC ECO:0000269|PubMed:19319195}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus
CC {ECO:0000250|UniProtKB:Q15397}. Nucleus, nucleoplasm
CC {ECO:0000250|UniProtKB:Q15397}. Chromosome
CC {ECO:0000250|UniProtKB:Q15397}.
CC -!- TISSUE SPECIFICITY: In adult, expressed at high levels in eye and ovary
CC and at lower levels in brain, testis and head kidney. In the adult
CC ovary, prominently expressed in early immature follicles.
CC {ECO:0000269|PubMed:19319195}.
CC -!- DEVELOPMENTAL STAGE: Expressed throughout embryogenesis. In the adult
CC ovary, strong expression detected in primitive stage I ovarian
CC follicles with levels declining sharply and becoming negligible in
CC subsequent stages of oocyte development. {ECO:0000269|PubMed:19319195}.
CC -!- DOMAIN: A 90 degree bend between Pumilio repeats 3 and 4 gives rise to
CC a L-shaped protein. {ECO:0000250|UniProtKB:Q15397}.
CC -!- DISRUPTION PHENOTYPE: Morpholino knockdown in embryos results in small
CC eyes, small head and brain edema at 1 and 2 days post-fertilization
CC (dpf). At 3 and 5 dpf, mutants exhibit features of an undifferentiated
CC retina with loss of detailed architecture and a significant reduction
CC in eye size. Structures such as the rod and cone layers are not
CC concentrically organized and retinal ganglion cells and plexiform
CC layers are not readily discernible. Mutants also show abnormal
CC primordial germ cell migration. {ECO:0000269|PubMed:19319195}.
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DR EMBL; CR628386; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; XP_003199363.1; XM_003199315.3.
DR AlphaFoldDB; X1WGX5; -.
DR SMR; X1WGX5; -.
DR STRING; 7955.ENSDARP00000129484; -.
DR PaxDb; X1WGX5; -.
DR Ensembl; ENSDART00000154037; ENSDARP00000129484; ENSDARG00000087779.
DR Ensembl; ENSDART00000189109; ENSDARP00000153216; ENSDARG00000087779.
DR GeneID; 553068; -.
DR CTD; 9933; -.
DR ZFIN; ZDB-GENE-030131-9808; pum3.
DR eggNOG; KOG2050; Eukaryota.
DR GeneTree; ENSGT00390000015757; -.
DR HOGENOM; CLU_013994_0_1_1; -.
DR OMA; WILDDVY; -.
DR OrthoDB; 845051at2759; -.
DR PRO; PR:X1WGX5; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 10.
DR Bgee; ENSDARG00000087779; Expressed in presomitic mesoderm and 46 other tissues.
DR ExpressionAtlas; X1WGX5; baseline.
DR GO; GO:0005694; C:chromosome; ISS:UniProtKB.
DR GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003729; F:mRNA binding; IBA:GO_Central.
DR GO; GO:0008354; P:germ cell migration; IMP:ZFIN.
DR GO; GO:0006417; P:regulation of translation; IBA:GO_Central.
DR Gene3D; 1.25.10.10; -; 2.
DR InterPro; IPR011989; ARM-like.
DR InterPro; IPR016024; ARM-type_fold.
DR InterPro; IPR012959; CPL_dom.
DR InterPro; IPR033133; PUM-HD.
DR InterPro; IPR040059; PUM3.
DR InterPro; IPR001313; Pumilio_RNA-bd_rpt.
DR PANTHER; PTHR13389; PTHR13389; 1.
DR Pfam; PF08144; CPL; 1.
DR Pfam; PF00806; PUF; 2.
DR SMART; SM00025; Pumilio; 6.
DR SUPFAM; SSF48371; SSF48371; 2.
DR PROSITE; PS50302; PUM; 5.
DR PROSITE; PS50303; PUM_HD; 1.
PE 2: Evidence at transcript level;
KW Chromosome; DNA-binding; Nucleus; Reference proteome; Repeat; RNA-binding.
FT CHAIN 1..629
FT /note="Pumilio homolog 3"
FT /id="PRO_0000435333"
FT DOMAIN 120..473
FT /note="PUM-HD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00318"
FT REPEAT 160..195
FT /note="Pumilio 1"
FT /evidence="ECO:0000250|UniProtKB:Q15397"
FT REPEAT 196..231
FT /note="Pumilio 2"
FT /evidence="ECO:0000250|UniProtKB:Q15397"
FT REPEAT 232..260
FT /note="Pumilio 3"
FT /evidence="ECO:0000250|UniProtKB:Q15397"
FT REPEAT 272..308
FT /note="Pumilio 4"
FT /evidence="ECO:0000250|UniProtKB:Q15397"
FT REPEAT 309..344
FT /note="Pumilio 5"
FT /evidence="ECO:0000250|UniProtKB:Q15397"
FT REPEAT 345..380
FT /note="Pumilio 6"
FT /evidence="ECO:0000250|UniProtKB:Q15397"
FT REPEAT 381..418
FT /note="Pumilio 7"
FT /evidence="ECO:0000250|UniProtKB:Q15397"
FT REPEAT 419..487
FT /note="Pumilio 8"
FT /evidence="ECO:0000250|UniProtKB:Q15397"
FT REPEAT 488..534
FT /note="Pumilio 9"
FT /evidence="ECO:0000250|UniProtKB:Q15397"
FT REPEAT 535..579
FT /note="Pumilio 10"
FT /evidence="ECO:0000250|UniProtKB:Q15397"
FT REPEAT 580..618
FT /note="Pumilio 11"
FT /evidence="ECO:0000250|UniProtKB:Q15397"
FT REGION 1..92
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 88..100
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000250|UniProtKB:Q15397"
FT COMPBIAS 1..21
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 35..49
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 69..92
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 85
FT /note="D -> A (in Ref. 1; no nucleotide entry)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 629 AA; 71359 MW; 73853BC76FC54523 CRC64;
MEGKPRKKSF TPRDGKKPSF KSKGKPGGKP QGKRPFKPHN NDKGKGFRKS GGEGGPQKFN
RKPTDGKFAK KRKFPGDRIK QEEGDERKKP KWDEFKQKKK ELKLNRQQTD RKESYQIVSR
AKQVWEMVRR KDCDKQKRTK LMKELQDLVK GKIKTIAFAH DSTRVLQCFI QFGSDKQRKE
VFDELKEHIV ELSKSKYARN IVKKFLMYGS KEQVGEVMLA FKGKVRQMLR HSEASSVVEY
AYNDKAILSQ RLMLTEELYG NTFTVLKSSV CPTLEKVLEA NPGKLESILD EMKQILTPMA
QKEAVIKHSL VHKVFLDFFE HAPDKQRTEM IESIREAVVY MAHTHDGARV TMHCLWHGTT
KDRKVIVKTM KSYIAKFAMG EYAHLVLLAA FDCIDDTKLV KQIIISEMVS SLSEIISNKH
GKKVLLYLLS PRDPAHLLPE IIQVLEKGDG NAHSKKDVLI RRKELLEAAS PSLLNHLCEN
AQSMVMDKSC CVVVSDILGS AVGDLRPAME AVAALADGPL IPGGKDGQLH MAEHPAGHLV
LKWLIEQDTK MKDTEREERF SRILLEKVGL ENLKTWASVN RGAIILCCLL QSADESVAEE
VKAMLKSSIP ELQRLQNSKG IEVLLEKLA
