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Q9C5X4 · ATX1_ARATH

Function

function

Isoform 1

Binds to the promoter and regulates the transcription of target genes, maintaining them in an active state; at promoters, required for TATA binding proteins (TBPs, e.g. TBP1 and TBP2) and RNA polymerase II (Pol II) recruitment, and, in a subsequent event, is recruited by a phosphorylated form of Pol II to the +300-bp region of transcribed sequences to trimethylates nucleosomes (PubMed:21266657, PubMed:23284292).
Histone trimethyltransferase that trimethylates 'Lys-4' of histone H3 (H3K4me3); H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation and is required for efficient elongation of transcription but not for transcription initiation (PubMed:17881378, PubMed:17965588, PubMed:18375658, PubMed:23284292).
Methylates only a limited fraction of nucleosomes of target genes (e.g. FLC, NAP, XTH33 and WRKY70) (PubMed:18375658).
Necessary for WDR5A occupancy at WRKY70 and LTP7 genes (PubMed:23284292).
Required to maintain the active state of class A (AP1 and AP2), class B (PI and AP3) and class C (AG, AGAMOUS) floral homeotic genes at early stages of flower development (PubMed:17881378).
Together with CLF, modulates AG nucleosome methylation statement (PubMed:17881378).
Involved in epigenetic regulation (e.g. H3K4me3) of the floral repressors FLC, FT and SOC1 to prevent the transition from vegetative to reproductive development, independently of the photoperiod; binds the active FLC locus before flowering, but this interaction is released upon the transition to flowering (PubMed:18375656, PubMed:24102415, PubMed:30150325).
Regulates floral organ identity and flowering transition. Functions as a receptor for the lipid messenger phosphatidylinositol 5-phosphate (PI5P), which negatively regulates its transcriptional activation activity. Exhibits histone methylase activity and subsequent transcriptional regulation on WRKY70 gene, and, to a lower extent on secondary defense-response targets salicylic acid (SA)-responsive gene PR1 and jasmonic acid (JA)-responsive gene THI2.1 (PubMed:17965588).
Involved in response to dehydration stress-response in both abscisic acid (ABA)-dependent and ABA-independent pathways; this includes specific genes (e.g. COR15A, ADH1, CBF4, RD29A, RD29B, RD26, ABF3, NCED3 and ABA3) epigenetic regulation (e.g. H3K4me3 and Pol II recruitment) to promote their transcription and influence ABA production (PubMed:19901554, PubMed:21309869).
Implicated in stomatal closure regulation (PubMed:21309869).
Indirect repressor of XTH genes (XTH33) (PubMed:19154201).
Necessary for the phosphorylation of Pol II NRPB1 (e.g. Ser5P and Ser2P) at the promoters of target genes, thus regulating both early and late stages of transcription (PubMed:21266657).
Controls root growth and architecture by regulating the timing of root development, stem cell niche maintenance (e.g. quiescent center (QC)), and cell patterning during primary and lateral root development (PubMed:25205583).
Modulates cell cycle duration, cell production, and the transition from cell proliferation in the root apical meristem (RAM) to cell elongation (PubMed:25205583).

Isoform 3

Trimethylates A4/EF1A post-translationally at Lys-396 (PubMed:21245040).
Required for actin cytoskeleton organization (PubMed:21245040).

Catalytic activity

Features

Showing features for binding site.

TypeIDPosition(s)Description
Binding site908S-adenosyl-L-methionine (UniProtKB | ChEBI)
Binding site954S-adenosyl-L-methionine (UniProtKB | ChEBI)
Binding site977-978S-adenosyl-L-methionine (UniProtKB | ChEBI)
Binding site980Zn2+ (UniProtKB | ChEBI)
Binding site1026Zn2+ (UniProtKB | ChEBI)
Binding site1028Zn2+ (UniProtKB | ChEBI)
Binding site1033Zn2+ (UniProtKB | ChEBI)

