ATX2_ARATH
ID ATX2_ARATH Reviewed; 1083 AA.
AC P0CB22; Q8RXL4; Q9MA43;
DT 01-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-SEP-2009, sequence version 1.
DT 03-AUG-2022, entry version 89.
DE RecName: Full=Histone-lysine N-methyltransferase ATX2 {ECO:0000303|PubMed:11418242};
DE EC=2.1.1.- {ECO:0000269|PubMed:18375658};
DE AltName: Full=Protein SET DOMAIN GROUP 30 {ECO:0000303|PubMed:11691919};
DE AltName: Full=Trithorax-homolog protein 2 {ECO:0000303|PubMed:11418242};
DE Short=TRX-homolog protein 2 {ECO:0000303|PubMed:11418242};
GN Name=ATX2 {ECO:0000303|PubMed:11418242};
GN Synonyms=SDG30 {ECO:0000303|PubMed:11691919},
GN SET30 {ECO:0000303|PubMed:11691919};
GN OrderedLocusNames=At1g05830 {ECO:0000312|Araport:AT1G05830};
GN ORFNames=T20M3.10 {ECO:0000312|EMBL:AAF29390.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP TISSUE SPECIFICITY.
RX PubMed=11418242; DOI=10.1016/s0378-1119(01)00524-8;
RA Alvarez-Venegas R., Avramova Z.;
RT "Two Arabidopsis homologs of the animal trithorax genes: a new structural
RT domain is a signature feature of the trithorax gene family.";
RL Gene 271:215-221(2001).
RN [5]
RP NOMENCLATURE.
RX PubMed=11691919; DOI=10.1093/nar/29.21.4319;
RA Baumbusch L.O., Thorstensen T., Krauss V., Fischer A., Naumann K.,
RA Assalkhou R., Schulz I., Reuter G., Aalen R.B.;
RT "The Arabidopsis thaliana genome contains at least 29 active genes encoding
RT SET domain proteins that can be assigned to four evolutionarily conserved
RT classes.";
RL Nucleic Acids Res. 29:4319-4333(2001).
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE,
RP AND CATALYTIC ACTIVITY.
RC STRAIN=cv. Columbia;
RX PubMed=18375658; DOI=10.1105/tpc.107.056614;
RA Saleh A., Alvarez-Venegas R., Yilmaz M., Le O., Hou G., Sadder M.,
RA Al-Abdallat A., Xia Y., Lu G., Ladunga I., Avramova Z.;
RT "The highly similar Arabidopsis homologs of trithorax ATX1 and ATX2 encode
RT proteins with divergent biochemical functions.";
RL Plant Cell 20:568-579(2008).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia, and cv. Wassilewskija;
RX PubMed=18375656; DOI=10.1105/tpc.108.058172;
RA Pien S., Fleury D., Mylne J.S., Crevillen P., Inze D., Avramova Z.,
RA Dean C., Grossniklaus U.;
RT "ARABIDOPSIS TRITHORAX1 dynamically regulates FLOWERING LOCUS C activation
RT via histone 3 lysine 4 trimethylation.";
RL Plant Cell 20:580-588(2008).
RN [8]
RP REVIEW.
RX PubMed=19412892; DOI=10.1387/ijdb.082664za;
RA Avramova Z.;
RT "Evolution and pleiotropy of TRITHORAX function in Arabidopsis.";
RL Int. J. Dev. Biol. 53:371-381(2009).
RN [9]
RP REVIEW.
RX PubMed=25047977; DOI=10.1016/j.pbi.2014.07.004;
RA Fromm M., Avramova Z.;
RT "ATX1/AtCOMPASS and the H3K4me3 marks: how do they activate Arabidopsis
RT genes?";
RL Curr. Opin. Plant Biol. 21:75-82(2014).
RN [10]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=24102415; DOI=10.1111/nph.12493;
RA Shafiq S., Berr A., Shen W.-H.;
RT "Combinatorial functions of diverse histone methylations in Arabidopsis
RT thaliana flowering time regulation.";
RL New Phytol. 201:312-322(2014).
