ATXR6_ARATH
ID ATXR6_ARATH Reviewed; 349 AA.
AC Q9FNE9;
DT 02-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Histone-lysine N-methyltransferase ATXR6;
DE EC=2.1.1.369 {ECO:0000269|PubMed:19503079, ECO:0000269|PubMed:35298257};
DE AltName: Full=Protein SET DOMAIN GROUP 34;
DE AltName: Full=Trithorax-related protein 6;
DE Short=TRX-related protein 6;
GN Name=ATXR6; Synonyms=SDG34, SET34; OrderedLocusNames=At5g24330;
GN ORFNames=MOP9.18;
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=9405937; DOI=10.1093/dnares/4.4.291;
RA Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence
RT features of the regions of 1,044,062 bp covered by thirteen physically
RT assigned P1 clones.";
RL DNA Res. 4:291-300(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10048488; DOI=10.1093/dnares/5.6.379;
RA Asamizu E., Sato S., Kaneko T., Nakamura Y., Kotani H., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence
RT features of the regions of 1,081,958 bp covered by seventeen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:379-391(1998).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Shinn P., Chen H., Cheuk R.F., Kim C.J., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (APR-2004) to the EMBL/GenBank/DDBJ databases.
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, INTERACTION WITH PCNA1 AND PCNA2, TISSUE SPECIFICITY, AND
RP SUBCELLULAR LOCATION.
RX PubMed=16771839; DOI=10.1111/j.1365-313x.2006.02799.x;
RA Raynaud C., Sozzani R., Glab N., Domenichini S., Perennes C., Cella R.,
RA Kondorosi E., Bergounioux C.;
RT "Two cell-cycle regulated SET-domain proteins interact with proliferating
RT cell nuclear antigen (PCNA) in Arabidopsis.";
RL Plant J. 47:395-407(2006).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
RX PubMed=19503079; DOI=10.1038/nsmb.1611;
RA Jacob Y., Feng S., LeBlanc C.A., Bernatavichute Y.V., Stroud H., Cokus S.,
RA Johnson L.M., Pellegrini M., Jacobsen S.E., Michaels S.D.;
RT "ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin
RT structure and gene silencing.";
RL Nat. Struct. Mol. Biol. 16:763-768(2009).
RN [8]
RP INTERACTION WITH IPS1.
RX PubMed=19812700; DOI=10.1371/journal.pone.0007364;
RA Meng P.H., Raynaud C., Tcherkez G., Blanchet S., Massoud K.,
RA Domenichini S., Henry Y., Soubigou-Taconnat L., Lelarge-Trouverie C.,
RA Saindrenan P., Renou J.P., Bergounioux C.;
RT "Crosstalks between myo-inositol metabolism, programmed cell death and
RT basal immunity in Arabidopsis.";
RL PLoS ONE 4:E7364-E7364(2009).
RN [9]
RP FUNCTION, INTERACTION WITH HTR1, AND MUTAGENESIS OF LEU-49; GLN-92; ILE-95;
RP PHE-98; PHE-99 AND TYR-243.
RX PubMed=20631708; DOI=10.1038/nature09290;
RA Jacob Y., Stroud H., Leblanc C., Feng S., Zhuo L., Caro E., Hassel C.,
RA Gutierrez C., Michaels S.D., Jacobsen S.E.;
RT "Regulation of heterochromatic DNA replication by histone H3 lysine 27
RT methyltransferases.";
RL Nature 466:987-991(2010).
RN [10]
RP FUNCTION.
RX PubMed=22549957; DOI=10.1101/gad.182865.111;
RA Pontvianne F., Blevins T., Chandrasekhara C., Feng W., Stroud H.,
RA Jacobsen S.E., Michaels S.D., Pikaard C.S.;
RT "Histone methyltransferases regulating rRNA gene dose and dosage control in
RT Arabidopsis.";
RL Genes Dev. 26:945-957(2012).
RN [11]
RP INTERACTION WITH IPS1.
RX PubMed=23341037; DOI=10.1093/nar/gks1458;
RA Latrasse D., Jegu T., Meng P.H., Mazubert C., Hudik E., Delarue M.,
RA Charon C., Crespi M., Hirt H., Raynaud C., Bergounioux C., Benhamed M.;
RT "Dual function of MIPS1 as a metabolic enzyme and transcriptional
RT regulator.";
RL Nucleic Acids Res. 41:2907-2917(2013).
RN [12]
RP SUBSTRATE SPECIFICITY, AND MUTAGENESIS OF GLU-186; MET-190; ARG-309 AND
RP TYR-339.