GO annotations

AspectTerm
Cellular Componentchromatin
Cellular Componentcytoplasm
Cellular Componentnucleus
Cellular Componentperinuclear region of cytoplasm
Cellular Componentplasma membrane
Cellular ComponentSet1C/COMPASS complex
Molecular Functionchromatin binding
Molecular Functionhistone H3K4 trimethyltransferase activity
Molecular Functionmetal ion binding
Molecular Functionphosphatidylinositol-5-phosphate binding
Molecular Functionprotein methyltransferase activity
Molecular Functiontranscription cis-regulatory region binding
Biological Processabscisic acid-activated signaling pathway
Biological Processactin cytoskeleton organization
Biological Processchromatin remodeling
Biological Processepigenetic regulation of gene expression
Biological Processmethylation
Biological Processnegative regulation of flower development
Biological Processpeptidyl-lysine methylation
Biological Processquiescent center organization
Biological Processregulation of DNA-templated transcription
Biological Processregulation of flower development
Biological Processregulation of lateral root development
Biological Processregulation of root development
Biological Processregulation of root morphogenesis
Biological Processregulation of stomatal closure
Biological Processregulation of transcription by RNA polymerase II
Biological Processresponse to water deprivation
Biological Processspecification of floral organ identity
Biological Processvegetative to reproductive phase transition of meristem

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    Histone H3-lysine(4) N-trimethyltransferase ATX1
  • EC number
  • Alternative names
    • Protein SET DOMAIN GROUP 27
    • Protein-lysine N-trimethyltransferase ATX1-SoloSET
      (EC:2.1.1.-
      ) . EC:2.1.1.- (UniProtKB | ENZYME | Rhea)
    • Trithorax-homolog protein 1
      (TRX-homolog protein 1
      )

Gene names

    • Name
      ATX1
    • Synonyms
      SDG27
      , SET27
      , TRX1
    • ORF names
      T9H9.17
    • Ordered locus names
      At2g31650

Organism names

  • Taxonomic identifier
  • Strains
    • cv. Wassilewskija
    • cv. Columbia
    • cv. Wassilewskija-2
  • Taxonomic lineage
    Eukaryota > Viridiplantae > Streptophyta > Embryophyta > Tracheophyta > Spermatophyta > Magnoliopsida > eudicotyledons > Gunneridae > Pentapetalae > rosids > malvids > Brassicales > Brassicaceae > Camelineae > Arabidopsis

Accessions

  • Primary accession
    Q9C5X4
  • Secondary accessions
    • Q84WP4
    • Q9SIP3

Proteomes

Organism-specific databases

Genome annotation databases

Subcellular Location

Isoform 1

Nucleus
Cytoplasm
Note: Shifts from nucleus to cytoplasm as PIP5 levels increase. When in the nucleus, associated with chromatin. When cytoplasmic, mostly localized along the plasma membrane, associated with PIP5.

