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Protein

Pancreas/duodenum homeobox protein 1

Gene

Pdx1

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

Functioni

Activates insulin and somatostatin gene transcription. Key regulator of islet peptide hormone expression but also responsible for the development of the pancreas, most probably by determining maturation and differentiation of common pancreatic precursor cells in the developing gut. As part of a PDX1:PBX1b:MEIS2b complex in pancreatic acinar cells is involved in the transcriptional activation of the ELA1 enhancer; the complex binds to the enhancer B element and cooperates with the transcription factor 1 complex (PTF1) bound to the enhancer A element. Binds the DNA sequence 5'-CC[CT]TAATGGG-3'.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi146 – 20560HomeoboxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • chromatin binding Source: Ensembl
  • core promoter sequence-specific DNA binding Source: RGD
  • protein complex binding Source: RGD
  • protein heterodimerization activity Source: RGD
  • RNA polymerase II core promoter proximal region sequence-specific DNA binding Source: Ensembl
  • sequence-specific DNA binding Source: RGD
  • transcription factor activity, sequence-specific DNA binding Source: RGD
  • transcription factor binding Source: RGD

GO - Biological processi

  • cell differentiation Source: RGD
  • central nervous system development Source: RGD
  • detection of glucose Source: BHF-UCL
  • digestive tract development Source: Ensembl
  • exocrine pancreas development Source: Ensembl
  • glucose homeostasis Source: RGD
  • glucose metabolic process Source: Ensembl
  • insulin secretion Source: Ensembl
  • liver development Source: Ensembl
  • morphogenesis of embryonic epithelium Source: Ensembl
  • negative regulation of cell proliferation Source: Ensembl
  • negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway Source: Ensembl
  • negative regulation of transcription, DNA-templated Source: RGD
  • negative regulation of transcription from RNA polymerase II promoter Source: Ensembl
  • negative regulation of type B pancreatic cell apoptotic process Source: Ensembl
  • nitric oxide mediated signal transduction Source: Ensembl
  • organ regeneration Source: RGD
  • organ senescence Source: RGD
  • pancreas development Source: RGD
  • positive regulation of cell death Source: RGD
  • positive regulation of cell proliferation Source: RGD
  • positive regulation of DNA binding Source: RGD
  • positive regulation of insulin secretion Source: RGD
  • positive regulation of insulin secretion involved in cellular response to glucose stimulus Source: Ensembl
  • positive regulation of transcription, DNA-templated Source: RGD
  • positive regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
  • regulation of gene expression Source: CACAO
  • regulation of transcription, DNA-templated Source: RGD
  • response to alkaloid Source: RGD
  • response to chlorate Source: RGD
  • response to cytokine Source: RGD
  • response to drug Source: RGD
  • response to fatty acid Source: RGD
  • response to glucocorticoid Source: RGD
  • response to glucose Source: RGD
  • response to iron(II) ion Source: RGD
  • response to leucine Source: RGD
  • response to lipid Source: RGD
  • response to nicotine Source: RGD
  • response to nutrient levels Source: RGD
  • response to organic cyclic compound Source: RGD
  • response to vitamin Source: RGD
  • response to wounding Source: RGD
  • smoothened signaling pathway Source: RGD
  • stem cell differentiation Source: RGD
  • transcription, DNA-templated Source: RGD
  • transcription from RNA polymerase II promoter Source: RGD
  • transdifferentiation Source: RGD
  • type B pancreatic cell differentiation Source: BHF-UCL
Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Pancreas/duodenum homeobox protein 1
Alternative name(s):
Insulin promoter factor 1
Short name:
IPF-1
Islet/duodenum homeobox 1
Short name:
IDX-1
Somatostatin-transactivating factor 1
Short name:
STF-1
Gene namesi
Name:Pdx1
Synonyms:Ipf1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 12

Organism-specific databases

RGDi62387. Pdx1.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation
  • Cytoplasmcytosol By similarity

GO - Cellular componenti

  • cytoplasm Source: RGD
  • cytosol Source: UniProtKB-SubCell
  • nuclear speck Source: Ensembl
  • nucleus Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 283283Pancreas/duodenum homeobox protein 1PRO_0000049150Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei151 – 1511Phosphothreonine; by PASKBy similarity
Modified residuei268 – 2681PhosphoserineCombined sources

Post-translational modificationi

Phosphorylated by the SAPK2 pathway at high intracellular glucose concentration. Phosphorylated by HIPK2 on Ser-268 upon glucose accumulation. This phoyphorylation mediates subnuclear localization shifting. Phosphorylation by PASK may lead to translocation into the cytosol (By similarity).By similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP52947.

PTM databases

iPTMnetiP52947.
PhosphoSiteiP52947.

Expressioni

Tissue specificityi

Duodenum and pancreas (Langerhans islet beta cells and small subsets of endocrine non-beta-cells, at low levels in acinar cells).

Gene expression databases

GenevisibleiP52947. RN.

