MIB1_DANRE
ID MIB1_DANRE Reviewed; 1030 AA.
AC Q804S5; Q8JHG3;
DT 05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=E3 ubiquitin-protein ligase mib1;
DE EC=2.3.2.27;
DE AltName: Full=Protein mind bomb;
DE AltName: Full=RING-type E3 ubiquitin transferase mib1 {ECO:0000305};
GN Name=mib1; Synonyms=mib;
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 [MRNA], ENZYME ACTIVITY, FUNCTION, SUBCELLULAR
RP LOCATION, INTERACTION WITH DLD, AND MUTAGENESIS OF CYS-1009 AND MET-1013.
RX PubMed=12530964; DOI=10.1016/s1534-5807(02)00409-4;
RA Itoh M., Kim C.-H., Palardy G., Oda T., Jiang Y.-J., Maust D., Yeo S.-Y.,
RA Lorick K., Wright G.J., Ariza-McNaughton L., Weissman A.M., Lewis J.,
RA Chandrasekharappa S.C., Chitnis A.B.;
RT "Mind bomb is a ubiquitin ligase that is essential for efficient activation
RT of Notch signaling by Delta.";
RL Dev. Cell 4:67-82(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-237, FUNCTION, AND DISRUPTION
RP PHENOTYPE.
RC TISSUE=Embryo;
RX PubMed=12006978; DOI=10.1038/ng896;
RA Golling G., Amsterdam A., Sun Z., Antonelli M., Maldonado E., Chen W.,
RA Burgess S., Haldi M., Artzt K., Farrington S., Lin S.-Y., Nissen R.M.,
RA Hopkins N.;
RT "Insertional mutagenesis in zebrafish rapidly identifies genes essential
RT for early vertebrate development.";
RL Nat. Genet. 31:135-140(2002).
RN [3]
RP FUNCTION.
RX PubMed=9806913; DOI=10.1242/dev.125.23.4637;
RA Haddon C., Jiang Y.-J., Smithers L., Lewis J.;
RT "Delta-Notch signalling and the patterning of sensory cell differentiation
RT in the zebrafish ear: evidence from the mind bomb mutant.";
RL Development 125:4637-4644(1998).
RN [4]
RP FUNCTION.
RX PubMed=10074451; DOI=10.1016/s0960-9822(99)80113-4;
RA Appel B., Fritz A., Westerfield M., Grunwald D.J., Eisen J.S., Riley B.B.;
RT "Delta-mediated specification of midline cell fates in zebrafish embryos.";
RL Curr. Biol. 9:247-256(1999).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, DOMAIN, AND INTERACTION WITH DLA AND DLD.
RX PubMed=15013799; DOI=10.1016/j.ydbio.2003.11.010;
RA Chen W., Corliss D.C.;
RT "Three modules of zebrafish Mind bomb work cooperatively to promote Delta
RT ubiquitination and endocytosis.";
RL Dev. Biol. 267:361-373(2004).
RN [6]
RP FUNCTION.
RX PubMed=14579383; DOI=10.1002/dvdy.10429;
RA Bingham S., Chaudhari S., Vanderlaan G., Itoh M., Chitnis A.,
RA Chandrasekhar A.;
RT "Neurogenic phenotype of mind bomb mutants leads to severe patterning
RT defects in the zebrafish hindbrain.";
RL Dev. Dyn. 228:451-463(2003).
RN [7]
RP FUNCTION.
RX PubMed=15689380; DOI=10.1242/dev.01644;
RA Crosnier C., Vargesson N., Gschmeissner S., Ariza-McNaughton L.,
RA Morrison A., Lewis J.;
RT "Delta-Notch signalling controls commitment to a secretory fate in the
RT zebrafish intestine.";
RL Development 132:1093-1104(2005).
CC -!- FUNCTION: E3 ubiquitin-protein ligase that mediates ubiquitination of
CC Delta receptors, which act as ligands of Notch proteins. Positively
CC regulates the Delta-mediated Notch signaling by ubiquitinating the
CC intracellular domain of Delta, leading to endocytosis of Delta
CC receptors. It thereby participates in many processes regulated by the
CC Notch signaling pathway, such as midline cell fate specification prior
CC to germ layer formation, patterning of sensory cell differentiation in
CC the ear, neurogenesis of the hindbrain and commitment to a secretory
CC fate in the intestine. Essential for early embryonic development.