Isoform 3

Cytoplasm

Keywords

Phenotypes & Variants

Disruption phenotype

Isoform 1

Decreased germination rates, larger stomatal apertures, more rapid transpiration and decreased tolerance to dehydration stress in atx1 plants partly due to reduced ABA biosynthesis as a result of decreased NCED3 transcript levels (PubMed:21309869).
Reduced trimethylated 'Lys-4' histone H3 (H3K4me3) but normal dimethylated 'Lys-4' histone H3 (H3K4me2) at NAP, XTH33, NCED3, LTP and WRKY70 nucleosomes leading to decreased transcript levels in atx1 plants (PubMed:18375658, PubMed:21266657).
Lower Pol II phosphorylation (e.g. Ser5P and Ser2P) and TBP (e.g. TBP1 and TBP2) occupancy at the promoters of NCED3, LTP and WRKY70 associated with reduced gene expression (PubMed:21266657).
Strongly reduced occupancy of WDR5A at WRKY70 and LTP7 genes (PubMed:23284292).
Accelerated transition from vegetative to reproductive development, under both long-day and short-day conditions, especially in medium-day conditions (12 hours light / 12 hours dark), due to FLC, FT and SOC1 epigenetic misregulation; specific depletion in H3K4me3 but increased H3K27me2 associated with reduced FLC, FT and SOC1 levels (PubMed:18375656, PubMed:21245040, PubMed:24102415).
Misexpression of AGAMOUS, recognizable phenotypes (e.g. small and slightly serrated leaves, and early flowering time) and loss of H3K4me3 histone H3-tail marks (PubMed:17881378).
Impaired in primary root growth with irregular shape and expanded quiescent center (QC) cells (PubMed:25205583).
Ectopic expression of QC-specific markers (e.g. QC46, WOX5 and SCR) in the primary RAM and in the developing lateral root primordia (PubMed:25205583).
Lack of coordination between cell division and cell growth leading to atypical distribution of T-divisions, the presence of oblique divisions, and abnormal cell patterning in the root apical meristem (RAM) (PubMed:25205583).
Reduced lateral root (LR) density within the branching zone (PubMed:25205583).
Altered transcription levels of target genes, including several endomembrane and cell wall-associated proteins coding genes, XTH genes being up-regulated (PubMed:18375658, PubMed:19154201).
Derepression of XTH33 in roots, stems and seedlings (PubMed:19154201).
Increased sensitivity to osmotic or dehydration stress due to an altered expression of genes involved in response to drought in both abscisic acid (ABA)-dependent and ABA-independent pathways (e.g. COR15A, ADH1, CBF4, RD29A, RD29B, RD26, ABF3, NCED3 and ABA3) (PubMed:19901554, PubMed:21309869).
Double mutant plants atx1 clf exhibits normal leaf-phenotype and flowering time (PubMed:17881378).
Reduced basal levels and induction of WRKY70 and of the salicylic acid (SA)-responsive gene PR1 upon pathogen infection by Pseudomonas syringae DC3000 or after SA treatment, but increased basal levels of the jasmonic acid (JA)-responsive gene THI2.1or after JA treatment (PubMed:17965588).

Isoform 3

Precocious flowering, asymmetric rosettes, aberrant flowers and chlorosis (PubMed:21245040).
Dramatically different pattern of reduced actin bundles and absent actin transvacuolar cytoplasmic strands (TVSs) (PubMed:21245040).

Features

Showing features for mutagenesis.

TypeIDPosition(s)Description
Mutagenesis927Deficient methyltransferase catalytic activity associated with early-flowering phenotype and reduced WRKY 70 and LTP7 transcripts levels but normal recruitment of WDR5A at target genes but without histone modification; when associated with A-945, A-954, A-1013 and A-1015.
Mutagenesis945Deficient methyltransferase catalytic activity associated with early-flowering phenotype and reduced WRKY 70 and LTP7 transcripts levels but normal recruitment of WDR5A at target genes but without histone modification; when associated with A-927, A-954, A-1013 and A-1015.
Mutagenesis947Repressed FLC transcription activation associated with reduced activation by SEC-mediated O-GlcNAcylation and lower methyltransferase catalytic activity.
Mutagenesis954Deficient methyltransferase catalytic activity associated with early-flowering phenotype and reduced WRKY 70 and LTP7 transcripts levels but normal recruitment of WDR5A at target genes but without histone modification; when associated with A-927, A-945, A-1013 and A-1015.
Mutagenesis1013Deficient methyltransferase catalytic activity associated with early-flowering phenotype and reduced WRKY 70 and LTP7 transcripts levels but normal recruitment of WDR5A at target genes but without histone modification; when associated with A-927, A-945, A-954 and A-1015.
Mutagenesis1015Deficient methyltransferase catalytic activity associated with early-flowering phenotype and reduced WRKY 70 and LTP7 transcripts levels but normal recruitment of WDR5A at target genes but without histone modification; when associated with A-927, A-945, A-954 and A-1013.

Variants

We now provide the "Disease & Variants" viewer in its own tab.