Interactioni

Subunit structurei

Interacts with the basic helix-loop-helix domains of TCF3(E47) and NEUROD1 and with HMG-I(Y). Interacts with SPOP and the methyltransferase SETD7. Part of a PDX1:PBX1b:MEIS2b complex (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
Psmd9Q9WTV53EBI-7626093,EBI-7626072

GO - Molecular functioni

  • protein complex binding Source: RGD
  • protein heterodimerization activity Source: RGD
  • transcription factor binding Source: RGD

Protein-protein interaction databases

IntActiP52947. 1 interaction.
MINTiMINT-1894530.
STRINGi10116.ENSRNOP00000066935.

Structurei

3D structure databases

ProteinModelPortaliP52947.
SMRiP52947. Positions 146-205.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni13 – 7361Transactivation domainAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi118 – 1236Antp-type hexapeptide
Motifi197 – 2037Nuclear localization signalBy similarity

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi42 – 487Poly-Pro
Compositional biasi216 – 2205Poly-Gly
Compositional biasi239 – 2446Poly-Pro

Domaini

The Antp-type hexapeptide mediates heterodimerization with PBX on a regulatory element of the somatostatin promoter.
The homeodomain, which contains the nuclear localization signal, not only mediates DNA-binding, but also acts as a protein-protein interaction domain for TCF3(E47), NEUROD1 and HMG-I(Y).By similarity

Sequence similaritiesi

Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation

Keywords - Domaini

Homeobox

Phylogenomic databases

eggNOGiKOG0489. Eukaryota.
ENOG410ZTBY. LUCA.
GeneTreeiENSGT00760000118940.
HOVERGENiHBG004525.
InParanoidiP52947.
KOiK07594.
OMAiPPPCLYM.
OrthoDBiEOG091G0GVH.
PhylomeDBiP52947.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR017995. Homeobox_antennapedia.
IPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR020479. Homeobox_metazoa.
IPR009057. Homeodomain-like.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
[Graphical view]
PRINTSiPR00025. ANTENNAPEDIA.
PR00024. HOMEOBOX.
SMARTiSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P52947-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNSEEQYYAA TQLYKDPCAF QRGPVPEFSA NPPACLYMGR QPPPPPPPQF
60 70 80 90 100
AGSLGTLEQG SPPDISPYEV PPLADDPAGA HLHHHLPAQL GLAHPPPGPF
110 120 130 140 150
PNGTETGGLE EPSRVHLPFP WMKSTKAHAW KSQWAGGAYA AEPEENKRTR
160 170 180 190 200
TAYTRAQLLE LEKEFLFNKY ISRPRRVELA VMLNLTERHI KIWFQNRRMK
210 220 230 240 250
WKKEEDKKRS SGTTSGGGGG EEPEQDCAVT SGEELLALPP PPPPGGAVPS
260 270 280
GVPAAAREGR LPSGLSASPQ PSSIAPLRPQ EPR
Length:283
Mass (Da):30,831
Last modified:October 1, 1996 - v1
Checksum:iC8C25FF2C75ED4E6
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti47 – 471P → T in AAA18355 (PubMed:7907546).Curated
Sequence conflicti240 – 2401P → K in AAA18355 (PubMed:7907546).Curated
Sequence conflicti247 – 2471A → V in AAA18355 (PubMed:7907546).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U04833 mRNA. Translation: AAA18355.1.
S67435 mRNA. Translation: AAB29317.1.
PIRiS42634.
RefSeqiNP_074043.3. NM_022852.3.
UniGeneiRn.54603.

Genome annotation databases

EnsembliENSRNOT00000071942; ENSRNOP00000066935; ENSRNOG00000046458.
GeneIDi29535.
KEGGirno:29535.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U04833 mRNA. Translation: AAA18355.1.
S67435 mRNA. Translation: AAB29317.1.
PIRiS42634.
RefSeqiNP_074043.3. NM_022852.3.
UniGeneiRn.54603.

3D structure databases

ProteinModelPortaliP52947.
SMRiP52947. Positions 146-205.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP52947. 1 interaction.
MINTiMINT-1894530.
STRINGi10116.ENSRNOP00000066935.

PTM databases

iPTMnetiP52947.
PhosphoSiteiP52947.

Proteomic databases

PaxDbiP52947.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000071942; ENSRNOP00000066935; ENSRNOG00000046458.
GeneIDi29535.
KEGGirno:29535.

Organism-specific databases

CTDi3651.
RGDi62387. Pdx1.

Phylogenomic databases

eggNOGiKOG0489. Eukaryota.
ENOG410ZTBY. LUCA.
GeneTreeiENSGT00760000118940.
HOVERGENiHBG004525.
InParanoidiP52947.
KOiK07594.
OMAiPPPCLYM.
OrthoDBiEOG091G0GVH.
PhylomeDBiP52947.

Miscellaneous databases

PROiP52947.

Gene expression databases

GenevisibleiP52947. RN.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR017995. Homeobox_antennapedia.
IPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR020479. Homeobox_metazoa.
IPR009057. Homeodomain-like.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
[Graphical view]
PRINTSiPR00025. ANTENNAPEDIA.
PR00024. HOMEOBOX.
SMARTiSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPDX1_RAT
AccessioniPrimary (citable) accession number: P52947
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: September 7, 2016
This is version 117 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.