ID ATXR2_ARATH Reviewed; 473 AA.
AC Q5PP37; Q9LSY2;
DT 02-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 04-JAN-2005, sequence version 1.
DT 24-JAN-2024, entry version 116.
DE RecName: Full=Histone-lysine N-methyltransferase ATXR2 {ECO:0000303|PubMed:11691919};
DE EC=2.1.1.- {ECO:0000255|PROSITE-ProRule:PRU00190};
DE AltName: Full=Protein SET DOMAIN GROUP 36;
DE AltName: Full=Trithorax-related protein 2 {ECO:0000303|PubMed:11691919};
DE Short=TRX-related protein 2 {ECO:0000303|PubMed:11691919};
GN Name=ATXR2 {ECO:0000303|PubMed:11691919}; Synonyms=SDG36, SET36;
GN OrderedLocusNames=At3g21820 {ECO:0000312|Araport:AT3G21820};
GN ORFNames=MSD21.13 {ECO:0000312|EMBL:BAB02844.1};
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=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(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 Shinn P., Chen H., Cheuk R.F., Kim C.J., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (FEB-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
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 (MAR-2005) 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, DISRUPTION PHENOTYPE, INTERACTION WITH ARF7 AND ARF19, AND
RP SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=29184030; DOI=10.1126/scisignal.aan0316;
RA Lee K., Park O.S., Seo P.J.;
RT "Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to
RT facilitate cellular dedifferentiation.";
RL Sci. Signal. 10:0-0(2017).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=29517958; DOI=10.1080/15592324.2018.1449543;
RA Lee K., Park O.-S., Seo P.J.;
RT "ATXR2 as a core regulator of de novo root organogenesis.";
RL Plant Signal. Behav. 13:e1449543-e1449543(2018).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH JMJ30.
RC STRAIN=cv. Columbia;
RX PubMed=29923261; DOI=10.1111/tpj.14002;
RA Lee K., Park O.-S., Seo P.J.;
RT "JMJ30-mediated demethylation of H3K9me3 drives tissue identity changes to
RT promote callus formation in Arabidopsis.";
RL Plant J. 95:961-975(2018).
CC -!- FUNCTION: Histone methyltransferase that methylates 'Lys-36' (H3K36me)
CC of histone H3 to produce H3K36me3 (PubMed:29184030). Promotes early
CC stages of cellular dedifferentiation through H3K36me3-dependent, and to
CC a lesser degree H3K4me3-dependent, activation of Lateral organ
CC Boundaries-Domain (LBD) (e.g. LBD16 and LBD29) genes (PubMed:29184030).
CC Positive regulator of root organogenesis including lateral root
CC formation as well as adventitious root formation from wounded leaf
CC tissues (PubMed:29517958). Recruited by JMJ30/ARF (e.g. ARF7 and ARF19)
CC complexes to promote the deposition of H3K36me3 and, to a lower extent,
CC H3K4me3 at LBD genes promoters, thus ensuring their stable activation
CC during callus formation on callus-inducing medium (CIM)
CC (PubMed:29923261, PubMed:29184030). {ECO:0000269|PubMed:29184030,
CC ECO:0000269|PubMed:29517958, ECO:0000269|PubMed:29923261}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-lysyl-[histone] + S-adenosyl-L-methionine = H(+) + N(6)-
CC methyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:10024, Rhea:RHEA-COMP:9845, Rhea:RHEA-COMP:9846,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:61929;
CC Evidence={ECO:0000250|UniProtKB:Q8VZJ1};
CC -!- SUBUNIT: Interacts with JMJ30 (PubMed:29923261). Binds to ARF7 and
CC ARF19 in the nucleus (PubMed:29184030). {ECO:0000269|PubMed:29184030,
CC ECO:0000269|PubMed:29923261}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:29184030}.
CC -!- DISRUPTION PHENOTYPE: Reduced callus formation from somatic cells
CC associated with an impaired reduction of H3K9me3 deposition and lower
CC accumulation of H3K36me3 at LBD16 and LBD29 loci during leaf-to-callus
CC transition (PubMed:29923261, PubMed:29184030). Lower lateral root
CC formation and impaired ability to form adventitious root formation from
CC wounded leaf tissues (PubMed:29517958). The double mutant jmj30-2
CC atxr2-1 is strongly impaired in callus formation (PubMed:29923261).
CC {ECO:0000269|PubMed:29184030, ECO:0000269|PubMed:29517958,
CC ECO:0000269|PubMed:29923261}.
