O80536 · PIF3_ARATH
- ProteinTranscription factor PIF3
- GenePIF3
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids524 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Transcription factor acting in the phytochrome signaling pathway (PubMed:10466729, PubMed:14508006).
Activates transcription by binding to the G box (5'-CACGTG-3'), particularly in the dark but barely in far-red light (PubMed:10797009, PubMed:31732705).
Acts as a negative regulator of phytochrome B signaling (PubMed:14508006).
Represses chlorophyll biosynthesis and photosynthesis in the dark (PubMed:23548744).
Recruits the histone deacetylase HDA15 to the promoters of chlorophyll biosynthetic and photosynthetic genes (PubMed:23548744).
HDA15 represses their transcription by histone deacetylation (PubMed:23548744).
Promotes the expression of MDP60 to modulate hypocotyl cell elongation in response to light and ethylene signaling (PubMed:29167353).
Required for submergence-induced and ethylene-dependent underwater hypocotyl elongation (PubMed:31638649).
Activates transcription by binding to the G box (5'-CACGTG-3'), particularly in the dark but barely in far-red light (PubMed:10797009, PubMed:31732705).
Acts as a negative regulator of phytochrome B signaling (PubMed:14508006).
Represses chlorophyll biosynthesis and photosynthesis in the dark (PubMed:23548744).
Recruits the histone deacetylase HDA15 to the promoters of chlorophyll biosynthetic and photosynthetic genes (PubMed:23548744).
HDA15 represses their transcription by histone deacetylation (PubMed:23548744).
Promotes the expression of MDP60 to modulate hypocotyl cell elongation in response to light and ethylene signaling (PubMed:29167353).
Required for submergence-induced and ethylene-dependent underwater hypocotyl elongation (PubMed:31638649).
Activity regulation
Sequestered by PhyA from its target genes promoters in far-red light.
GO annotations
all annotations | all molecular function | nucleotide binding | molecular_function | nucleic acid binding | dna binding | chromatin binding | dna-binding transcription factor activity | rna binding | cytoskeletal motor activity | catalytic activity | nuclease activity | signaling receptor binding | structural molecule activity | transporter activity | binding | protein binding | translation factor activity, rna binding | lipid binding | kinase activity | transferase activity | hydrolase activity | oxygen binding | enzyme regulator activity | carbohydrate binding | signaling receptor activity | translation regulator activity | transcription regulator activity | other molecular function | all biological process | carbohydrate metabolic process | generation of precursor metabolites and energy | nucleobase-containing compound metabolic process | dna metabolic process | translation | lipid metabolic process | transport | response to stress | cell cycle | cell communication | signal transduction | cell-cell signaling | multicellular organism development | circadian rhythm | biological_process | metabolic process | catabolic process | biosynthetic process | response to light stimulus | response to external stimulus | tropism | response to biotic stimulus | response to abiotic stimulus | response to endogenous stimulus | embryo development | post-embryonic development | fruit ripening | abscission | pollination | flower development | cellular process | programmed cell death | photosynthesis | cellular component organization | cell growth | protein metabolic process | cellular homeostasis | secondary metabolic process | reproductive process | cell differentiation | protein modification process | growth | epigenetic regulation of gene expression | response to chemical | anatomical structure development | regulation of molecular function | other biological process | all cellular component | cellular_component | extracellular region | cell wall | intracellular anatomical structure | nucleus | nuclear envelope | nucleoplasm | nucleolus | cytoplasm | mitochondrion | lysosome | endosome | vacuole | peroxisome | endoplasmic reticulum | golgi apparatus | cytosol | ribosome | cytoskeleton | plasma membrane | chloroplast | plastid | thylakoid | membrane | external encapsulating structure | other cellular component | |||
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Keywords
- Molecular function
- Biological process
Names & Taxonomy
Protein names
- Recommended nameTranscription factor PIF3
- Alternative names
Gene names
Organism names
- Strains
- Taxonomic lineageEukaryota > Viridiplantae > Streptophyta > Embryophyta > Tracheophyta > Spermatophyta > Magnoliopsida > eudicotyledons > Gunneridae > Pentapetalae > rosids > malvids > Brassicales > Brassicaceae > Camelineae > Arabidopsis
Accessions
- Primary accessionO80536
- Secondary accessions
Proteomes
Organism-specific databases
Genome annotation databases
Subcellular Location
Phenotypes & Variants
Disruption phenotype
Inhibited submergence-induced and ethylene-dependent underwater hypocotyl elongation.
