UBR3_DANRE
ID UBR3_DANRE Reviewed; 1863 AA.
AC F1QJX5; Q05AJ6; Q1JPS8; Q6AZB6;
DT 30-AUG-2017, integrated into UniProtKB/Swiss-Prot.
DT 30-AUG-2017, sequence version 2.
DT 03-AUG-2022, entry version 68.
DE RecName: Full=E3 ubiquitin-protein ligase ubr3 {ECO:0000303|PubMed:27195754};
DE EC=2.3.2.27 {ECO:0000250|UniProtKB:Q9W3M3};
DE AltName: Full=E3 ubiquitin-protein transferase ubr3 {ECO:0000305};
GN Name=ubr3 {ECO:0000312|ZFIN:ZDB-GENE-030131-1473};
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: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).
RN [2] {ECO:0000312|EMBL:AAH78396.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1245-1863.
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000305}
RP FUNCTION, DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RX PubMed=27195754; DOI=10.1371/journal.pgen.1006054;
RA Li T., Fan J., Blanco-Sanchez B., Giagtzoglou N., Lin G., Yamamoto S.,
RA Jaiswal M., Chen K., Zhang J., Wei W., Lewis M.T., Groves A.K.,
RA Westerfield M., Jia J., Bellen H.J.;
RT "Ubr3, a Novel Modulator of Hh Signaling Affects the Degradation of Costal-
RT 2 and Kif7 through Poly-ubiquitination.";
RL PLoS Genet. 12:E1006054-E1006054(2016).
CC -!- FUNCTION: E3 ubiquitin-protein ligase which is a component of the N-end
CC rule pathway (By similarity). Recognizes and binds to proteins bearing
CC specific N-terminal residues, leading to their ubiquitination and
CC subsequent degradation (By similarity). Positively regulates
CC hedgehog/shh-signaling pathways that function in eye development,
CC neuronal specification and somite development (PubMed:27195754).
CC Activation of shh up-regulates transcription of ubr3, which in turn
CC promotes hedgehog/shh signaling possibly by controlling negative
CC regulators such as Kif7 (PubMed:27195754).
CC {ECO:0000250|UniProtKB:Q9W3M3, ECO:0000269|PubMed:27195754}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC EC=2.3.2.27; Evidence={ECO:0000250|UniProtKB:Q9W3M3};
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC {ECO:0000250|UniProtKB:Q9W3M3}.
CC -!- DEVELOPMENTAL STAGE: Expressed in the embryonic retina, central nervous
CC system and trunk (at the protein level). {ECO:0000269|PubMed:27195754}.
CC -!- DISRUPTION PHENOTYPE: Heterozygotes fail to form cohesive and
CC stratified epithelium in their optic vesicles. Average somite angle is
CC increased by 30% and the posterior central nervous system displays a
CC gain of Rohon-Beard sensory neurons. Defects are the result of
CC decreased Hh/shh-signaling demonstrated by the reduced expression of
CC the Hh/shh target gene ptch2. {ECO:0000269|PubMed:27195754}.
CC -!- SIMILARITY: Belongs to the UBR1 family. {ECO:0000305}.
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DR EMBL; CABZ01051288; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CABZ01051289; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CABZ01051291; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CU639483; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CU986282; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; FP089512; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; FQ790221; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC078396; AAH78396.1; -; mRNA.
DR EMBL; BC116612; AAI16613.1; -; mRNA.
DR EMBL; BC124477; AAI24478.1; -; mRNA.
DR RefSeq; XP_017213227.1; XM_017357738.1.
DR AlphaFoldDB; F1QJX5; -.
DR SMR; F1QJX5; -.
DR STRING; 7955.ENSDARP00000111269; -.
DR PaxDb; F1QJX5; -.
DR Ensembl; ENSDART00000181059; ENSDARP00000156490; ENSDARG00000042508.
DR GeneID; 553247; -.
DR KEGG; dre:553247; -.
DR CTD; 130507; -.
DR ZFIN; ZDB-GENE-030131-1473; ubr3.
DR eggNOG; KOG1139; Eukaryota.
DR GeneTree; ENSGT00950000183075; -.
DR InParanoid; F1QJX5; -.
DR OrthoDB; 81415at2759; -.
DR PhylomeDB; F1QJX5; -.
DR TreeFam; TF323875; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:F1QJX5; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 9.
DR Bgee; ENSDARG00000042508; Expressed in cleaving embryo and 27 other tissues.
DR ExpressionAtlas; F1QJX5; baseline.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0000151; C:ubiquitin ligase complex; IBA:GO_Central.
DR GO; GO:0061630; F:ubiquitin protein ligase activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0048592; P:eye morphogenesis; IMP:ZFIN.
DR GO; GO:0016567; P:protein ubiquitination; IBA:GO_Central.
DR GO; GO:0071596; P:ubiquitin-dependent protein catabolic process via the N-end rule pathway; IBA:GO_Central.
DR InterPro; IPR044046; E3_ligase_UBR-like_C.
DR InterPro; IPR039164; UBR1-like.
DR InterPro; IPR001841; Znf_RING.
DR InterPro; IPR003126; Znf_UBR.
DR PANTHER; PTHR21497; PTHR21497; 1.
DR Pfam; PF18995; PRT6_C; 1.
DR Pfam; PF02207; zf-UBR; 1.
DR SMART; SM00396; ZnF_UBR1; 1.
DR PROSITE; PS50089; ZF_RING_2; 1.
