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P55055 (NR1H2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 155. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Oxysterols receptor LXR-beta
Alternative name(s):
Liver X receptor beta
Nuclear receptor NER
Nuclear receptor subfamily 1 group H member 2
Ubiquitously-expressed nuclear receptor
Gene names
Name:NR1H2
Synonyms:LXRB, NER, UNR
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length460 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Nuclear receptor. Binds preferentially to double-stranded oligonucleotide direct repeats having the consensus half-site sequence 5'-AGGTCA-3' and 4-nt spacing (DR-4). Regulates cholesterol uptake through MYLIP-dependent ubiquitination of LDLR, VLDLR and LRP8; DLDLR and LRP8. Interplays functionally with RORA for the regulation of genes involved in liver metabolism By similarity.

Subunit structure

Forms a heterodimer with RXR.

Subcellular location

Nucleus Potential.

Tissue specificity

Ubiquitous.

Sequence similarities

Belongs to the nuclear hormone receptor family. NR1 subfamily.

Contains 1 nuclear receptor DNA-binding domain.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   DomainZinc-finger
   LigandDNA-binding
Metal-binding
Zinc
   Molecular functionReceptor
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcellular lipid metabolic process

Inferred from electronic annotation. Source: Ensembl

cholesterol homeostasis

Inferred from electronic annotation. Source: Ensembl

gene expression

Traceable author statement. Source: Reactome

negative regulation of cholesterol storage

Inferred from mutant phenotype PubMed 17693624. Source: BHF-UCL

negative regulation of interferon-gamma-mediated signaling pathway

Non-traceable author statement PubMed 21268089. Source: BHF-UCL

negative regulation of lipid transport

Inferred from mutant phenotype PubMed 17693624. Source: BHF-UCL

negative regulation of macrophage derived foam cell differentiation

Inferred by curator PubMed 17693624. Source: BHF-UCL

negative regulation of pinocytosis

Inferred from mutant phenotype PubMed 17693624. Source: BHF-UCL

negative regulation of proteolysis

Inferred from electronic annotation. Source: Ensembl

negative regulation of transcription from RNA polymerase II promoter

Inferred from electronic annotation. Source: Ensembl

negative regulation of transcription, DNA-templated

Inferred from direct assay PubMed 12393874. Source: HGNC

positive regulation of cellular protein metabolic process

Inferred from mutant phenotype PubMed 17186944. Source: BHF-UCL

positive regulation of cholesterol efflux

Inferred from mutant phenotype PubMed 17186944. Source: BHF-UCL

positive regulation of cholesterol transport

Inferred from direct assay PubMed 16141411. Source: BHF-UCL

positive regulation of fatty acid biosynthetic process

Inferred from mutant phenotype PubMed 17186944. Source: BHF-UCL

positive regulation of high-density lipoprotein particle assembly

Inferred from electronic annotation. Source: Ensembl

positive regulation of lipid storage

Inferred from electronic annotation. Source: Ensembl

positive regulation of lipoprotein lipase activity

Inferred from mutant phenotype PubMed 17186944. Source: BHF-UCL

positive regulation of pancreatic juice secretion

Inferred from electronic annotation. Source: Ensembl

positive regulation of secretion of lysosomal enzymes

Inferred from electronic annotation. Source: Ensembl

positive regulation of transcription from RNA polymerase II promoter

Inferred from direct assay PubMed 20219900. Source: UniProtKB

positive regulation of triglyceride biosynthetic process

Inferred from mutant phenotype PubMed 17186944. Source: BHF-UCL

retinoic acid receptor signaling pathway

Inferred from electronic annotation. Source: Ensembl

transcription initiation from RNA polymerase II promoter

Traceable author statement. Source: Reactome

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytoplasm

Inferred from direct assay PubMed 12393874. Source: HGNC

nucleoplasm

Traceable author statement. Source: Reactome

nucleus

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: InterPro

ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity

Traceable author statement Ref.1. Source: ProtInc

sequence-specific DNA binding

Inferred from electronic annotation. Source: InterPro

sequence-specific DNA binding transcription factor activity

Inferred from electronic annotation. Source: InterPro

sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity

Inferred from electronic annotation. Source: Ensembl

steroid hormone receptor activity

Inferred from electronic annotation. Source: InterPro

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

MDFIQ997503EBI-745354,EBI-724076

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P55055-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: P55055-2)