CC -!- FUNCTION: Histone methyltransferase (PubMed:18375658). Dimethylates
CC 'Lys-4' of histone H3 (H3K4me2) (PubMed:18375658, PubMed:24102415). H3
CC 'Lys-4' methylation represents a specific tag for epigenetic
CC transcriptional activation (PubMed:18375658). Methylates only a limited
CC fraction of nucleosomes of target genes (e.g. NAP and XTH33)
CC (PubMed:18375658). Involved in epigenetic regulation of the floral
CC repressor FLC and FT to prevent the transition from vegetative to
CC reproductive development (PubMed:18375656, PubMed:24102415).
CC {ECO:0000269|PubMed:18375656, ECO:0000269|PubMed:18375658,
CC ECO:0000269|PubMed:24102415}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=N(6)-methyl-L-lysyl-[histone] + S-adenosyl-L-methionine = H(+)
CC + N(6),N(6)-dimethyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:21696, Rhea:RHEA-COMP:9846, Rhea:RHEA-COMP:15914,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:61929, ChEBI:CHEBI:61976;
CC Evidence={ECO:0000269|PubMed:18375658};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:21697;
CC Evidence={ECO:0000269|PubMed:18375658};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves and flowers and, to a
CC lower extent, in young seedlings. {ECO:0000269|PubMed:11418242,
CC ECO:0000269|PubMed:18375658}.
CC -!- DEVELOPMENTAL STAGE: Accumulates in adult plants, especially in rosette
CC leaves and roots (but not in the vasculature and in tips)
CC (PubMed:18375658). Weakly expressed in inflorescence nodes and at the
CC base of the flowers (PubMed:18375658). In flowers, present in pollen
CC and, at low levels, at the tips of the stigma (PubMed:18375658). In
CC seedlings, observed in the vasculature and in the shoot apical
CC meristems (PubMed:18375656). {ECO:0000269|PubMed:18375656,
CC ECO:0000269|PubMed:18375658}.
CC -!- PTM: Activated via O-glycosylation. {ECO:0000250|UniProtKB:Q9C5X4}.
CC -!- DISRUPTION PHENOTYPE: No obvious phenotype except a slightly delayed
CC abscission of sepals and petals after fertilization (PubMed:18375658).
CC Reduced dimethylated 'Lys-4' histone H3 (H3K4me2) but normal
CC trimethylated 'Lys-4' histone H3 (H3K4me3) at FLC, FT, NAP and XTH33
CC nucleosomes (PubMed:18375658, PubMed:24102415). Accelerated transition
CC from vegetative to reproductive development (early flowering),
CC especially in medium-day conditions (12 hours light / 12 hours dark),
CC due to FLC and FT epigenetic misregulation (PubMed:18375656,
CC PubMed:24102415). Altered transcription levels of target genes
CC (PubMed:18375658). Decreased XTH33 but normal WRKY70 transcript levels
CC in atx2 plants (PubMed:18375658). {ECO:0000269|PubMed:18375656,
CC ECO:0000269|PubMed:18375658, ECO:0000269|PubMed:24102415}.
CC -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC superfamily. Histone-lysine methyltransferase family. TRX/MLL
CC subfamily. {ECO:0000255|PROSITE-ProRule:PRU00190}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF29390.1; Type=Erroneous gene model prediction; Note=The predicted gene has been split into 2 genes: At1g05830 and At1g05835.; Evidence={ECO:0000305};
CC Sequence=AK226560; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AC009999; AAF29390.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE27900.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE27901.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59180.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59181.1; -; Genomic_DNA.
DR EMBL; AK226560; -; NOT_ANNOTATED_CDS; mRNA.
DR PIR; A86193; A86193.
DR RefSeq; NP_001077464.4; NM_001083995.4.
DR RefSeq; NP_001321563.1; NM_001331587.1.
DR RefSeq; NP_001321564.1; NM_001331588.1.
