VDRB_DANRE
ID VDRB_DANRE Reviewed; 422 AA.
AC Q1L673;
DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT 10-JUN-2008, sequence version 2.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Vitamin D3 receptor B;
DE Short=VDR-B;
DE AltName: Full=1,25-dihydroxyvitamin D3 receptor B;
DE AltName: Full=Nuclear receptor subfamily 1 group I member 1-B;
GN Name=vdrb; Synonyms=nr1i1b; ORFNames=gb:dq017633;
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 MRNA] OF 1-97.
RC TISSUE=Testis;
RA Chen F., Jin Y., Zeng K., Gnirke A., Baille M., Cheung L.M., Chong A.,
RA Garrick B., Murray L., Oliva J., Park C., Reyes J., Yang J., Amundsen C.,
RA Orton A., Shao A., Platt D., Swimmer C.;
RT "Exelixis Danio rerio EST project.";
RL Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 4-422, AND TISSUE SPECIFICITY.
RX PubMed=17997606; DOI=10.1371/journal.pgen.0030188;
RA Bertrand S., Thisse B., Tavares R., Sachs L., Chaumot A., Bardet P.-L.,
RA Escriva H., Duffraisse M., Marchand O., Safi R., Thisse C., Laudet V.;
RT "Unexpected novel relational links uncovered by extensive developmental
RT profiling of nuclear receptor expression.";
RL PLoS Genet. 3:E188-E188(2007).
CC -!- FUNCTION: Nuclear receptor for calcitriol, the active form of vitamin
CC D3 which mediates the action of this vitamin on cells. Enters the
CC nucleus upon vitamin D3 binding where it forms heterodimers with the
CC retinoid X receptor/RXR. The VDR-RXR heterodimers bind to specific
CC response elements on DNA and activate the transcription of vitamin D3-
CC responsive target genes. Recruited to promoters via its interaction
CC with BAZ1B/WSTF which mediates the interaction with acetylated
CC histones, an essential step for VDR-promoter association. Plays a
CC central role in calcium homeostasis. {ECO:0000250|UniProtKB:P11473}.
CC -!- SUBUNIT: Homodimer in the absence of bound vitamin D3. Heterodimer with
CC RXRA after vitamin D3 binding (By similarity). Interacts with ncoa1 and
CC possibly other coactivators, leading to a strong increase of
CC transcription of target genes (By similarity).
CC {ECO:0000250|UniProtKB:P11473, ECO:0000250|UniProtKB:Q9PTN2}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P11473,
CC ECO:0000255|PROSITE-ProRule:PRU00407}. Cytoplasm
CC {ECO:0000250|UniProtKB:P11473}. Note=Localizes mainly to the nucleus.
CC Translocated into the nucleus via both ligand-dependent and ligand-
CC independent pathways; ligand-independent nuclear translocation is
CC mediated by IPO4. {ECO:0000250|UniProtKB:P11473}.
CC -!- TISSUE SPECIFICITY: Detected in embryo 24 to 48 hours after
CC fertilization, and in intestinal bulb. {ECO:0000269|PubMed:17997606}.
CC -!- DOMAIN: Composed of three domains: a modulating N-terminal domain, a
CC DNA-binding domain and a C-terminal ligand-binding domain.
CC {ECO:0000250|UniProtKB:P11473}.
CC -!- DOMAIN: The 9aaTAD motif is a transactivation domain present in a large
CC number of yeast and animal transcription factors.
CC {ECO:0000250|UniProtKB:P11473}.
CC -!- SIMILARITY: Belongs to the nuclear hormone receptor family.
CC {ECO:0000305}.
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DR EMBL; EB970525; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; DQ017633; AAY85288.1; -; mRNA.
DR RefSeq; NP_001153457.1; NM_001159985.1.
DR RefSeq; XP_005166104.1; XM_005166047.3.
DR AlphaFoldDB; Q1L673; -.
DR SMR; Q1L673; -.
DR STRING; 7955.ENSDARP00000125655; -.
DR PaxDb; Q1L673; -.
DR Ensembl; ENSDART00000104116; ENSDARP00000094891; ENSDARG00000070721.
DR Ensembl; ENSDART00000150885; ENSDARP00000125655; ENSDARG00000070721.
DR GeneID; 564511; -.
DR KEGG; dre:564511; -.
DR CTD; 564511; -.
DR ZFIN; ZDB-GENE-080403-10; vdrb.
DR eggNOG; KOG3575; Eukaryota.
DR GeneTree; ENSGT00940000155473; -.
DR HOGENOM; CLU_007368_12_0_1; -.
DR InParanoid; Q1L673; -.
DR OMA; RPEHSMQ; -.
DR OrthoDB; 297114at2759; -.
DR PhylomeDB; Q1L673; -.
DR TreeFam; TF316304; -.
DR Reactome; R-DRE-196791; Vitamin D (calciferol) metabolism.
DR Reactome; R-DRE-383280; Nuclear Receptor transcription pathway.