Features
Showing features for natural variant.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Natural variant | 124 | in strain: cv. An-2 and cv. Su-0 | ||||
Sequence: E → D | ||||||
Natural variant | 141 | in strain: cv. An-2 and cv. Su-0 | ||||
Sequence: K → N | ||||||
Natural variant | 176 | in strain: cv. An-2 and cv. Su-0 | ||||
Sequence: Q → H | ||||||
Natural variant | 186 | in strain: cv. An-2 and cv. Su-0 | ||||
Sequence: Q → K | ||||||
Natural variant | 209 | in strain: cv. An-2 and cv. Su-0 | ||||
Sequence: F → L | ||||||
Natural variant | 220 | in strain: cv. An-2 and cv. Su-0 | ||||
Sequence: T → I | ||||||
Natural variant | 236 | in strain: cv. An-2 and cv. Su-0 | ||||
Sequence: V → I |
Variants
We now provide the "Disease & Variants" viewer in its own tab.
The viewer provides 39 variants from UniProt as well as other sources including ClinVar and dbSNP.
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000127428 | 1-524 | Transcription factor PIF3 | |||
Sequence: MPLFELFRLTKAKLESAQDRNPSPPVDEVVELVWENGQISTQSQSSRSRNIPPPQANSSRAREIGNGSKTTMVDEIPMSVPSLMTGLSQDDDFVPWLNHHPSLDGYCSDFLRDVSSPVTVNEQESDMAVNQTAFPLFQRRKDGNESAPAASSSQYNGFQSHSLYGSDRARDLPSQQTNPDRFTQTQEPLITSNKPSLVNFSHFLRPATFAKTTNNNLHDTKEKSPQSPPNVFQTRVLGAKDSEDKVLNESVASATPKDNQKACLISEDSCRKDQESEKAVVCSSVGSGNSLDGPSESPSLSLKRKHSNIQDIDCHSEDVEEESGDGRKEAGPSRTGLGSKRSRSAEVHNLSERRRRDRINEKMRALQELIPNCNKVDKASMLDEAIEYLKSLQLQVQIMSMASGYYLPPAVMFPPGMGHYPAAAAAMAMGMGMPYAMGLPDLSRGGSSVNHGPQFQVSGMQQQPVAMGIPRVSGGGIFAGSSTIGNGSTRDLSGSKDQTTTNNNSNLKPIKRKQGSSDQFCGSS |
Post-translational modification
Phosphorylated by PHYA; this phosphorylation is repressed by PIA2.
Dephosphorylated by TOPP4 during photomorphogenesis, leading to subsequent degradation of PIF3 by the proteasomal pathway.
Keywords
- PTM
Proteomic databases
PTM databases
Expression
Tissue specificity
Expressed in stems, leaves, seedlings, fruits and flowers, and, to a lower extent, in roots.
Induction
By UV treatment (PubMed:12679534).
Repressed by red (R) and far red (FR) light treatments in a phyB- and phyA-dependent manner, and via a PTAC12/HMR/PAP5 regulated process (PubMed:25944101).
Up-regulated by abscisic acid (ABA), ethylene (ACC), auxin (IAA), salt (NaCl), cold and heat (PubMed:23708772).
Follows a tenous circadian rhythm with slightly higher levels at the end of the light phase (PubMed:23708772).
Repressed by red (R) and far red (FR) light treatments in a phyB- and phyA-dependent manner, and via a PTAC12/HMR/PAP5 regulated process (PubMed:25944101).
