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Protein

WD repeat-containing protein 48

Gene

wdr48

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at transcript leveli

Functioni

Regulator of deubiquitinating complexes. Acts as a strong activator of USP1 and USP46. Enhances the USP1-mediated deubiquitination of FANCD2; USP1 being almost inactive by itself. Also activates deubiquitinating activity of complexes containing USP12. Activates deubiquitination by increasing the catalytic turnover without increasing the affinity of deubiquitinating enzymes for the substrate. May play a role in vesicular transport or membrane fusion events necessary for transport to lysosomes.By similarity

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Ubl conjugation pathway

Names & Taxonomyi

Protein namesi
Recommended name:
WD repeat-containing protein 48
Alternative name(s):
USP1-associated factor 1
Gene namesi
Name:wdr48
Synonyms:uaf1
ORF Names:ch211-190k17.1
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Chromosome 2

Organism-specific databases

ZFINiZDB-GENE-030131-6622. wdr48b.

Subcellular locationi

  • Nucleus By similarity
  • Cytoplasm By similarity
  • Lysosome By similarity
  • Late endosome By similarity

  • Note: Mainly in cytoplasmic compartments.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endosome, Lysosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 677677WD repeat-containing protein 48PRO_0000051404Add
BLAST

Proteomic databases

PaxDbiQ6PFM9.

Expressioni

Gene expression databases

BgeeiQ6PFM9.

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000056247.

Structurei

3D structure databases

ProteinModelPortaliQ6PFM9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati28 – 6740WD 1Add
BLAST
Repeati73 – 11240WD 2Add
BLAST
Repeati115 – 15440WD 3Add
BLAST
Repeati166 – 20540WD 4Add
BLAST
Repeati208 – 24740WD 5Add
BLAST
Repeati250 – 28940WD 6Add
BLAST
Repeati292 – 33443WD 7Add
BLAST
Repeati358 – 39740WD 8Add
BLAST

Domaini

The WD repeats are required for the interaction with deubiquitinating enzymes USP1, USP12 and USP46.By similarity

Sequence similaritiesi

Belongs to the WD repeat WDR48 family.Curated
Contains 8 WD repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

eggNOGiKOG0308. Eukaryota.
ENOG410XRJ5. LUCA.
GeneTreeiENSGT00820000127095.
HOGENOMiHOG000007343.
HOVERGENiHBG079413.
InParanoidiQ6PFM9.
KOiK15361.
OMAiXACKVED.
OrthoDBiEOG7JDQX1.
PhylomeDBiQ6PFM9.
TreeFamiTF315205.

Family and domain databases

Gene3Di2.130.10.10. 2 hits.
InterProiIPR021772. DUF3337.
IPR020472. G-protein_beta_WD-40_rep.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF11816. DUF3337. 1 hit.
PF00400. WD40. 4 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00320. WD40. 7 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS00678. WD_REPEATS_1. 2 hits.
PS50082. WD_REPEATS_2. 5 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q6PFM9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATLHRQNAA GRRKVQVSYV IRDEVEKYNR NGVNALQLDP ALNRLFTAGR
60 70 80 90 100
DSIIRIWSVN QHKQDPYIAS MEHHTDWVND IILCCNGKTL ISASSDTTVK
110 120 130 140 150
VWNAHKGFCM STLRTHKDYV KALAYAKDKE LVASAGLDRQ IFLWDVNTLT
160 170 180 190 200
ALTASNNTVT TSSLSGNKDS IYSLAMNQTG TVIISGSTEK VLRVWDPRTC
210 220 230 240 250
AKLMKLKGHT DNVKSLLLNR DGTQCLSGSS DGTIRLWSLG QQRCIATYRV
260 270 280 290 300
HDEGVWALQV NEAFTHIYSG GRDRKIYCTD LRNPDMRVLI CEEKAPVLRM
310 320 330 340 350
ELDRSADPPQ SIWVSTTKSF VNKWSLKAMH NFRASGDYDN DCSAPLTPLC
360 370 380 390 400
TQPEQVIKGG TSIVQCHILN DKRHILTKDT NNSVAFWDVL KACKGEDLGK
410 420 430 440 450
VDFDEEVKKR FKMVYVPNWF SVDLKTGMLT ITLDESDCFA AWVAAKDAGF
460 470 480 490 500
TSPDGSDPKL NLGGLLLQAL LEFWPRTHIN PMEEEENELN HVNGEQESRI
510 520 530 540 550
QKGNGYFQVP PHTPVIFGEA GGRTLFRLLC RDSGGETESM LLNETVPQWV
560 570 580 590 600
IDITVDKNMP KFNKIPFYLQ PHSSSGAKTL KKDRLSASDM LQVRKVMEHV
610 620 630 640 650
YEKIINLDTE SQATSSSAND KPGEQEKEED VSVMAEEKIE LMCLDQVLDP
660 670
NMDLRTVKHF IWKSGGDLTI HYRQKST
Length:677
Mass (Da):76,230
Last modified:July 7, 2009 - v2
Checksum:i02CA845B9FF77E3C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti344 – 3441A → T in AAH57489 (Ref. 2) Curated
Sequence conflicti609 – 6091T → M in AAH57489 (Ref. 2) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX284666 Genomic DNA. Translation: CAQ15013.1.
BC057489 mRNA. Translation: AAH57489.1.
RefSeqiNP_999874.1. NM_214709.1.
UniGeneiDr.5219.

Genome annotation databases

EnsembliENSDART00000056248; ENSDARP00000056247; ENSDARG00000038543.
GeneIDi334682.
KEGGidre:334682.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX284666 Genomic DNA. Translation: CAQ15013.1.
BC057489 mRNA. Translation: AAH57489.1.
RefSeqiNP_999874.1. NM_214709.1.
UniGeneiDr.5219.

3D structure databases

ProteinModelPortaliQ6PFM9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000056247.

Proteomic databases

PaxDbiQ6PFM9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000056248; ENSDARP00000056247; ENSDARG00000038543.
GeneIDi334682.
KEGGidre:334682.

Organism-specific databases

CTDi334682.
ZFINiZDB-GENE-030131-6622. wdr48b.

Phylogenomic databases

eggNOGiKOG0308. Eukaryota.
ENOG410XRJ5. LUCA.
GeneTreeiENSGT00820000127095.
HOGENOMiHOG000007343.
HOVERGENiHBG079413.
InParanoidiQ6PFM9.
KOiK15361.
OMAiXACKVED.
OrthoDBiEOG7JDQX1.
PhylomeDBiQ6PFM9.
TreeFamiTF315205.

Miscellaneous databases

NextBioi20810509.
PROiQ6PFM9.

Gene expression databases

BgeeiQ6PFM9.

Family and domain databases

Gene3Di2.130.10.10. 2 hits.
InterProiIPR021772. DUF3337.
IPR020472. G-protein_beta_WD-40_rep.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF11816. DUF3337. 1 hit.
PF00400. WD40. 4 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00320. WD40. 7 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS00678. WD_REPEATS_1. 2 hits.
PS50082. WD_REPEATS_2. 5 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Tuebingen.
  2. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: AB.
    Tissue: Embryo.

Entry informationi

Entry nameiWDR48_DANRE
AccessioniPrimary (citable) accession number: Q6PFM9
Secondary accession number(s): B0S5N8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: July 7, 2009
Last modified: May 11, 2016
This is version 91 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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.