CC {ECO:0000269|PubMed:10074451, ECO:0000269|PubMed:12006978,
CC ECO:0000269|PubMed:12530964, ECO:0000269|PubMed:14579383,
CC ECO:0000269|PubMed:15013799, ECO:0000269|PubMed:15689380,
CC ECO:0000269|PubMed:9806913}.
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;
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC -!- SUBUNIT: Interacts with deltaA (dla) and deltaD (dld).
CC {ECO:0000269|PubMed:12530964, ECO:0000269|PubMed:15013799}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton, microtubule organizing
CC center, centrosome, centriolar satellite {ECO:0000250}. Cytoplasm. Cell
CC membrane. Note=Localizes to the plasma membrane.
CC -!- DOMAIN: The N-terminal domain (1-440) mediates the interaction with
CC Delta receptors. {ECO:0000269|PubMed:15013799}.
CC -!- DOMAIN: The ANK repeats are involved in Delta receptor internalization.
CC {ECO:0000269|PubMed:15013799}.
CC -!- DOMAIN: The RING fingers mediate the E3 ligase activity. The third RING
CC finger probably plays a central role in this process. The role of the
CC other RING fingers remains unclear. {ECO:0000269|PubMed:15013799}.
CC -!- DISRUPTION PHENOTYPE: Mutants have a disorganized brain and neural
CC tube, bent tail and very small or absent otoliths.
CC {ECO:0000269|PubMed:12006978}.
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DR EMBL; AF537301; AAO37830.1; -; mRNA.
DR EMBL; AF506233; AAM34677.1; -; mRNA.
DR RefSeq; NP_775393.2; NM_173286.3.
DR AlphaFoldDB; Q804S5; -.
DR SMR; Q804S5; -.
DR BioGRID; 87906; 62.
DR STRING; 7955.ENSDARP00000109025; -.
DR PaxDb; Q804S5; -.
DR PeptideAtlas; Q804S5; -.
DR Ensembl; ENSDART00000165634; ENSDARP00000139883; ENSDARG00000102184.
DR GeneID; 352910; -.
DR KEGG; dre:352910; -.
DR CTD; 57534; -.
DR ZFIN; ZDB-GENE-030404-2; mib1.
DR eggNOG; KOG0504; Eukaryota.
DR eggNOG; KOG4582; Eukaryota.
DR GeneTree; ENSGT00940000156781; -.
DR HOGENOM; CLU_007287_1_0_1; -.
DR InParanoid; Q804S5; -.
DR SignaLink; Q804S5; -.
DR UniPathway; UPA00143; -.
DR PRO; PR:Q804S5; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 2.
DR Bgee; ENSDARG00000102184; Expressed in muscle tissue and 28 other tissues.
DR ExpressionAtlas; Q804S5; baseline.
DR GO; GO:0005737; C:cytoplasm; IDA:ZFIN.
DR GO; GO:0031410; C:cytoplasmic vesicle; IDA:ZFIN.
DR GO; GO:0030139; C:endocytic vesicle; IDA:ZFIN.
DR GO; GO:0005815; C:microtubule organizing center; IEA:UniProtKB-SubCell.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IGI:ZFIN.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0032991; C:protein-containing complex; IPI:ZFIN.
DR GO; GO:0000151; C:ubiquitin ligase complex; IC:ZFIN.
DR GO; GO:0042802; F:identical protein binding; IPI:ZFIN.
DR GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:ZFIN.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0048899; P:anterior lateral line development; IMP:ZFIN.
DR GO; GO:0001568; P:blood vessel development; IMP:ZFIN.
DR GO; GO:0048514; P:blood vessel morphogenesis; IMP:ZFIN.
DR GO; GO:0007420; P:brain development; IMP:ZFIN.