The viewer provides 73 variants from UniProt as well as other sources including ClinVar and dbSNP.

Go to variant viewer

PTM/Processing

Features

Showing features for chain, glycosylation.

Type
IDPosition(s)Description
ChainPRO_00002333541-1062Histone H3-lysine4 N-trimethyltransferase ATX1
Glycosylation947O-linked (GlcNAc) serine

Post-translational modification

Activated via O-glycosylation by SEC; this modification triggers FLC locus H3K4me3 histone modification, thus preventing premature flowering.

Keywords

Proteomic databases

PTM databases

Expression

Tissue specificity

Isoform 1

Strongly expressed in cotyledons, but weak levels in the first true leaves, except at the hydothodes (PubMed:21245040).
Ubiquitous with higher levels in dividing tissues, including inflorescence meristem and flower primordia (PubMed:11418242, PubMed:12699618, PubMed:18375658).
Expressed also in leaves (especially at hydathodes), in growing inflorescence stems and in the mature flowers (PubMed:18375658).

Isoform 3

Strongly expressed in young seedlings.

Developmental stage

Isoform 1

Expression is associated with the initiation of flower organs and ovules (PubMed:12699618, PubMed:18375658).
Accumulates in the tissues of young seedlings but also in adult plants (PubMed:18375658, PubMed:21245040).
In flowers, present in sepals, in the vasculature of petals, and in the filaments of the stamens and, at low levels, at the tips of the stigma (PubMed:18375658).
In seedlings, observed in the vasculature of the cotyledons, hypocotyls, stems, and the first pair of leaves (PubMed:18375656, PubMed:21245040).
Just prior to flowering, a strong reduction in expression levels occurs in the vasculature (PubMed:18375656).

Isoform 3

Expressed in young seedlings (PubMed:21245040).
Later in development, confined to cells at attachment sites of organ to stems (PubMed:21245040).

Gene expression databases

Interaction

Subunit

Isoform 1

Interacts with PIP5 (PubMed:16585509).
Interacts with WDR5A (PubMed:19567704, PubMed:23284292).
Binds to CLF in the nucleus (PubMed:17881378).
Interacts with NRPB1 CTD domain, especially when NRPB1 is phosphorylated on 'Ser-5' of the heptapeptide repeat (PubMed:21266657).
Component of a nuclear protein complex containing at least TATA binding proteins (TBPs, e.g. TBP1 and TBP2) and ATX1 (PubMed:21266657).
Associates with ULT1 for trimethylating 'Lys-4' on histone H3 (H3K4me3) at flower MADS box gene loci (PubMed:23632855).
Interacts with SEC (PubMed:30150325).

Isoform 3

Interacts with A4/EF1A in the cytoplasm on the nuclear periphery.

Protein-protein interaction databases

Structure

Family & Domains

Features

Showing features for region, domain, compositional bias, zinc finger.

Type
IDPosition(s)Description
Region159-184Disordered
Domain301-365PWWP
Region401-424Disordered
Compositional bias404-423Polar residues
Domain441-500FYR N-terminal
Domain504-586FYR C-terminal
Zinc finger591-647Phorbol-ester/DAG-type
Region599-1062Interaction with PIP5
Zinc finger609-660PHD-type 1
Zinc finger665-698C2HC pre-PHD-type
Zinc finger722-785PHD-type 2
Domain898-1016SET
Domain1022-1038Post-SET

Sequence similarities

Keywords

Phylogenomic databases

Family and domain databases

Sequence & Isoforms

Align isoforms (3)
  • Sequence status
    Complete

This entry describes 3 isoforms produced by Alternative splicing.

Q9C5X4-1

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.

