RXRAB_DANRE
ID RXRAB_DANRE Reviewed; 379 AA.
AC Q90415;
DT 27-SEP-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Retinoic acid receptor RXR-alpha-B;
DE AltName: Full=Nuclear receptor subfamily 2 group B member 1-B;
DE AltName: Full=Retinoid X receptor alpha-B;
GN Name=rxrab; Synonyms=nr2b1b, rxra, rxrg;
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] {ECO:0000305, ECO:0000312|EMBL:AAC59719.1}
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND DEVELOPMENTAL STAGE.
RX PubMed=7565671; DOI=10.1128/mcb.15.10.5226;
RA Jones B.B., Ohno C.K., Allenby G., Boffa M.B., Levin A.A., Grippo J.F.,
RA Petkovich M.;
RT "New retinoid X receptor subtypes in zebra fish (Danio rerio)
RT differentially modulate transcription and do not bind 9-cis retinoic
RT acid.";
RL Mol. Cell. Biol. 15:5226-5234(1995).
RN [2]
RP TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RX PubMed=16448862; DOI=10.1016/j.modgep.2005.10.005;
RA Tallafuss A., Hale L.A., Yan Y.-L., Dudley L., Eisen J.S.,
RA Postlethwait J.H.;
RT "Characterization of retinoid-X receptor genes rxra, rxrba, rxrbb and rxrg
RT during zebrafish development.";
RL Gene Expr. Patterns 6:556-565(2006).
RN [3]
RP TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RX PubMed=17195188; DOI=10.1002/dvdy.21049;
RA Waxman J.S., Yelon D.;
RT "Comparison of the expression patterns of newly identified zebrafish
RT retinoic acid and retinoid X receptors.";
RL Dev. Dyn. 236:587-595(2007).
RN [4]
RP DEVELOPMENTAL STAGE.
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: Receptor for retinoic acid that acts as a transcription
CC factor (PubMed:7565671). Forms homo- or heterodimers with retinoic acid
CC receptors (rars) and binds to target response elements in response to
CC their ligands, all-trans or 9-cis retinoic acid, to regulate gene
CC expression in various biological processes (By similarity). The rar/rxr
CC heterodimers bind to the retinoic acid response elements (RARE)
CC composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5 to regulate
CC transcription (By similarity). The high affinity ligand for rxrs is 9-
CC cis retinoic acid (By similarity). In the absence of ligand, the
CC rar/rxr heterodimers associate with a multiprotein complex containing
CC transcription corepressors that induce histone deacetylation, chromatin
CC condensation and transcriptional suppression (By similarity). On ligand
CC binding, the corepressors dissociate from the receptors and
CC coactivators are recruited leading to transcriptional activation (By
CC similarity). {ECO:0000250|UniProtKB:P19793,
CC ECO:0000269|PubMed:7565671}.
CC -!- SUBUNIT: Homodimer. Heterodimer; with a rar molecule. Binds DNA
CC preferentially as a rar/rxr heterodimer.
CC {ECO:0000250|UniProtKB:P19793}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00407}.
CC -!- TISSUE SPECIFICITY: Uniform expression from the blastula to mid-
CC gastrula stages. At 12 hours post-fertilization (hpf), expressed
CC strongly in the tail and weakly elsewhere. At 24 hpf, weak expression
CC in the forebrain, eyes and pharyngeal endoderm and continued expression
CC in the tail mesoderm. At 48 hpf, anterior expression limited to ventral
CC cells underlying the head, medial expression in the pectoral fin bud
CC mesoderm and continued tail expression. {ECO:0000269|PubMed:16448862,
CC ECO:0000269|PubMed:17195188}.
CC -!- DEVELOPMENTAL STAGE: Expressed both maternally and zygotically.
CC {ECO:0000269|PubMed:16448862, ECO:0000269|PubMed:17195188,
CC ECO:0000269|PubMed:17997606, ECO:0000269|PubMed:7565671}.
CC -!- DOMAIN: Composed of three domains: a modulating N-terminal domain, a
CC DNA-binding domain and a C-terminal ligand-binding domain.
CC -!- SIMILARITY: Belongs to the nuclear hormone receptor family. NR2
CC subfamily. {ECO:0000255}.
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DR EMBL; U29894; AAC59719.1; -; mRNA.
DR PIR; I50514; I50514.
DR RefSeq; NP_571228.1; NM_131153.1.
DR AlphaFoldDB; Q90415; -.
DR SMR; Q90415; -.
DR STRING; 7955.ENSDARP00000004918; -.
DR PaxDb; Q90415; -.
DR PRIDE; Q90415; -.
DR GeneID; 793011; -.
DR KEGG; dre:793011; -.
DR CTD; 793011; -.
DR ZFIN; ZDB-GENE-990415-243; rxrab.
DR eggNOG; KOG3575; Eukaryota.
DR InParanoid; Q90415; -.
DR OrthoDB; 912470at2759; -.