Up-regulated by abscisic acid (ABA), ethylene (ACC), auxin (IAA), salt (NaCl), cold and heat (PubMed:23708772).
Follows a tenous circadian rhythm with slightly higher levels at the end of the light phase (PubMed:23708772).
Developmental stage
Accumulates progressively in maturating seeds to reach a peak in dry seeds (PubMed:23708772).
Expressed upon seed imbibition (PubMed:23708772).
Expressed upon seed imbibition (PubMed:23708772).
Gene expression databases
Interaction
Subunit
Homodimer (PubMed:25944101).
Can form a heterodimer with REP1 and PIF4. Phytochrome B binds specifically to DNA-bound PIF3, but only upon red light induced conversion to the Pfr form (PfrB). Reconversion to Pr form causes rapid dissociation. Interacts with APRR1/TOC1. Binds to PIA2; this interaction may trigger the repression of PHYA-mediated phosphorylation (PubMed:27143545).
Interacts with TOPP4 (Probable) (PubMed:11828023, PubMed:12826627, PubMed:12897250, PubMed:26704640, PubMed:27143545).
Interacts with FYPP1 and FYPP3 (PubMed:31527236).
Interacts with HDA15 in the dark (PubMed:23548744).
Associates to PTAC12/HMR/PAP5 which acts as a transcriptional coactivator (PubMed:25944101).
Binds to PhyA (PubMed:31732705).
Can form a heterodimer with REP1 and PIF4. Phytochrome B binds specifically to DNA-bound PIF3, but only upon red light induced conversion to the Pfr form (PfrB). Reconversion to Pr form causes rapid dissociation. Interacts with APRR1/TOC1. Binds to PIA2; this interaction may trigger the repression of PHYA-mediated phosphorylation (PubMed:27143545).
Interacts with TOPP4 (Probable) (PubMed:11828023, PubMed:12826627, PubMed:12897250, PubMed:26704640, PubMed:27143545).
Interacts with FYPP1 and FYPP3 (PubMed:31527236).
Interacts with HDA15 in the dark (PubMed:23548744).
Associates to PTAC12/HMR/PAP5 which acts as a transcriptional coactivator (PubMed:25944101).
Binds to PhyA (PubMed:31732705).
Binary interactions
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | O80536 | HFR1 Q9FE22 | 6 | EBI-625701, EBI-626001 | |
BINARY | O80536 | PHYA P14712 | 8 | EBI-625701, EBI-624446 | |
BINARY | O80536 | PHYB P14713 | 22 | EBI-625701, EBI-300727 | |
BINARY | O80536 | PIF1 Q8GZM7 | 6 | EBI-625701, EBI-630400 | |
BINARY | O80536 | PIF3 O80536 | 3 | EBI-625701, EBI-625701 | |
BINARY | O80536 | PIF4 Q8W2F3-2 | 3 | EBI-625701, EBI-625732 | |
BINARY | O80536 | RGA Q9SLH3 | 6 | EBI-625701, EBI-963624 |
Protein-protein interaction databases
Structure
Family & Domains
Features
Showing features for compositional bias, region, domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 38-66 | Polar residues | ||||
Sequence: QISTQSQSSRSRNIPPPQANSSRAREIGN | ||||||
Region | 38-70 | Disordered | ||||
Sequence: QISTQSQSSRSRNIPPPQANSSRAREIGNGSKT | ||||||
Region | 141-194 | Disordered | ||||
Sequence: KDGNESAPAASSSQYNGFQSHSLYGSDRARDLPSQQTNPDRFTQTQEPLITSNK | ||||||
Compositional bias | 145-194 | Polar residues | ||||
Sequence: ESAPAASSSQYNGFQSHSLYGSDRARDLPSQQTNPDRFTQTQEPLITSNK | ||||||
Region | 239-259 | Disordered | ||||
Sequence: AKDSEDKVLNESVASATPKDN | ||||||
Compositional bias | 281-305 | Polar residues | ||||
Sequence: VCSSVGSGNSLDGPSESPSLSLKRK | ||||||
Region | 281-358 | Disordered | ||||
Sequence: VCSSVGSGNSLDGPSESPSLSLKRKHSNIQDIDCHSEDVEEESGDGRKEAGPSRTGLGSKRSRSAEVHNLSERRRRDR | ||||||
Compositional bias | 306-329 | Basic and acidic residues | ||||