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=BAB02844.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB025634; BAB02844.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE76555.1; -; Genomic_DNA.
DR EMBL; BT020260; AAV84481.1; -; mRNA.
DR EMBL; BT021112; AAX12882.1; -; mRNA.
DR EMBL; AK221711; BAD95436.1; -; mRNA.
DR RefSeq; NP_188819.2; NM_113077.5.
DR AlphaFoldDB; Q5PP37; -.
DR STRING; 3702.Q5PP37; -.
DR iPTMnet; Q5PP37; -.
DR PaxDb; 3702-AT3G21820-1; -.
DR ProteomicsDB; 241102; -.
DR EnsemblPlants; AT3G21820.1; AT3G21820.1; AT3G21820.
DR GeneID; 821736; -.
DR Gramene; AT3G21820.1; AT3G21820.1; AT3G21820.
DR KEGG; ath:AT3G21820; -.
DR Araport; AT3G21820; -.
DR TAIR; AT3G21820; ATXR2.
DR eggNOG; KOG2084; Eukaryota.
DR HOGENOM; CLU_034791_0_0_1; -.
DR InParanoid; Q5PP37; -.
DR OMA; TYHSLLC; -.
DR OrthoDB; 56553at2759; -.
DR PhylomeDB; Q5PP37; -.
DR PRO; PR:Q5PP37; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q5PP37; baseline and differential.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0046975; F:histone H3K36 methyltransferase activity; IMP:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:1990110; P:callus formation; IMP:TAIR.
DR GO; GO:0040029; P:epigenetic regulation of gene expression; IMP:UniProtKB.
DR GO; GO:0010452; P:histone H3-K36 methylation; IMP:TAIR.
DR GO; GO:0010311; P:lateral root formation; IMP:UniProtKB.
DR GO; GO:0062211; P:root regeneration; IMP:UniProtKB.
DR CDD; cd20071; SET_SMYD; 1.
DR Gene3D; 6.10.140.2220; -; 1.
DR Gene3D; 2.170.270.10; SET domain; 1.
DR InterPro; IPR044237; ATXR2-like.
DR InterPro; IPR001214; SET_dom.
DR InterPro; IPR046341; SET_dom_sf.
DR InterPro; IPR002893; Znf_MYND.
DR PANTHER; PTHR47436; HISTONE-LYSINE N-METHYLTRANSFERASE ATXR2; 1.
DR PANTHER; PTHR47436:SF1; SET DOMAIN-CONTAINING PROTEIN; 1.
DR Pfam; PF00856; SET; 1.
DR Pfam; PF01753; zf-MYND; 1.
DR SMART; SM00317; SET; 1.
DR SUPFAM; SSF144232; HIT/MYND zinc finger-like; 1.
DR SUPFAM; SSF82199; SET domain; 1.
DR PROSITE; PS50280; SET; 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..473
FT /note="Histone-lysine N-methyltransferase ATXR2"
FT /id="PRO_0000233359"
FT DOMAIN 33..441
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT ZN_FING 134..203
FT /note="MYND-type; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 176
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 180
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 199
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 203
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 440
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
SQ SEQUENCE 473 AA; 52803 MW; 2EFE76512D6F74D7 CRC64;
MDSVYKTDEN FAADVAALLA PLPTPQLQEY FNKLITSRRC NGIEVKNNGT IGKGVYANSE
FDEDELILKD EILVGIQHSS NKVDCLVCSF CFRFIGSIEK QIGRKLYFKN LGVSGCCDDD
SSEEDECVKY NGNEEQCGGS SSSHNTLPEG VVSSLMNGEM ALPHTDKFPL PSPLSCPGGC
QEAFYCSESC AAADWESSHS LLCTGERSES ISREALGEFI KHANDTNDIF LLAAKAIAFT
ILRYRKLKAE HVDKKAKQSE PKQSLLLEAW KPVSIGYKRR WWDCIALPDD VDPTDEGAFR
MQIKNLACTS LELLKIAIFD KECEALFSLE IYGNIIGMFE LNNLDLVVAS PVEDYFLYID
DLPDAEKEET EEITRPFLDA LGDEYSDCCQ GTAFFPLQSC MNHSCCPNAK AFKREEDRDG
QAVIIALRRI SKNEEVTISY IDEELPYKER QALLADYGFS CKCSKCLEDS SSI
//