DR GO; GO:0007417; P:central nervous system development; IMP:ZFIN.
DR GO; GO:0060216; P:definitive hemopoiesis; IMP:ZFIN.
DR GO; GO:0007368; P:determination of left/right symmetry; IMP:ZFIN.
DR GO; GO:0048066; P:developmental pigmentation; IMP:ZFIN.
DR GO; GO:0021536; P:diencephalon development; IMP:ZFIN.
DR GO; GO:0048546; P:digestive tract morphogenesis; IMP:ZFIN.
DR GO; GO:0031076; P:embryonic camera-type eye development; IMP:ZFIN.
DR GO; GO:0009880; P:embryonic pattern specification; IMP:ZFIN.
DR GO; GO:0006897; P:endocytosis; IBA:GO_Central.
DR GO; GO:0001885; P:endothelial cell development; IMP:ZFIN.
DR GO; GO:0002064; P:epithelial cell development; IMP:ZFIN.
DR GO; GO:0021508; P:floor plate formation; IMP:ZFIN.
DR GO; GO:0048859; P:formation of anatomical boundary; IMP:ZFIN.
DR GO; GO:0048699; P:generation of neurons; IMP:ZFIN.
DR GO; GO:0010001; P:glial cell differentiation; IMP:ZFIN.
DR GO; GO:0021986; P:habenula development; IMP:ZFIN.
DR GO; GO:0035315; P:hair cell differentiation; IMP:ZFIN.
DR GO; GO:0007507; P:heart development; IMP:ZFIN.
DR GO; GO:0002244; P:hematopoietic progenitor cell differentiation; IMP:ZFIN.
DR GO; GO:0060218; P:hematopoietic stem cell differentiation; IMP:ZFIN.
DR GO; GO:0030097; P:hemopoiesis; IMP:ZFIN.
DR GO; GO:0030902; P:hindbrain development; IMP:ZFIN.
DR GO; GO:0060113; P:inner ear receptor cell differentiation; IMP:ZFIN.
DR GO; GO:0048892; P:lateral line nerve development; IMP:ZFIN.
DR GO; GO:0030318; P:melanocyte differentiation; IMP:ZFIN.
DR GO; GO:0003407; P:neural retina development; IMP:ZFIN.
DR GO; GO:0022008; P:neurogenesis; IMP:ZFIN.
DR GO; GO:0048666; P:neuron development; IMP:ZFIN.
DR GO; GO:0030182; P:neuron differentiation; IMP:ZFIN.
DR GO; GO:0048663; P:neuron fate commitment; IMP:ZFIN.
DR GO; GO:0048665; P:neuron fate specification; IMP:ZFIN.
DR GO; GO:0007219; P:Notch signaling pathway; IMP:ZFIN.
DR GO; GO:0060035; P:notochord cell development; IMP:ZFIN.
DR GO; GO:0030903; P:notochord development; IMP:ZFIN.
DR GO; GO:0003408; P:optic cup formation involved in camera-type eye development; IMP:ZFIN.
DR GO; GO:0071599; P:otic vesicle development; IMP:ZFIN.
DR GO; GO:0050931; P:pigment cell differentiation; IMP:ZFIN.
DR GO; GO:0008284; P:positive regulation of cell population proliferation; IGI:ZFIN.
DR GO; GO:0045747; P:positive regulation of Notch signaling pathway; IMP:ZFIN.
DR GO; GO:0031398; P:positive regulation of protein ubiquitination; IPI:ZFIN.
DR GO; GO:0048916; P:posterior lateral line development; IMP:ZFIN.
DR GO; GO:0048920; P:posterior lateral line neuromast primordium migration; IGI:ZFIN.
DR GO; GO:0039022; P:pronephric duct development; IMP:ZFIN.
DR GO; GO:0048793; P:pronephros development; IMP:ZFIN.
DR GO; GO:0051865; P:protein autoubiquitination; IDA:ZFIN.
DR GO; GO:0016567; P:protein ubiquitination; IDA:ZFIN.
DR GO; GO:0045685; P:regulation of glial cell differentiation; IMP:ZFIN.
