ID   WDR48_DANRE             Reviewed;         677 AA.
AC   Q6PFM9; B0S5N8;
DT   20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT   07-JUL-2009, sequence version 2.
DT   03-AUG-2022, entry version 121.
DE   RecName: Full=WD repeat-containing protein 48;
DE   AltName: Full=USP1-associated factor 1;
GN   Name=wdr48; Synonyms=uaf1; ORFNames=ch211-190k17.1;
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;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Tuebingen;
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).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=AB; TISSUE=Embryo;
RG   NIH - Zebrafish Gene Collection (ZGC) project;
RL   Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Regulator of deubiquitinating complexes, which acts as a
CC       strong activator of usp1, usp12 and usp46. Enhances the usp1-mediated
CC       deubiquitination of fancd2; usp1 being almost inactive by itself.
CC       Activates deubiquitination by increasing the catalytic turnover without
CC       increasing the affinity of deubiquitinating enzymes for the substrate.
CC       Also activates deubiquitinating activity of complexes containing usp12.
CC       Together with rad51ap1, promotes DNA repair by stimulating rad51-
CC       mediated homologous recombination. Binds single-stranded DNA (ssDNA)
CC       and double-stranded DNA (dsDNA). DNA-binding is required both for usp1-
CC       mediated deubiquitination of fancd2 and stimulation of rad51-mediated
CC       homologous recombination: both wdr48/uaf1 and rad51ap1 have coordinated
CC       role in DNA-binding during these processes. Together with atad5 and by
CC       regulating usp1 activity, has a role in pcna-mediated translesion
CC       synthesis (TLS) by deubiquitinating monoubiquitinated pcna. Together
CC       with atad5, has a role in recruiting rad51 to stalled forks during
CC       replication stress. {ECO:0000250|UniProtKB:Q8TAF3}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q8TAF3}. Cytoplasm
CC       {ECO:0000250|UniProtKB:Q8TAF3}. Lysosome
CC       {ECO:0000250|UniProtKB:Q8TAF3}. Late endosome
CC       {ECO:0000250|UniProtKB:Q8TAF3}. Note=Mainly in cytoplasmic
CC       compartments. {ECO:0000250|UniProtKB:Q8TAF3}.
CC   -!- DOMAIN: The WD repeats are required for the interaction with
CC       deubiquitinating enzymes USP1, USP12 and USP46.
CC       {ECO:0000250|UniProtKB:Q8TAF3}.
CC   -!- SIMILARITY: Belongs to the WD repeat WDR48 family. {ECO:0000305}.
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DR   EMBL; BX284666; CAQ15013.1; -; Genomic_DNA.
DR   EMBL; BC057489; AAH57489.1; -; mRNA.
DR   RefSeq; NP_999874.1; NM_214709.1.
DR   AlphaFoldDB; Q6PFM9; -.
DR   SMR; Q6PFM9; -.
DR   STRING; 7955.ENSDARP00000056247; -.
DR   PaxDb; Q6PFM9; -.
DR   Ensembl; ENSDART00000056248; ENSDARP00000056247; ENSDARG00000038543.
DR   GeneID; 334682; -.
DR   KEGG; dre:334682; -.
DR   CTD; 334682; -.
DR   ZFIN; ZDB-GENE-030131-6622; wdr48b.
DR   eggNOG; KOG0308; Eukaryota.
DR   GeneTree; ENSGT00920000149157; -.
DR   HOGENOM; CLU_014960_0_1_1; -.
DR   InParanoid; Q6PFM9; -.
DR   OMA; ILQMYRI; -.
DR   OrthoDB; 261328at2759; -.
DR   PhylomeDB; Q6PFM9; -.
DR   TreeFam; TF315205; -.
DR   PRO; PR:Q6PFM9; -.
DR   Proteomes; UP000000437; Genome assembly.
DR   Proteomes; UP000814640; Chromosome 2.
DR   Bgee; ENSDARG00000038543; Expressed in early embryo and 26 other tissues.
DR   GO; GO:0005770; C:late endosome; IEA:UniProtKB-SubCell.
DR   GO; GO:0005764; C:lysosome; IEA:UniProtKB-SubCell.
DR   GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR   GO; GO:0035800; F:deubiquitinase activator activity; ISS:UniProtKB.
DR   GO; GO:0003677; F:DNA binding; ISS:UniProtKB.