DR Reactome; R-DRE-4090294; SUMOylation of intracellular receptors.
DR PRO; PR:Q1L673; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 6.
DR Bgee; ENSDARG00000070721; Expressed in retina and 20 other tissues.
DR ExpressionAtlas; Q1L673; baseline.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0004879; F:nuclear receptor activity; IDA:ZFIN.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0030154; P:cell differentiation; IBA:GO_Central.
DR GO; GO:0003146; P:heart jogging; IMP:ZFIN.
DR GO; GO:0001947; P:heart looping; IMP:ZFIN.
DR GO; GO:0060119; P:inner ear receptor cell development; IMP:ZFIN.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0071599; P:otic vesicle development; IMP:ZFIN.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR CDD; cd06955; NR_DBD_VDR; 1.
DR Gene3D; 1.10.565.10; -; 1.
DR Gene3D; 3.30.50.10; -; 1.
DR InterPro; IPR042153; DBD_VDR.
DR InterPro; IPR035500; NHR-like_dom_sf.
DR InterPro; IPR000536; Nucl_hrmn_rcpt_lig-bd.
DR InterPro; IPR001723; Nuclear_hrmn_rcpt.
DR InterPro; IPR000324; VitD_rcpt.
DR InterPro; IPR001628; Znf_hrmn_rcpt.
DR InterPro; IPR013088; Znf_NHR/GATA.
DR Pfam; PF00104; Hormone_recep; 1.
DR Pfam; PF00105; zf-C4; 1.
DR PRINTS; PR00398; STRDHORMONER.
DR PRINTS; PR00047; STROIDFINGER.
DR PRINTS; PR00350; VITAMINDR.
DR SMART; SM00430; HOLI; 1.
DR SMART; SM00399; ZnF_C4; 1.
DR SUPFAM; SSF48508; SSF48508; 1.
DR PROSITE; PS51843; NR_LBD; 1.
DR PROSITE; PS00031; NUCLEAR_REC_DBD_1; 1.
DR PROSITE; PS51030; NUCLEAR_REC_DBD_2; 1.
PE 2: Evidence at transcript level;
KW Cytoplasm; DNA-binding; Metal-binding; Nucleus; Receptor;
KW Reference proteome; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..422
FT /note="Vitamin D3 receptor B"
FT /id="PRO_0000337879"
FT DOMAIN 126..418
FT /note="NR LBD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01189"
FT DNA_BIND 20..95
FT /note="Nuclear receptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 23..43
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 59..78
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT REGION 96..125
FT /note="Hinge"
FT /evidence="ECO:0000250|UniProtKB:P11473"
FT REGION 106..128
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 145..190
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 243..261
FT /note="Interaction with coactivator LXXLL motif"
FT /evidence="ECO:0000250|UniProtKB:P13053"
FT MOTIF 411..419
FT /note="9aaTAD"
FT /evidence="ECO:0000250|UniProtKB:P11473"
FT COMPBIAS 166..190
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 142
FT /ligand="calciol"
FT /ligand_id="ChEBI:CHEBI:28940"
FT /evidence="ECO:0000250|UniProtKB:P11473"
FT BINDING 224..234
FT /ligand="calciol"
FT /ligand_id="ChEBI:CHEBI:28940"
FT /evidence="ECO:0000250|UniProtKB:P11473"
FT BINDING 268..275
FT /ligand="calciol"
FT /ligand_id="ChEBI:CHEBI:28940"
FT /evidence="ECO:0000250|UniProtKB:P11473"
FT BINDING 302
FT /ligand="calciol"
FT /ligand_id="ChEBI:CHEBI:28940"
FT /evidence="ECO:0000250|UniProtKB:P11473"
FT BINDING 392
FT /ligand="calciol"
FT /ligand_id="ChEBI:CHEBI:28940"
FT /evidence="ECO:0000250|UniProtKB:P11473"
SQ SEQUENCE 422 AA; 47663 MW; 843F9B8183F77BF4 CRC64;
MESAVSTSTQ VPDEFDRNVP RICGVCGDKA TGFHFNAMTC EGCKGFFRRS MKRKASFTCP
FNGSCTITKD NRRHCQACRL KRCLDIGMMK EFILTDEEVQ RKKELIQRRK DEEAHREAQK
PRLSDEQRNI IDTLVDAHHK TYDDSYSDFS RFRPPVREGP VTRSASRAAS LHSLSDASSD
SFSHSPESGD RKMNLSNLLM MYQEQGLSSS PDSKEEDGSS LSMLPHLADL VSYSIQKVIG
FAKMIPGFRE LTAEDQIALL KSSAIEVIML RSNQSFSLED MSWSCGGPEF KYCVNDVTKA
GHTLELLEPL VKFQVGLKKL NLHEEEHVLL MAICLLSPDR PGVQDHVRVE ALQDKVSEVL
QAYIRAHHPG GRLLYAKMIQ KLADLRSLNE EHSKQYRSLS FQPEHSMQLT PLVLEVFGGQ
VT