RX PubMed=24626927; DOI=10.1126/science.1248357;
RA Jacob Y., Bergamin E., Donoghue M.T., Mongeon V., LeBlanc C., Voigt P.,
RA Underwood C.J., Brunzelle J.S., Michaels S.D., Reinberg D., Couture J.F.,
RA Martienssen R.A.;
RT "Selective methylation of histone H3 variant H3.1 regulates heterochromatin
RT replication.";
RL Science 343:1249-1253(2014).
RN [13]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=35298257; DOI=10.1126/science.abm5320;
RA Davarinejad H., Huang Y.C., Mermaz B., LeBlanc C., Poulet A., Thomson G.,
RA Joly V., Munoz M., Arvanitis-Vigneault A., Valsakumar D., Villarino G.,
RA Ross A., Rotstein B.H., Alarcon E.I., Brunzelle J.S., Voigt P., Dong J.,
RA Couture J.F., Jacob Y.;
RT "The histone H3.1 variant regulates TONSOKU-mediated DNA repair during
RT replication.";
RL Science 375:1281-1286(2022).
CC -!- FUNCTION: Histone methyltransferase that specifically monomethylates
CC 'Lys-27' of histone H3 (H3K27me1). Has higher activity on nucleosomes
CC containing H3.1 than H3.3. Involved in the formation of constitutive
CC heterochromatin and the silencing of heterochromatic elements. May act
CC as a positive regulator of the G1-S transition. Influences which sets
CC of rRNA gene variants are expressed or silenced. Up-regulated by E2FB.
CC {ECO:0000269|PubMed:16771839, ECO:0000269|PubMed:19503079,
CC ECO:0000269|PubMed:20631708, ECO:0000269|PubMed:22549957,
CC ECO:0000269|PubMed:35298257}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysyl(27)-[histone H3] + S-adenosyl-L-methionine = H(+) +
CC N(6)-methyl-L-lysyl(27)-[histone H3] + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:60296, Rhea:RHEA-COMP:15544, Rhea:RHEA-COMP:15548,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; EC=2.1.1.369;
CC Evidence={ECO:0000269|PubMed:19503079, ECO:0000269|PubMed:35298257};
CC -!- SUBUNIT: Interacts with PCNA1 and PCNA2. Interacts (via PHD domain)
CC with HTR1 (via N-terminus). Interacts with IPS1.
CC {ECO:0000269|PubMed:16771839, ECO:0000269|PubMed:19812700,
CC ECO:0000269|PubMed:20631708, ECO:0000269|PubMed:23341037}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16771839}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves, roots, stems, flowers and
CC siliques. Up-regulated in tissues where cell division is active.
CC {ECO:0000269|PubMed:16771839}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype. Atxr5 and atxr6 double
CC mutant is smaller than wild-type plants, shows partial decondensation
CC of the chromocenter, decreased H3K27 monomethylation and increased DNA
CC re-replication. {ECO:0000269|PubMed:19503079}.
CC -!- MISCELLANEOUS: The binding to histone H3.2 is unaffected by mono-, di,
CC or trimethylation at H3K9, but is strongly reduced by increasing levels
CC of H3K4 methylation. {ECO:0000305|PubMed:20631708}.
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}.
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DR EMBL; AB006701; BAB10399.1; -; Genomic_DNA.
DR EMBL; AB016884; BAB10399.1; JOINED; Genomic_DNA.
DR EMBL; CP002688; AED93294.1; -; Genomic_DNA.
DR EMBL; BT012223; AAS76710.1; -; mRNA.
DR EMBL; BT012421; AAS92337.1; -; mRNA.
DR RefSeq; NP_197821.1; NM_122341.3.
DR AlphaFoldDB; Q9FNE9; -.
DR SMR; Q9FNE9; -.
DR BioGRID; 17778; 4.
DR DIP; DIP-48530N; -.
DR IntAct; Q9FNE9; 2.
DR STRING; 3702.AT5G24330.1; -.
DR PaxDb; Q9FNE9; -.
DR PRIDE; Q9FNE9; -.
DR EnsemblPlants; AT5G24330.1; AT5G24330.1; AT5G24330.
DR GeneID; 832503; -.
DR Gramene; AT5G24330.1; AT5G24330.1; AT5G24330.
DR KEGG; ath:AT5G24330; -.
DR Araport; AT5G24330; -.
DR TAIR; locus:2169779; AT5G24330.
DR eggNOG; KOG1083; Eukaryota.
DR HOGENOM; CLU_051756_0_0_1; -.
DR InParanoid; Q9FNE9; -.
