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Protein

Hepatocyte nuclear factor 4-alpha

Gene

Hnf4a

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Transcriptionally controlled transcription factor. Binds to DNA sites required for the transcription of alpha 1-antitrypsin, apolipoprotein CIII, transthyretin genes and HNF1-alpha. May be essential for development of the liver, kidney and intestine.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi57 – 132Nuclear receptorPROSITE-ProRule annotationAdd BLAST76
Zinc fingeri60 – 80NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri96 – 120NR C4-typePROSITE-ProRule annotationAdd BLAST25

GO - Molecular functioni

  • DNA binding Source: RGD
  • fatty acid binding Source: RGD
  • fatty-acyl-CoA binding Source: RGD
  • palmitoyl-CoA hydrolase activity Source: RGD
  • protein homodimerization activity Source: RGD
  • repressing transcription factor binding Source: BHF-UCL
  • RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding Source: InterPro
  • sequence-specific DNA binding Source: RGD
  • steroid hormone receptor activity Source: RGD
  • transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding Source: BHF-UCL
  • transcription factor activity, sequence-specific DNA binding Source: RGD
  • transcription factor binding Source: RGD
  • zinc ion binding Source: InterPro

GO - Biological processi

  • acyl-CoA metabolic process Source: RGD
  • aging Source: RGD
  • cell-cell junction organization Source: RGD
  • cell differentiation Source: RGD
  • cellular response to hypoxia Source: RGD
  • establishment of tissue polarity Source: RGD
  • negative regulation of activation of JAK2 kinase activity Source: RGD
  • negative regulation of cell proliferation Source: RGD
  • negative regulation of mitotic cell cycle Source: RGD
  • negative regulation of protein import into nucleus, translocation Source: RGD
  • negative regulation of sequence-specific DNA binding transcription factor activity Source: RGD
  • negative regulation of tyrosine phosphorylation of Stat5 protein Source: RGD
  • positive regulation of fatty acid biosynthetic process Source: RGD
  • positive regulation of gluconeogenesis Source: RGD
  • positive regulation of transcription, DNA-templated Source: BHF-UCL
  • positive regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
  • regulation of microvillus assembly Source: RGD
  • regulation of transcription, DNA-templated Source: RGD
  • response to cAMP Source: RGD
  • response to drug Source: RGD
  • response to glucose Source: RGD
Complete GO annotation...

Keywords - Molecular functioni

Receptor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Hepatocyte nuclear factor 4-alpha
Short name:
HNF-4-alpha
Alternative name(s):
Nuclear receptor subfamily 2 group A member 1
Transcription factor 14
Short name:
TCF-14
Transcription factor HNF-4
Gene namesi
Name:Hnf4a
Synonyms:Hnf-4, Hnf4, Nr2a1, Tcf14
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi2810. Hnf4a.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: RGD
  • nucleus Source: BHF-UCL
  • transcription factor complex Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi142 – 143SS → AG: Loss of phosphorylation, no effect on DNA-binding. 1 Publication2
Mutagenesisi142 – 143SS → LE: Loss of phosphorylation, no effect on DNA-binding. 1 Publication2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000535601 – 474Hepatocyte nuclear factor 4-alphaAdd BLAST474

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei142Phosphoserine; by PKA1 Publication1
Modified residuei143Phosphoserine; by PKA1 Publication1
Modified residuei144PhosphotyrosineBy similarity1
Modified residuei166PhosphothreonineBy similarity1
Modified residuei167PhosphoserineBy similarity1
Cross-linki234Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki307Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei313Phosphoserine; by AMPKBy similarity1
Modified residuei429PhosphothreonineBy similarity1
Modified residuei432PhosphothreonineCombined sources1
Modified residuei436PhosphoserineCombined sources1
Modified residuei458N6-acetyllysineBy similarity1

Post-translational modificationi

Phosphorylation at Ser-313 by AMPK reduces the ability to form homodimers and bind DNA (By similarity). Phosphorylated in the recognition sequence R-R-S-S near the DNA-binding domain; phosphorylation results in decrease in DNA-binding activity. Phosphorylation of HNF4 depends on the diet and is decreased by a carbohydrate-rich diet and is increased by fasting.By similarity1 Publication
The N-terminus is blocked.
Acetylation at Lys-458 lowers transcriptional activation by about two-fold.By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiP22449.
PRIDEiP22449.

PTM databases

iPTMnetiP22449.
PhosphoSitePlusiP22449.

Expressioni

Tissue specificityi

Liver, kidney and intestine.

Interactioni

Subunit structurei

Homodimerization is required for HNF4-alpha to bind to its recognition site. Interacts with PER2.

Binary interactionsi

WithEntry#Exp.IntActNotes
Fabp1P026923EBI-5261592,EBI-1209448

GO - Molecular functioni

  • protein homodimerization activity Source: RGD
  • repressing transcription factor binding Source: BHF-UCL
  • transcription factor binding Source: RGD

Protein-protein interaction databases

BioGridi247763. 1 interactor.
IntActiP22449. 2 interactors.
STRINGi10116.ENSRNOP00000011978.