DR GO; GO:0045664; P:regulation of neuron differentiation; IMP:ZFIN.
DR GO; GO:0008593; P:regulation of Notch signaling pathway; IMP:ZFIN.
DR GO; GO:0002090; P:regulation of receptor internalization; IDA:ZFIN.
DR GO; GO:0048259; P:regulation of receptor-mediated endocytosis; IMP:ZFIN.
DR GO; GO:0021654; P:rhombomere boundary formation; IMP:ZFIN.
DR GO; GO:0021546; P:rhombomere development; IMP:ZFIN.
DR GO; GO:0001756; P:somitogenesis; IMP:ZFIN.
DR GO; GO:0021519; P:spinal cord association neuron specification; IMP:ZFIN.
DR GO; GO:0021510; P:spinal cord development; IMP:ZFIN.
DR GO; GO:0021520; P:spinal cord motor neuron cell fate specification; IMP:ZFIN.
DR GO; GO:0002040; P:sprouting angiogenesis; IGI:ZFIN.
DR GO; GO:0061195; P:taste bud formation; IMP:ZFIN.
DR GO; GO:0061551; P:trigeminal ganglion development; IMP:ZFIN.
DR GO; GO:0070086; P:ubiquitin-dependent endocytosis; IPI:ZFIN.
DR GO; GO:0001570; P:vasculogenesis; IMP:ZFIN.
DR GO; GO:0021514; P:ventral spinal cord interneuron differentiation; IMP:ZFIN.
DR GO; GO:0021521; P:ventral spinal cord interneuron specification; IMP:ZFIN.
DR CDD; cd02339; ZZ_Mind_bomb; 1.
DR Gene3D; 1.25.40.20; -; 3.
DR Gene3D; 3.30.40.10; -; 3.
DR Gene3D; 3.30.60.90; -; 1.
DR InterPro; IPR002110; Ankyrin_rpt.
DR InterPro; IPR036770; Ankyrin_rpt-contain_sf.
DR InterPro; IPR042056; MIB1/2_ZZ.
DR InterPro; IPR010606; Mib_Herc2.
DR InterPro; IPR037252; Mib_Herc2_sf.
DR InterPro; IPR040847; SH3_15.
DR InterPro; IPR001841; Znf_RING.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR InterPro; IPR000433; Znf_ZZ.
DR InterPro; IPR043145; Znf_ZZ_sf.
DR Pfam; PF12796; Ank_2; 2.
DR Pfam; PF13637; Ank_4; 1.
DR Pfam; PF06701; MIB_HERC2; 2.
DR Pfam; PF18346; SH3_15; 2.
DR Pfam; PF00569; ZZ; 1.
DR PRINTS; PR01415; ANKYRIN.
DR SMART; SM00248; ANK; 8.
DR SMART; SM00184; RING; 3.
DR SMART; SM00291; ZnF_ZZ; 1.
DR SUPFAM; SSF159034; SSF159034; 2.
DR SUPFAM; SSF48403; SSF48403; 1.
DR PROSITE; PS50297; ANK_REP_REGION; 1.
DR PROSITE; PS50088; ANK_REPEAT; 6.
DR PROSITE; PS51416; MIB_HERC2; 2.
DR PROSITE; PS50089; ZF_RING_2; 3.
DR PROSITE; PS01357; ZF_ZZ_1; 1.
DR PROSITE; PS50135; ZF_ZZ_2; 1.
PE 1: Evidence at protein level;
KW ANK repeat; Cell membrane; Coiled coil; Cytoplasm; Cytoskeleton;
KW Developmental protein; Membrane; Metal-binding; Notch signaling pathway;
KW Reference proteome; Repeat; Transferase; Ubl conjugation pathway; Zinc;
KW Zinc-finger.