DR RefSeq; NP_172074.6; NM_100464.7.
DR AlphaFoldDB; P0CB22; -.
DR SMR; P0CB22; -.
DR STRING; 3702.AT1G05830.1; -.
DR iPTMnet; P0CB22; -.
DR PaxDb; P0CB22; -.
DR PRIDE; P0CB22; -.
DR ProteomicsDB; 240917; -.
DR EnsemblPlants; AT1G05830.1; AT1G05830.1; AT1G05830.
DR EnsemblPlants; AT1G05830.2; AT1G05830.2; AT1G05830.
DR EnsemblPlants; AT1G05830.3; AT1G05830.3; AT1G05830.
DR EnsemblPlants; AT1G05830.4; AT1G05830.4; AT1G05830.
DR GeneID; 837093; -.
DR Gramene; AT1G05830.1; AT1G05830.1; AT1G05830.
DR Gramene; AT1G05830.2; AT1G05830.2; AT1G05830.
DR Gramene; AT1G05830.3; AT1G05830.3; AT1G05830.
DR Gramene; AT1G05830.4; AT1G05830.4; AT1G05830.
DR KEGG; ath:AT1G05830; -.
DR Araport; AT1G05830; -.
DR TAIR; locus:2198743; AT1G05830.
DR eggNOG; KOG1080; Eukaryota.
DR HOGENOM; CLU_005729_0_0_1; -.
DR InParanoid; P0CB22; -.
DR OMA; CELKEWT; -.
DR OrthoDB; 181572at2759; -.
DR PhylomeDB; P0CB22; -.
DR PRO; PR:P0CB22; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; P0CB22; baseline and differential.
DR Genevisible; P0CB22; AT.
DR GO; GO:0000785; C:chromatin; IBA:GO_Central.
DR GO; GO:0048188; C:Set1C/COMPASS complex; IDA:TAIR.
DR GO; GO:0042800; F:histone methyltransferase activity (H3-K4 specific); IMP:TAIR.
DR GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0044648; P:histone H3-K4 dimethylation; IDA:UniProtKB.
DR GO; GO:0051568; P:histone H3-K4 methylation; IMP:TAIR.
DR GO; GO:0040029; P:regulation of gene expression, epigenetic; IMP:UniProtKB.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IMP:TAIR.
DR GO; GO:0010228; P:vegetative to reproductive phase transition of meristem; IMP:UniProtKB.
DR CDD; cd15662; ePHD_ATX1_2_like; 1.
DR CDD; cd15494; PHD_ATX1_2_like; 1.
DR Gene3D; 2.170.270.10; -; 1.
DR Gene3D; 3.30.40.10; -; 2.
DR InterPro; IPR041956; ATX1/2_ePHD.
DR InterPro; IPR042010; ATX1/2_PHD.
DR InterPro; IPR034732; EPHD.
DR InterPro; IPR003889; FYrich_C.
DR InterPro; IPR003888; FYrich_N.
DR InterPro; IPR003616; Post-SET_dom.
DR InterPro; IPR000313; PWWP_dom.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF05965; FYRC; 1.
DR Pfam; PF05964; FYRN; 1.
DR Pfam; PF00855; PWWP; 1.
DR Pfam; PF00856; SET; 1.
DR SMART; SM00542; FYRC; 1.
DR SMART; SM00541; FYRN; 1.
DR SMART; SM00249; PHD; 2.
DR SMART; SM00293; PWWP; 1.
DR SMART; SM00317; SET; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR SUPFAM; SSF82199; SSF82199; 1.
DR PROSITE; PS51805; EPHD; 1.
DR PROSITE; PS51543; FYRC; 1.
DR PROSITE; PS51542; FYRN; 1.
DR PROSITE; PS50868; POST_SET; 1.
DR PROSITE; PS50812; PWWP; 1.