Structurei

Secondary structure

1474
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi152 – 164Combined sources13
Helixi184 – 203Combined sources20
Helixi206 – 209Combined sources4
Helixi213 – 222Combined sources10
Helixi224 – 234Combined sources11
Turni235 – 238Combined sources4
Beta strandi239 – 244Combined sources6
Beta strandi250 – 254Combined sources5
Helixi256 – 258Combined sources3
Turni259 – 261Combined sources3
Helixi262 – 271Combined sources10
Helixi273 – 279Combined sources7
Helixi283 – 294Combined sources12
Helixi305 – 324Combined sources20
Beta strandi326 – 328Combined sources3
Helixi333 – 338Combined sources6
Helixi341 – 360Combined sources20
Helixi368 – 373Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1M7WX-ray2.80A/B/C/D142-391[»]
ProteinModelPortaliP22449.
SMRiP22449.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP22449.

Family & Domainsi

Sequence similaritiesi

Contains 1 nuclear receptor DNA-binding domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri60 – 80NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri96 – 120NR C4-typePROSITE-ProRule annotationAdd BLAST25

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG4215. Eukaryota.
ENOG410XQT8. LUCA.
HOGENOMiHOG000260822.
HOVERGENiHBG005606.
InParanoidiP22449.
KOiK07292.
PhylomeDBiP22449.

Family and domain databases

Gene3Di1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProiIPR003068. COUP_TF.
IPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR01282. COUPTNFACTOR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTiSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMiSSF48508. SSF48508. 1 hit.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform Long (identifier: P22449-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MRLSKTLADM DMADYSAALD PAYTTLEFEN VQVLTMGNDT SPSEGANLNS
60 70 80 90 100
SNSLGVSALC AICGDRATGK HYGASSCDGC KGFFRRSVRK NHMYSCRFSR
110 120 130 140 150
QCVVDKDKRN QCRYCRLKKC FRAGMKKEAV QNERDRISTR RSSYEDSSLP
160 170 180 190 200
SINALLQAEV LSQQITSPIS GINGDIRAKK IANITDVCES MKEQLLVLVE
210 220 230 240 250
WAKYIPAFCE LLLDDQVALL RAHAGEHLLL GATKRSMVFK DVLLLGNDYI
260 270 280 290 300
VPRHCPELAE MSRVSIRILD ELVLPFQELQ IDDNEYACLK AIIFFDPDAK
310 320 330 340 350
GLSDPGKIKR LRSQVQVSLE DYINDRQYDS RGRFGELLLL LPTLQSITWQ
360 370 380 390 400
MIEQIQFIKL FGMAKIDNLL QEMLLGGSAS DAPHAHHPLH PHLMQEHMGT
410 420 430 440 450
NVIVANTMPS HLSNGQMCEW PRPRGQAATP ETPQPSPPSG SGSESYKLLP
460 470
GAITTIVKPP SAIPQPTITK QEAI
Length:474
Mass (Da):52,712
Last modified:May 29, 2007 - v3
Checksum:iE6DECA74FEA65E75
GO
Isoform Short (identifier: P22449-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     418-428: CEWPRPRGQAA → S

Show »
Length:464
Mass (Da):51,546
Checksum:i6B0961382FB9A0F7
GO

Sequence cautioni

The sequence BAA01411 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence CAA40412 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti180K → R in CAA40412 (PubMed:2279702).Curated1
Sequence conflicti183N → S in CAA40412 (PubMed:2279702).Curated1
Sequence conflicti378S → L in ABM69090 (Ref. 3) Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_003677418 – 428CEWPRPRGQAA → S in isoform Short. 2 PublicationsAdd BLAST11

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D10554 mRNA. Translation: BAA01411.1. Different initiation.
X57133 mRNA. Translation: CAA40412.1. Different initiation.
EF193392 mRNA. Translation: ABM69090.1.
PIRiA36471.
S23502.
RefSeqiNP_071516.2. NM_022180.2.
UniGeneiRn.12238.

Genome annotation databases

GeneIDi25735.
KEGGirno:25735.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D10554 mRNA. Translation: BAA01411.1. Different initiation.
X57133 mRNA. Translation: CAA40412.1. Different initiation.
EF193392 mRNA. Translation: ABM69090.1.
PIRiA36471.
S23502.
RefSeqiNP_071516.2. NM_022180.2.
UniGeneiRn.12238.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1M7WX-ray2.80A/B/C/D142-391[»]
ProteinModelPortaliP22449.
SMRiP22449.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi247763. 1 interactor.
IntActiP22449. 2 interactors.
STRINGi10116.ENSRNOP00000011978.

PTM databases

iPTMnetiP22449.
PhosphoSitePlusiP22449.

Proteomic databases

PaxDbiP22449.
PRIDEiP22449.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi25735.
KEGGirno:25735.

Organism-specific databases

CTDi3172.
RGDi2810. Hnf4a.

Phylogenomic databases

eggNOGiKOG4215. Eukaryota.
ENOG410XQT8. LUCA.
HOGENOMiHOG000260822.
HOVERGENiHBG005606.
InParanoidiP22449.
KOiK07292.
PhylomeDBiP22449.

Miscellaneous databases

EvolutionaryTraceiP22449.
PROiP22449.

Family and domain databases

Gene3Di1.10.565.10. 1 hit.
3.30.50.10. 1 hit.
InterProiIPR003068. COUP_TF.
IPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR01282. COUPTNFACTOR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTiSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMiSSF48508. SSF48508. 1 hit.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiHNF4A_RAT
AccessioniPrimary (citable) accession number: P22449
Secondary accession number(s): A2ICG9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: May 29, 2007
Last modified: November 2, 2016
This is version 164 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

DNA-binding activity of phosphorylated protein is reduced by fasting and by inducers of intracellular cyclic AMP.
Binds fatty acids.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.