  • Length
    1,062
  • Mass (Da)
    119,711
  • Last updated
    2006-05-02 v2
  • MD5 Checksum
    DE1225D69BF8D139ABF1888EAD75CB8E
MACFSNETQIEIDVHDLVEAPIRYDSIESIYSIPSSALCCVNAVGSHSLMSKKVKAQKLPMIEQFEIEGSGVSASDDCCRSDDYKLRIQRPEIVRVYYRRRKRPLRECLLDQAVAVKTESVELDEIDCFEEKKRRKIGNCELVKSGMESIGLRRCKENNAFSGNKQNGSSRRKGSSSKNQDKATLASRSAKKWVRLSYDGVDPTSFIGLQCKVFWPLDALWYEGSIVGYSAERKRYTVKYRDGCDEDIVFDREMIKFLVSREEMELLHLKFCTSNVTVDGRDYDEMVVLAATLDECQDFEPGDIVWAKLAGHAMWPAVIVDESIIGERKGLNNKVSGGGSLLVQFFGTHDFARIKVKQAISFIKGLLSPSHLKCKQPRFEEGMQEAKMYLKAHRLPERMSQLQKGADSVDSDMANSTEEGNSGGDLLNDGEVWLRPTEHVDFRHIIGDLLIINLGKVVTDSQFFKDENHIWPEGYTAMRKFTSLTDHSASALYKMEVLRDAETKTHPLFIVTADSGEQFKGPTPSACWNKIYNRIKKVQNSDSPNILGEELNGSGTDMFGLSNPEVIKLVQDLSKSRPSSHVSMCKNSLGRHQNQPTGYRPVRVDWKDLDKCNVCHMDEEYENNLFLQCDKCRMMVHAKCYGELEPCDGALWLCNLCRPGAPDMPPRCCLCPVVGGAMKPTTDGRWAHLACAIWIPETCLSDVKKMEPIDGVNKVSKDRWKLMCTICGVSYGACIQCSNNSCRVAYHPLCARAAGLCVELENDMSVEGEEADQCIRMLSFCKRHRQTSTACLGSEDRIKSATHKTSEYLPPPNPSGCARTEPYNCFGRRGRKEPEALAAASSKRLFVENQPYVIGGYSRLEFSTYKSIHGSKVSQMNTPSNILSMAEKYRYMRETYRKRLAFGKSGIHGFGIFAKLPHRAGDMMIEYTGELVRPSIADKREQLIYNSMVGAGTYMFRIDDERVIDATRTGSIAHLINHSCVPNCYSRVITVNGDEHIIIFAKRHIPKWEELTYDYRFFSIGERLSCSCGFPGCRGVVNDTEAEEQHAKICVPRCDLIDWTAE

Q9C5X4-2

  • Name
    2
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical

Q9C5X4-3

  • Name
    3
  • Synonyms
    SoloSET
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical

Sequence caution

The sequence AAD24842.1 differs from that shown. Reason: Erroneous gene model prediction

Features

Showing features for alternative sequence, sequence conflict, compositional bias.

Type
IDPosition(s)Description
Alternative sequenceVSP_0181321-583in isoform 2
Alternative sequenceVSP_0605261-875in isoform 3
Sequence conflict4in Ref. 1; AAK01237
Sequence conflict23in Ref. 1; AAK01237
Sequence conflict194in Ref. 1; AAK01237
Sequence conflict313in Ref. 1; AAK01237
Compositional bias404-423Polar residues
Sequence conflict667in Ref. 1; AAK01237

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
AF329273
EMBL· GenBank· DDBJ
AAK01237.1
EMBL· GenBank· DDBJ
mRNA
AC007071
EMBL· GenBank· DDBJ
AAD24842.1
EMBL· GenBank· DDBJ
Genomic DNA Sequence problems.
CP002685
EMBL· GenBank· DDBJ
AEC08569.1
EMBL· GenBank· DDBJ
Genomic DNA
BT002941
EMBL· GenBank· DDBJ
AAO22754.1
EMBL· GenBank· DDBJ
mRNA

Genome annotation databases

Similar Proteins

Disclaimer

Any 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. Our staff consists of biologists and biochemists that are not trained to give medical advice.
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