DR PROSITE; PS51157; ZF_UBR; 1.
PE 2: Evidence at transcript level;
KW Metal-binding; Reference proteome; Transferase; Ubl conjugation pathway;
KW Zinc; Zinc-finger.
FT CHAIN 1..1863
FT /note="E3 ubiquitin-protein ligase ubr3"
FT /id="PRO_0000441158"
FT ZN_FING 80..151
FT /note="UBR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00508"
FT ZN_FING 1270..1328
FT /note="RING-type; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT REGION 302..330
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 970..995
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1128..1152
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 303..317
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 970..986
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1135..1152
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 1375..1386
FT /note="Missing (in Ref. 2; AAI16613/AAI24478)"
FT /evidence="ECO:0000305"
FT CONFLICT 1588
FT /note="I -> V (in Ref. 2; AAH78396)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1863 AA; 210579 MW; EF37E9021465A19F CRC64;
MMAASLLRRD KKSTAAHLKA DLKRTDNSSG LRQLQELLDS VLNPERGSDP EALDWCKWLL
AGGDGFDEFC RTVRSYDNAT LCGLVWTANF VAYRCRTCGI SPCMSLCAEC FNNGDHTGHD
FNMFRSQAGG ACDCGDGNVM RESGFCNRHR LKTGENVPSV PRDLLLMSEM VLPRFIITII
QYLRDGYTEP ESAADRDLQK VLQQLDPHIS FLEELTKMGG AMRTVLTKIL TDQQTFKELS
MGQEDNVYAK KNYEKYLSAL KSSGLVSVEE KGAAGGAGDG TSDAAAGAGA LSLLGATATA
SLDDSSKEED QDGLQGVGQR KRVKLSSSTK DPSIMDTLKH KCFLEELLFW TIKYEFPQKM
VTFLLNMLPD QDYKITFTKT FVQHYAFIMK TLMKSHESDT MSNRIVHISV QLFSNEELAR
HVTEECQLLD IMVTVLLYMM ESCLIKSELQ DEENNRHVVV NCGEALLKNN TYWPLVSDFI
NILSHQSVAK RFLEDHSLLL LWMSFVSFFQ GMNLNKRELN EHVEFESQTY YAAFAAELEA
CAQPMWGLLT HCKVKETQDY TKTVVRYCLE TLQMWFDAIG FVDEPSLNQL TFHLPLHRYY
AMFLSKGVKC QGLDLDSLLP DQEMLMKIMV HPLQIQASLS EIHSNMWVRN GLQIKGQAMT
YVQSHFCNSM IDPDIYLLQV CASRLDPDYF ISSVFERFKV VDLLTMASQH QNAVLDSEQE
RPMLEGALTF LVILCSLRIH LGMSDDEILR AEMVSQLCMN DRTHSSLLDL IPENPNPKSG
VVPGSCSFEE MLSGVADFKA PVFEPGGSMQ QGMYTPKAEV WEKEFDPIMV ILRTVYRRDV
QSAMDRYSAF LKQSGVHTGN PWPPYKERTP LHPCYKGLVR LLHCKTLHIV IFTLLYKIWM
DHQNMSEHVL CMVLYLIELG LDNQVQDDKV EEEPCIEEHC HDSWFPGTSL LSNLHHVINF
VRVRVPETAP EVERKRERER ERETPPSTSS ESATFGQNLR EAQVFSLVAE RRRKFQEIIN
RSNHEASQAV RPKSSASRWL PPGTPPQLVT EILEIRESML SLLVKLHQKL SAKQNSLSLS
WLAEVDPAHH AHGDGLTAIE RILAKASARS RHSKRCLQEI CGKVCPPIPP KKISPGDKKS
MDKEERRQRA RERQQKLLAE FASRQKSFME TAMDVESPEA DAVMDVSSEE SLDSEVLYDC
VICGQSGPST EDRPTGLVVL LQASSVLGHR CRSDMPKRLP TTDEEHIYPE DTCGATHDVR
LSLMQRYFKD SSCLQSVSIG WDGGVYVQTC GHTLHIDCHK SYMESLRNDQ VLQGISVDKG
EFTCPLCRQF ANSVLPCRPG RGMETGAWHA PSTKSMSTLV KEVEDLQEQL GIFPVRASIK
QRDPILIESN LSKEMESVIK DIKNTTQKKY MDYGKNPGSP DNDFLFMYSV ARTNLELELV
HRGGNLCSGG ASAAAKRSCL NQLFHVLAMH MRLYSIDSAY NPWTRLTLST QSRENEYCDE
ERPEVPMLFR DVPSLLIIFI LTMPQPLRKE HFTCVVKVLY SLQFTQALAA LSIRFSREER
LAWSNTGAAK KNLPNSDKSW ESLLGHMISE LTKAKDVYDT NSEETSALSS SVWSPQSIEF
RLQQFCLPFL RLSCLLQHHL YGDSLPGCLV EEEFSLLTRC LGLAASVQCS GSMSSAACLE
WNISAFDLIS QWCSEVVALS DTPSQQSASL LGQDPQWAAP RLLQLPDNYN TIFQYYHRKS
CSSCGKTPKD PALCLVCGAF VCLKGHCCKQ QGVCECVLHS QHCGAATGIF LLINASVIII
IRGHRFCLWG SVYLDAHGEE DRDLRRGKPL YLCEERYRVL EQQWVAHTFD HINKRWGPHY
NGL
