ATXR5_ARATH
ID ATXR5_ARATH Reviewed; 379 AA.
AC Q8VZJ1; F4KFB9; Q1AJM5; Q9FXW6; Q9LXE2;
DT 02-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 14-MAY-2014, sequence version 2.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=Histone-lysine N-methyltransferase ATXR5;
DE EC=2.1.1.369 {ECO:0000269|PubMed:19503079, ECO:0000269|PubMed:35298257};
DE AltName: Full=Protein SET DOMAIN GROUP 15;
DE AltName: Full=Trithorax-related protein 5;
DE Short=TRX-related protein 5;
DE Flags: Precursor;
GN Name=ATXR5; Synonyms=SDG15, SET15; OrderedLocusNames=At5g09790;
GN ORFNames=17I14.20, MTH16.26;
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 [MRNA] (ISOFORM 1), ALTERNATIVE SPLICING, INTERACTION
RP WITH PCNA1 AND PCNA2, TISSUE SPECIFICITY, AND 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 [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10470850; DOI=10.1093/dnares/6.3.183;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Kotani H.,
RA Miyajima N., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. IX. Sequence
RT features of the regions of 1,011,550 bp covered by seventeen P1 and TAC
RT clones.";
RL DNA Res. 6:183-195(1999).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
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 [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, AND INTERACTION WITH HTR1.
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 SUBSTRATE SPECIFICITY.
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 [12]
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 much higher activity on
CC nucleosomes containing H3.1 than H3.3. Involved in the formation of
CC constitutive heterochromatin and the silencing of heterochromatic
CC elements. Influences which sets of rRNA gene variants are expressed or
CC silenced. {ECO:0000269|PubMed:19503079, ECO:0000269|PubMed:20631708,
CC ECO:0000269|PubMed:22549957, 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: Isoform 1 but not isoform 2 interacts with PCNA1 and PCNA2.
CC Interacts (via PHD domain) with HTR1 (via N-terminus). Isoform 2
CC interacts with IPS1. {ECO:0000269|PubMed:16771839,
CC ECO:0000269|PubMed:19812700, ECO:0000269|PubMed:20631708}.
CC -!- INTERACTION:
CC Q8VZJ1-1; Q9FEN9: SHL; NbExp=3; IntAct=EBI-15200822, EBI-4458733;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16771839}. Plastid,
CC chloroplast {ECO:0000269|PubMed:16771839}. Note=Never found in plastids
CC and the nucleus within the same cell.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8VZJ1-2; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8VZJ1-1; Sequence=VSP_054858;
CC -!- TISSUE SPECIFICITY: Expressed in leaves, roots, stems, flowers,
CC siliques and developing pollen. Up-regulated in tissues where cell
CC division is active. {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 -!- MISCELLANEOUS: [Isoform 1]: Major isoform.
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=BAB09537.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; DQ074689; AAZ31374.1; -; mRNA.
DR EMBL; AB020752; BAB09537.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL353994; CAB89351.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91447.1; -; Genomic_DNA.
DR EMBL; AY064131; AAL36039.1; -; mRNA.
DR EMBL; AY120701; AAM52244.1; -; mRNA.
DR PIR; T49919; T49919.
DR RefSeq; NP_001078559.1; NM_001085090.2. [Q8VZJ1-2]
DR RefSeq; NP_001318519.1; NM_001343068.1.
DR AlphaFoldDB; Q8VZJ1; -.
DR SMR; Q8VZJ1; -.
DR BioGRID; 16117; 11.
DR DIP; DIP-48529N; -.
DR IntAct; Q8VZJ1; 11.
DR STRING; 3702.AT5G09790.2; -.
DR PaxDb; Q8VZJ1; -.
DR PRIDE; Q8VZJ1; -.
DR ProteomicsDB; 241105; -. [Q8VZJ1-2]
DR EnsemblPlants; AT5G09790.2; AT5G09790.2; AT5G09790. [Q8VZJ1-2]
DR GeneID; 830839; -.
DR Gramene; AT5G09790.2; AT5G09790.2; AT5G09790. [Q8VZJ1-2]
DR KEGG; ath:AT5G09790; -.
DR Araport; AT5G09790; -.
DR TAIR; locus:2144841; AT5G09790.
DR eggNOG; KOG1083; Eukaryota.
DR HOGENOM; CLU_051756_0_0_1; -.
DR InParanoid; Q8VZJ1; -.
DR BRENDA; 2.1.1.369; 399.
DR PRO; PR:Q8VZJ1; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8VZJ1; baseline and differential.
DR Genevisible; Q8VZJ1; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
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:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0009294; P:DNA-mediated transformation; IMP:TAIR.
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:0009555; P:pollen development; IMP:TAIR.
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 Pfam; PF00856; SET; 1.
DR SMART; SM00249; PHD; 1.
DR SMART; SM00317; SET; 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 Alternative splicing; Chloroplast; Chromatin regulator; Metal-binding;
KW Methyltransferase; Nucleus; Plastid; Reference proteome;
KW S-adenosyl-L-methionine; Transferase; Transit peptide; Zinc; Zinc-finger.
FT TRANSIT 1..44
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 45..379
FT /note="Histone-lysine N-methyltransferase ATXR5"
FT /id="PRO_0000429173"
FT DOMAIN 245..367
FT /note="SET"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT ZN_FING 64..114
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 1..42
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 122..129
FT /note="PIP motif"
FT COMPBIAS 1..15
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 221
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 255..257
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 317..321
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 339
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 366
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT BINDING 369..370
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 373
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT VAR_SEQ 120..146
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_054858"
FT CONFLICT 347
FT /note="R -> P (in Ref. 1; AAZ31374)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 379 AA; 43034 MW; F5A792C7E491BB48 CRC64;
MATWNASSPA ASPCSSRRRT KAPARRPSSE SPPPRKMKSM AEIMAKSVPV VEQEEEEDED
SYSNVTCEKC GSGEGDDELL LCDKCDRGFH MKCLRPIVVR VPIGTWLCVD CSDQRPVRRL
SQKKILHFFR IEKHTHQTDK LELSQEETRK RRRSCSLTVK KRRRKLLPLV PSEDPDQRLA
QMGTLASALT ALGIKYSDGL NYVPGMAPRS ANQSKLEKGG MQVLCKEDLE TLEQCQSMYR
RGECPPLVVV FDPLEGYTVE ADGPIKDLTF IAEYTGDVDY LKNREKDDCD SIMTLLLSED
PSKTLVICPD KFGNISRFIN GINNHNPVAK KKQNCKCVRY SINGECRVLL VATRDISKGE
RLYYDYNGYE HEYPTHHFL