DR PROSITE; PS50280; SET; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; Glycoprotein; Metal-binding; Methyltransferase;
KW Nucleus; Reference proteome; Repeat; S-adenosyl-L-methionine; Transferase;
KW Zinc; Zinc-finger.
FT CHAIN 1..1083
FT /note="Histone-lysine N-methyltransferase ATX2"
FT /id="PRO_0000233355"
FT DOMAIN 315..379
FT /note="PWWP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00162"
FT DOMAIN 457..516
FT /note="FYR N-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00875"
FT DOMAIN 520..604
FT /note="FYR C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00876"
FT DOMAIN 919..1037
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT DOMAIN 1043..1059
FT /note="Post-SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00155"
FT ZN_FING 626..677
FT /note="PHD-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 682..715
FT /note="C2HC pre-PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT ZN_FING 739..807
FT /note="PHD-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT REGION 422..443
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 682..807
FT /note="Extended PHD domain (ePHD)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01146"
FT MOTIF 77..84
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT BINDING 929
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 975
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 998..999
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q03164"
FT BINDING 1001
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 1036
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 1047
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00155"
FT BINDING 1049
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00155"
FT BINDING 1054
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00155"
FT CARBOHYD 968
FT /note="O-linked (GlcNAc) serine"
FT /evidence="ECO:0000250|UniProtKB:Q9C5X4"
SQ SEQUENCE 1083 AA; 123287 MW; 2F773B9406BE6102 CRC64;
MISMSCVPKE EEGEDTQIKT ELHDHAADNP VRYASLESVY SVSSSSSSLC CKTAAGSHKK
VNALKLPMSD SFELQPHRRP EIVHVYCRRK RRRRRRRESF LELAILQNEG VERDDRIVKI
ESAELDDEKE EENKKKKQKK RRIGNGELMK LGVDSTTLSV SATPPLRGCR IKAVCSGNKQ
DGSSRSKRNT VKNQEKVVTA SATAKKWVRL SYDGVDPKHF IGLQCKVFWP LDAVWYPGSI
VGYNVETKHH IVKYGDGDGE ELALRREKIK FLISRDDMEL LNMKFGTNDV VVDGQDYDEL
VILAASFEEC QDFEPRDIIW AKLTGHAMWP AIIVDESVIV KRKGLNNKIS GGRSVLVQFF
GTHDFARIQV KQAVSFLKGL LSRSPLKCKQ PRFEEAMEEA KMYLKEYKLP GRMDQLQKVA
DTDCSERINS GEEDSSNSGD DYTKDGEVWL RPTELGDCLH RIGDLQIINL GRIVTDSEFF
KDSKHTWPEG YTATRKFISL KDPNASAMYK MEVLRDAESK TRPVFRVTTN SGEQFKGDTP
SACWNKIYNR IKKIQIASDN PDVLGEGLHE SGTDMFGFSN PEVDKLIQGL LQSRPPSKVS
QRKYSSGKYQ DHPTGYRPVR VEWKDLDKCN VCHMDEEYEN NLFLQCDKCR MMVHTRCYGQ
LEPHNGILWL CNLCRPVALD IPPRCCLCPV VGGAMKPTTD GRWAHLACAI WIPETCLLDV
KKMEPIDGVK KVSKDRWKLL CSICGVSYGA CIQCSNNTCR VAYHPLCARA AGLCVELADE
DRLFLLSMDD DEADQCIRLL SFCKRHRQTS NYHLETEYMI KPAHNIAEYL PPPNPSGCAR
TEPYNYLGRR GRKEPEALAG ASSKRLFVEN QPYIVGGYSR HEFSTYERIY GSKMSQITTP
SNILSMAEKY TFMKETYRKR LAFGKSGIHG FGIFAKLPHR AGDMVIEYTG ELVRPPIADK
REHLIYNSMV GAGTYMFRID NERVIDATRT GSIAHLINHS CEPNCYSRVI SVNGDEHIII
FAKRDVAKWE ELTYDYRFFS IDERLACYCG FPRCRGVVND TEAEERQANI HASRCELKEW
TES