DR OMA; RASNTKF; -.
DR OrthoDB; 1014608at2759; -.
DR PhylomeDB; Q9FNE9; -.
DR BRENDA; 2.1.1.369; 399.
DR PRO; PR:Q9FNE9; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FNE9; baseline and differential.
DR Genevisible; Q9FNE9; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0042393; F:histone binding; IBA:GO_Central.
DR GO; GO:0046976; F:histone methyltransferase activity (H3-K27 specific); IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR GO; GO:0009901; P:anther dehiscence; IMP:TAIR.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0070734; P:histone H3-K27 methylation; IDA:TAIR.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IBA:GO_Central.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0051726; P:regulation of cell cycle; IEP:TAIR.
DR GO; GO:0006275; P:regulation of DNA replication; IGI:TAIR.
DR Gene3D; 2.170.270.10; -; 1.
DR Gene3D; 3.30.40.10; -; 1.
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; PF00628; PHD; 1.
DR SMART; SM00249; PHD; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR SUPFAM; SSF82199; SSF82199; 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; Metal-binding; Methyltransferase; Nucleus;
KW Reference proteome; S-adenosyl-L-methionine; Transferase; Zinc;
KW Zinc-finger.
FT CHAIN 1..349
FT /note="Histone-lysine N-methyltransferase ATXR6"
FT /id="PRO_0000233363"
FT DOMAIN 214..337
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT ZN_FING 32..82
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 1..28
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 105..126
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 92..99
FT /note="PIP motif"
FT BINDING 190
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 224..226
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 287..291
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 309
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 339..340
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 343
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 349
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT MUTAGEN 49
FT /note="L->W: Loss of methylation activity."
FT /evidence="ECO:0000269|PubMed:20631708"
FT MUTAGEN 92
FT /note="Q->A: Loss of methylation activity."
FT /evidence="ECO:0000269|PubMed:20631708"
FT MUTAGEN 95
FT /note="I->A: Loss of methylation activity."
FT /evidence="ECO:0000269|PubMed:20631708"
FT MUTAGEN 98
FT /note="F->A: Loss of methylation activity."
FT /evidence="ECO:0000269|PubMed:20631708"
FT MUTAGEN 99
FT /note="F->A: Loss of methylation activity."
FT /evidence="ECO:0000269|PubMed:20631708"
FT MUTAGEN 186
FT /note="E->D: 24% methylation activity on histone H3.1 and
FT loss of methylation activity on histone H3.3."
FT /evidence="ECO:0000269|PubMed:24626927"
FT MUTAGEN 186
FT /note="E->S,A: Loss of methylation activity."
FT /evidence="ECO:0000269|PubMed:24626927"
FT MUTAGEN 190
FT /note="M->A: 87% methylation activity on histone H3.1 and
FT 2% methylation activity on histone H3.3."
FT /evidence="ECO:0000269|PubMed:24626927"
FT MUTAGEN 243
FT /note="Y->N: Loss of methylation activity."
FT /evidence="ECO:0000269|PubMed:20631708"
FT MUTAGEN 309
FT /note="R->A: 2% methylation activity on histone H3.1 and 2%
FT methylation activity on histone H3.3."
FT /evidence="ECO:0000269|PubMed:24626927"
FT MUTAGEN 309
FT /note="R->Q: Loss of methylation activity."
FT /evidence="ECO:0000269|PubMed:24626927"
FT MUTAGEN 339
FT /note="Y->A: 98% methylation activity on histone H3.1 and
FT 22% methylation activity on histone H3.3."
FT /evidence="ECO:0000269|PubMed:24626927"
SQ SEQUENCE 349 AA; 39640 MW; ED8D4FA7C92283BA CRC64;
MVAVRRRRTQ ASNPRSEPPQ HMSDHDSDSD WDTVCEECSS GKQPAKLLLC DKCDKGFHLF
CLRPILVSVP KGSWFCPSCS KHQIPKSFPL IQTKIIDFFR IKRSPDSSQI SSSSDSIGKK
RKKTSLVMSK KKRRLLPYNP SNDPQRRLEQ MASLATALRA SNTKFSNELT YVSGKAPRSA
NQAAFEKGGM QVLSKEGVET LALCKKMMDL GECPPLMVVF DPYEGFTVEA DRFIKDWTII
TEYVGDVDYL SNREDDYDGD SMMTLLHASD PSQCLVICPD RRSNIARFIS GINNHSPEGR
KKQNLKCVRF NINGEARVLL VANRDISKGE RLYYDYNGYE HEYPTEHFV