The sequence of this isoform differs from the canonical sequence as follows:
     61-158: VIPDPEEEPE...CKEAGMREQC → G
Note: No experimental confirmation.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 460460Oxysterols receptor LXR-beta
PRO_0000053532

Regions

DNA binding84 – 16178Nuclear receptor
Zinc finger87 – 10721NR C4-type
Zinc finger125 – 14925NR C4-type
Region230 – 460231Ligand-binding Potential
Compositional bias190 – 1956Poly-Ser

Natural variations

Alternative sequence61 – 15898VIPDP…MREQC → G in isoform 2.
VSP_053789
Natural variant21S → F.
Corresponds to variant rs41379547 [ dbSNP | Ensembl ].
VAR_050579

Experimental info

Sequence conflict1751Q → QQ in AAA61783. Ref.1
Sequence conflict1751Q → QQ in BAF83544. Ref.2
Sequence conflict1751Q → QQ in BAG60288. Ref.2
Sequence conflict1751Q → QQ in AAH07790. Ref.4
Sequence conflict1751Q → QQ in AAH33500. Ref.4
Sequence conflict1751Q → QQ in AAH47750. Ref.4
Sequence conflict1751Q → QQ in AAH74500. Ref.4
Sequence conflict1751Q → QQ in AAA58594. Ref.5
Sequence conflict2441D → G in BAG60288. Ref.2

Secondary structure

.............................. 460
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 18, 2010. Version 2.
Checksum: 9465A6FFB7FCFD2F

FASTA46050,974
        10         20         30         40         50         60 
MSSPTTSSLD TPLPGNGPPQ PGAPSSSPTV KEEGPEPWPG GPDPDVPGTD EASSACSTDW 

        70         80         90        100        110        120 
VIPDPEEEPE RKRKKGPAPK MLGHELCRVC GDKASGFHYN VLSCEGCKGF FRRSVVRGGA 

       130        140        150        160        170        180 
RRYACRGGGT CQMDAFMRRK CQQCRLRKCK EAGMREQCVL SEEQIRKKKI RKQQQESQSQ 

       190        200        210        220        230        240 
SQSPVGPQGS SSSASGPGAS PGGSEAGSQG SGEGEGVQLT AAQELMIQQL VAAQLQCNKR 

       250        260        270        280        290        300 
SFSDQPKVTP WPLGADPQSR DARQQRFAHF TELAIISVQE IVDFAKQVPG FLQLGREDQI 

       310        320        330        340        350        360 
ALLKASTIEI MLLETARRYN HETECITFLK DFTYSKDDFH RAGLQVEFIN PIFEFSRAMR 

       370        380        390        400        410        420 
RLGLDDAEYA LLIAINIFSA DRPNVQEPGR VEALQQPYVE ALLSYTRIKR PQDQLRFPRM 

       430        440        450        460 
LMKLVSLRTL SSVHSEQVFA LRLQDKKLPP LLSEIWDVHE 

« Hide

Isoform 2 [UniParc].

Checksum: E1F0B75FDA51C249
Show »