DR PhylomeDB; Q90415; -.
DR SignaLink; Q90415; -.
DR PRO; PR:Q90415; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Unplaced.
DR GO; GO:0090575; C:RNA polymerase II transcription regulator complex; IBA:GO_Central.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:UniProtKB.
DR GO; GO:0004879; F:nuclear receptor activity; IDA:ZFIN.
DR GO; GO:0003707; F:nuclear steroid receptor activity; IEA:InterPro.
DR GO; GO:0044323; F:retinoic acid-responsive element binding; IBA:GO_Central.
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:0048856; P:anatomical structure development; IBA:GO_Central.
DR GO; GO:0030154; P:cell differentiation; IBA:GO_Central.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; ISS:UniProtKB.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0032526; P:response to retinoic acid; IBA:GO_Central.
DR GO; GO:0048384; P:retinoic acid receptor signaling pathway; IBA:GO_Central.
DR Gene3D; 1.10.565.10; -; 1.
DR Gene3D; 3.30.50.10; -; 1.
DR InterPro; IPR035500; NHR-like_dom_sf.
DR InterPro; IPR021780; Nuc_recep-AF1.
DR InterPro; IPR000536; Nucl_hrmn_rcpt_lig-bd.
DR InterPro; IPR001723; Nuclear_hrmn_rcpt.
DR InterPro; IPR000003; Retinoid-X_rcpt/HNF4.
DR InterPro; IPR001628; Znf_hrmn_rcpt.
DR InterPro; IPR013088; Znf_NHR/GATA.
DR Pfam; PF00104; Hormone_recep; 1.
DR Pfam; PF11825; Nuc_recep-AF1; 1.
DR Pfam; PF00105; zf-C4; 1.
DR PRINTS; PR00545; RETINOIDXR.
DR PRINTS; PR00398; STRDHORMONER.
DR PRINTS; PR00047; STROIDFINGER.
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 DNA-binding; Metal-binding; Nucleus; Receptor; Reference proteome;
KW Transcription; Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..379
FT /note="Retinoic acid receptor RXR-alpha-B"
FT /id="PRO_0000053579"
FT DOMAIN 144..375
FT /note="NR LBD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01189"
FT DNA_BIND 51..126
FT /note="Nuclear receptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 54..74
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT ZN_FING 90..109
FT /note="NR C4-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00407"
FT REGION 1..53
FT /note="Modulating"
FT /evidence="ECO:0000250"
FT REGION 1..24
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 79..84
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000250|UniProtKB:P19793"
FT REGION 120..141
FT /note="Hinge"
FT /evidence="ECO:0000250"
FT REGION 265..285
FT /note="Required for nuclear export"
FT /evidence="ECO:0000250|UniProtKB:P19793"
FT REGION 364..375
FT /note="AF-2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01189"
FT COMPBIAS 1..21
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 54
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P19793"
FT BINDING 57
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P19793"
FT BINDING 71
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P19793"
FT BINDING 74
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P19793"
FT BINDING 90
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P19793"
FT BINDING 96
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P19793"
FT BINDING 106
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P19793"
FT BINDING 109
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P19793"
FT BINDING 233
FT /ligand="9-cis-retinoate"
FT /ligand_id="ChEBI:CHEBI:78630"
FT /evidence="ECO:0000250|UniProtKB:P19793"
FT BINDING 233
FT /ligand="all-trans-retinoate"
FT /ligand_id="ChEBI:CHEBI:35291"
FT /evidence="ECO:0000250|UniProtKB:P19793"
FT BINDING 244
FT /ligand="9-cis-retinoate"
FT /ligand_id="ChEBI:CHEBI:78630"
FT /evidence="ECO:0000250|UniProtKB:P19793"
FT BINDING 244
FT /ligand="all-trans-retinoate"
FT /ligand_id="ChEBI:CHEBI:35291"
FT /evidence="ECO:0000250|UniProtKB:P19793"
SQ SEQUENCE 379 AA; 42556 MW; 317EA9E9DE455D16 CRC64;
MPVPEQKQTV QLSSPMNAVS SSEDIKPPLG LNGVMKVPAH RIGTLSLSLT KHICAICGDR
SSGKHYGVYS CEGCKGFFKR TVRKDLTYTC RDNKDCMIDK RQRNRCQYCR YQKCLAMGMK
REAVQEERQR AKERSEAEFG GCANEDMPVE KILEAELAVE PKTETYVEAN LSPSANSPND
PVTNICQAAD KQLFTLVEWA KRIPHFSDLP LDDQVILLRA GWNELLIASF SHRSIAVKDG
ILLATGLHVH RNSAHTAGVG AIFDRVLTEL VSKMRDMQMD KTELGCLRAI VLFNPDSKGL
SNPSEVEALR ERVYASLEAY CKHKYPDQPG RFAKLLLRLP ALRSIGLKCL EHLFFFKLIG
DTPIDTFLME MLEAPHQIT