DR   GO; GO:0003690; F:double-stranded DNA binding; ISS:UniProtKB.
DR   GO; GO:0003697; F:single-stranded DNA binding; ISS:UniProtKB.
DR   GO; GO:0043130; F:ubiquitin binding; IBA:GO_Central.
DR   GO; GO:0006974; P:cellular response to DNA damage stimulus; ISS:UniProtKB.
DR   GO; GO:0000724; P:double-strand break repair via homologous recombination; IBA:GO_Central.
DR   GO; GO:1905168; P:positive regulation of double-strand break repair via homologous recombination; ISS:UniProtKB.
DR   GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
DR   Gene3D; 2.130.10.10; -; 2.
DR   InterPro; IPR020472; G-protein_beta_WD-40_rep.
DR   InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR   InterPro; IPR001680; WD40_repeat.
DR   InterPro; IPR019775; WD40_repeat_CS.
DR   InterPro; IPR036322; WD40_repeat_dom_sf.
DR   InterPro; IPR021772; WDR48/Bun107.
DR   Pfam; PF11816; DUF3337; 1.
DR   Pfam; PF00400; WD40; 4.
DR   PRINTS; PR00320; GPROTEINBRPT.
DR   SMART; SM00320; WD40; 7.
DR   SUPFAM; SSF50978; SSF50978; 1.
DR   PROSITE; PS00678; WD_REPEATS_1; 2.
DR   PROSITE; PS50082; WD_REPEATS_2; 5.
DR   PROSITE; PS50294; WD_REPEATS_REGION; 1.
PE   2: Evidence at transcript level;
KW   Cytoplasm; DNA damage; DNA repair; DNA-binding; Endosome; Lysosome;
KW   Nucleus; Reference proteome; Repeat; Ubl conjugation pathway; WD repeat.
FT   CHAIN           1..677
FT                   /note="WD repeat-containing protein 48"
FT                   /id="PRO_0000051404"
FT   REPEAT          28..67
FT                   /note="WD 1"
FT   REPEAT          73..112
FT                   /note="WD 2"
FT   REPEAT          115..154
FT                   /note="WD 3"
FT   REPEAT          166..205
FT                   /note="WD 4"
FT   REPEAT          208..247
FT                   /note="WD 5"
FT   REPEAT          250..289
FT                   /note="WD 6"
FT   REPEAT          292..334
FT                   /note="WD 7"
FT   REPEAT          358..397
FT                   /note="WD 8"
FT   REGION          611..632
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   CONFLICT        344
FT                   /note="A -> T (in Ref. 2; AAH57489)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        609
FT                   /note="T -> M (in Ref. 2; AAH57489)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   677 AA;  76230 MW;  02CA845B9FF77E3C CRC64;
     MATLHRQNAA GRRKVQVSYV IRDEVEKYNR NGVNALQLDP ALNRLFTAGR DSIIRIWSVN
     QHKQDPYIAS MEHHTDWVND IILCCNGKTL ISASSDTTVK VWNAHKGFCM STLRTHKDYV
     KALAYAKDKE LVASAGLDRQ IFLWDVNTLT ALTASNNTVT TSSLSGNKDS IYSLAMNQTG
     TVIISGSTEK VLRVWDPRTC AKLMKLKGHT DNVKSLLLNR DGTQCLSGSS DGTIRLWSLG
     QQRCIATYRV HDEGVWALQV NEAFTHIYSG GRDRKIYCTD LRNPDMRVLI CEEKAPVLRM
     ELDRSADPPQ SIWVSTTKSF VNKWSLKAMH NFRASGDYDN DCSAPLTPLC TQPEQVIKGG
     TSIVQCHILN DKRHILTKDT NNSVAFWDVL KACKGEDLGK VDFDEEVKKR FKMVYVPNWF
     SVDLKTGMLT ITLDESDCFA AWVAAKDAGF TSPDGSDPKL NLGGLLLQAL LEFWPRTHIN
     PMEEEENELN HVNGEQESRI QKGNGYFQVP PHTPVIFGEA GGRTLFRLLC RDSGGETESM
     LLNETVPQWV IDITVDKNMP KFNKIPFYLQ PHSSSGAKTL KKDRLSASDM LQVRKVMEHV
     YEKIINLDTE SQATSSSAND KPGEQEKEED VSVMAEEKIE LMCLDQVLDP NMDLRTVKHF
     IWKSGGDLTI HYRQKST