FT CHAIN 1..1030
FT /note="E3 ubiquitin-protein ligase mib1"
FT /id="PRO_0000055945"
FT DOMAIN 6..74
FT /note="MIB/HERC2 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00749"
FT DOMAIN 143..221
FT /note="MIB/HERC2 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00749"
FT REPEAT 430..460
FT /note="ANK 1"
FT REPEAT 463..492
FT /note="ANK 2"
FT REPEAT 496..525
FT /note="ANK 3"
FT REPEAT 529..558
FT /note="ANK 4"
FT REPEAT 562..591
FT /note="ANK 5"
FT REPEAT 595..627
FT /note="ANK 6"
FT REPEAT 631..661
FT /note="ANK 7"
FT REPEAT 665..694
FT /note="ANK 8"
FT REPEAT 698..727
FT /note="ANK 9"
FT ZN_FING 80..132
FT /note="ZZ-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT ZN_FING 817..852
FT /note="RING-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT ZN_FING 864..899
FT /note="RING-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT ZN_FING 987..1020
FT /note="RING-type 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT COILED 957..986
FT /evidence="ECO:0000255"
FT BINDING 85
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT BINDING 88
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT BINDING 100
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT BINDING 103
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT BINDING 109
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT BINDING 112
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT BINDING 118
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT BINDING 122
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00228"
FT MUTAGEN 1009
FT /note="C->S: In tfi101; induces neurogenic defects due to
FT reduced notch signaling."
FT /evidence="ECO:0000269|PubMed:12530964"
FT MUTAGEN 1013
FT /note="M->R: In ta52b; induces neurogenic defects due to
FT reduced notch signaling."
FT /evidence="ECO:0000269|PubMed:12530964"
FT CONFLICT 236..237
FT /note="EQ -> KI (in Ref. 2; AAM34677)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1030 AA; 112688 MW; DAB541D403215A02 CRC64;
MTTGRNNRVM MEGVGARVIR GPDWKWGKQD GGEGHVGTVR SFESPEEVVV VWDNGTAANY
RCSGAYDVRI LDSAPTGIKH DGTMCDTCRQ QPIIGIRWKC AECTNYDLCT TCYHGDKHHL
RHRFYRITTP GSERVLLESR RKSKKITARG IFAGGRVVRG VDWQWEDQDG GNGRRGKVTE
IQDWSAASPH SAAYVLWDNG AKNLYRVGFE GMSDLKCVQD AKGGTFYRDH CPVLGEQNGN
RNPGGLQIGD LVNIDLDLEI VQSLQHGHGG WTDGMFETLT TTGTVCGIDE DHDIVVQYPS
GNRWTFNPAV LTKANVVRSG EVAAGAEGGS SQFMVGDLVQ ICYDIDRIKL LQRGHGEWAE
AMLPTLGKVG RVQQIYSDSD LKVEVCGTSW TYNPAAVTKV APAGSAVTNA SGERLSQLLK
KLFETQESGD INEELVKAAA NGDLAKVEDI LKRPDVDVNG QCAGHTAMQA ASQNGHVDVL
KLLLKHSVDL EAEDKDGDRA VHHASFGDEG SVIEVLHRGG ADLNARNKRR QTPLHIAVNK
GHLQVVKTLL DFGCHPSLQD SEGDTPLHDA ISKKRDDMLS VLLEAGADVT ITNNNGFNAL
HHAALRGNPS AMRVLLSKLP RPWIVDEKKD DGYTALHLAA LNNHVEVAEL LVHQGNANLD
VQNVNQQTAL HLAVERQHTQ IVRLLVRAEA KLDVQDKDGD TPLHEALRHH TLSQLRQLQD
MQDVSKVEPW EPSKNTLIMG LGTQGAEKKS AASIACFLAA NGADLTIRNK KGQSPLDLCP
DPSLCKALAK CHKEKTSGQV GSRSPSLNSN NETLEECMVC SDMKRDTLFG PCGHIATCSL
CSPRVKKCLI CKEQVQSRTK IEECVVCSDK KAAVLFQPCG HMCACENCAS LMKKCVQCRA
VVERRTPFVL CCGGKGMEDA TDDEDLTGGS NSMAGGSQDL LQPNNLALSW SSGNIPALQR
DKDNTNVNAD VQKLQQQLQD IKEQTMCPVC LDRLKNMIFM CGHGTCQLCG DRMSECPICR
KAIERRILLY