Sequence: HSNIQDIDCHSEDVEEESGDGRKE | ||||||
Domain | 343-392 | bHLH | ||||
Sequence: RSAEVHNLSERRRRDRINEKMRALQELIPNCNKVDKASMLDEAIEYLKSL | ||||||
Region | 483-524 | Disordered | ||||
Sequence: TIGNGSTRDLSGSKDQTTTNNNSNLKPIKRKQGSSDQFCGSS |
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length524
- Mass (Da)56,990
- Last updated1998-11-01 v1
- Checksum1044AC01D598DE7C
Features
Showing features for sequence conflict, compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 15 | in Ref. 3; AAC99771 | ||||
Sequence: E → D | ||||||
Compositional bias | 38-66 | Polar residues | ||||
Sequence: QISTQSQSSRSRNIPPPQANSSRAREIGN | ||||||
Compositional bias | 145-194 | Polar residues | ||||
Sequence: ESAPAASSSQYNGFQSHSLYGSDRARDLPSQQTNPDRFTQTQEPLITSNK | ||||||
Compositional bias | 281-305 | Polar residues | ||||
Sequence: VCSSVGSGNSLDGPSESPSLSLKRK | ||||||
Compositional bias | 306-329 | Basic and acidic residues | ||||
Sequence: HSNIQDIDCHSEDVEEESGDGRKE | ||||||
Sequence conflict | 344 | in Ref. 3; AAC99771 | ||||
Sequence: S → L |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AF100166 EMBL· GenBank· DDBJ | AAC95156.1 EMBL· GenBank· DDBJ | mRNA | ||
AF251693 EMBL· GenBank· DDBJ | AAL55715.1 EMBL· GenBank· DDBJ | mRNA | ||
AF088280 EMBL· GenBank· DDBJ | AAC99771.1 EMBL· GenBank· DDBJ | mRNA | ||
AC003970 EMBL· GenBank· DDBJ | AAC33213.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
CP002684 EMBL· GenBank· DDBJ | AEE28457.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
CP002684 EMBL· GenBank· DDBJ | AEE28458.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
CP002684 EMBL· GenBank· DDBJ | ANM60410.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
CP002684 EMBL· GenBank· DDBJ | ANM60411.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
CP002684 EMBL· GenBank· DDBJ | ANM60412.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
CP002684 EMBL· GenBank· DDBJ | ANM60413.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AK117255 EMBL· GenBank· DDBJ | BAC41930.1 EMBL· GenBank· DDBJ | mRNA | ||
EF193482 EMBL· GenBank· DDBJ | ABP96435.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193483 EMBL· GenBank· DDBJ | ABP96436.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193484 EMBL· GenBank· DDBJ | ABP96437.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193485 EMBL· GenBank· DDBJ | ABP96438.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193486 EMBL· GenBank· DDBJ | ABP96439.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193487 EMBL· GenBank· DDBJ | ABP96440.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193488 EMBL· GenBank· DDBJ | ABP96441.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193489 EMBL· GenBank· DDBJ | ABP96442.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193490 EMBL· GenBank· DDBJ | ABP96443.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193491 EMBL· GenBank· DDBJ | ABP96444.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193492 EMBL· GenBank· DDBJ | ABP96445.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193493 EMBL· GenBank· DDBJ | ABP96446.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193494 EMBL· GenBank· DDBJ | ABP96447.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193495 EMBL· GenBank· DDBJ | ABP96448.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
EF193496 EMBL· GenBank· DDBJ | ABP96449.1 EMBL· GenBank· DDBJ | Genomic DNA |