FASTA36339,920

References

« Hide 'large scale' references
[1]"NER, a new member of the gene family encoding the human steroid hormone nuclear receptor."
Shinar D.M., Endo N., Rutledge S.J., Vogel R., Rodan G.A., Schmidt A.
Gene 147:273-276(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
Tissue: Osteosarcoma and Skin.
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
Tissue: Mammary gland.
[3]"The DNA sequence and biology of human chromosome 19."
Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V. expand/collapse author list , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M.
Nature 428:529-535(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Blood, Brain, Placenta and Uterus.
[5]"Ubiquitous receptor: a novel receptor that modulates gene activation by retinoic acid and thyroid hormone receptors."
Song C., Konkontis J.M., Hiipakka R.A., Liao S.
Submitted (SEP-1994) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 7-460 (ISOFORM 1).
[6]"The three-dimensional structure of the liver X receptor beta reveals a flexible ligand-binding pocket that can accommodate fundamentally different ligands."
Farnegardh M., Bonn T., Sun S., Ljunggren J., Ahola H., Wilhelmsson A., Gustafsson J.-A., Carlquist M.
J. Biol. Chem. 278:38821-38828(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 208-460 IN COMPLEX WITH SYNTHETIC LIGANDS.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U07132 mRNA. Translation: AAA61783.1.
AK290855 mRNA. Translation: BAF83544.1.
AK297978 mRNA. Translation: BAG60288.1.
AC008655 Genomic DNA. No translation available.
BC007790 mRNA. Translation: AAH07790.1.
BC033500 mRNA. Translation: AAH33500.1.
BC047750 mRNA. Translation: AAH47750.1.
BC074500 mRNA. Translation: AAH74500.1.
U14534 mRNA. Translation: AAA58594.1.
PIRJC4014.
RefSeqNP_001243576.1. NM_001256647.1.
NP_009052.3. NM_007121.5.
UniGeneHs.432976.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1P8DX-ray2.80A/B213-460[»]
1PQ6X-ray2.40A/B/C/D212-460[»]
1PQ9X-ray2.10A/B/C/D212-460[»]
1PQCX-ray2.80A/B/C/D212-460[»]
1UPVX-ray2.10A208-460[»]
1UPWX-ray2.40A208-460[»]
3KFCX-ray2.40A/B/C/D212-460[»]
3L0EX-ray2.30A212-460[»]
4DK7X-ray2.45A/C218-460[»]
4DK8X-ray2.75A/C218-460[»]
ProteinModelPortalP55055.
SMRP55055. Positions 85-459.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid113222. 54 interactions.
DIPDIP-53004N.
IntActP55055. 26 interactions.
MINTMINT-1444220.
STRING9606.ENSP00000253727.

Chemistry

BindingDBP55055.
ChEMBLCHEMBL4093.
GuidetoPHARMACOLOGY601.

PTM databases

PhosphoSiteP55055.

Polymorphism databases

DMDM296439251.

Proteomic databases

PaxDbP55055.
PRIDEP55055.

Protocols and materials databases

DNASU7376.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000253727; ENSP00000253727; ENSG00000131408.
ENST00000411902; ENSP00000396151; ENSG00000131408.
ENST00000593926; ENSP00000471194; ENSG00000131408.
GeneID7376.
KEGGhsa:7376.

Organism-specific databases

CTD7376.
GeneCardsGC19P050879.
HGNCHGNC:7965. NR1H2.
HPAHPA056838.
MIM600380. gene.
neXtProtNX_P55055.
PharmGKBPA31750.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG285805.
HOGENOMHOG000220845.
HOVERGENHBG108655.
InParanoidP55055.
KOK08535.
OMARRYACRG.
PhylomeDBP55055.
TreeFamTF352167.

Enzyme and pathway databases

ReactomeREACT_71. Gene Expression.
SignaLinkP55055.

Gene expression databases

ArrayExpressP55055.
BgeeP55055.
CleanExHS_NR1H2.
GenevestigatorP55055.

Family and domain databases

Gene3D1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProIPR023257. Liver_X_rcpt.
IPR008946. Nucl_hormone_rcpt_ligand-bd.
IPR000536. Nucl_hrmn_rcpt_lig-bd_core.
IPR001723. Str_hrmn_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSPR02034. LIVERXRECPTR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMSSF48508. SSF48508. 1 hit.
PROSITEPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSNR1H2. human.
EvolutionaryTraceP55055.
GeneWikiLiver_X_receptor_beta.
GenomeRNAi7376.
NextBio28886.
PROP55055.
SOURCESearch...

Entry information

Entry nameNR1H2_HUMAN
AccessionPrimary (citable) accession number: P55055
Secondary accession number(s): A8K490 expand/collapse secondary AC list , B4DNM6, E7EWA6, Q12970, Q5I0Y1
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: May 18, 2010
Last modified: April 16, 2014
This is version 155 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 19

Human chromosome 19: entries, gene names and cross-references to MIM