ID   SUVH2_ARATH             Reviewed;         651 AA.
AC   O22781;
DT   09-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-JAN-1998, sequence version 1.
DT   27-MAR-2024, entry version 161.
DE   RecName: Full=Histone-lysine N-methyltransferase family member SUVH2;
DE   AltName: Full=Cytosine-HMTase 2;
DE   AltName: Full=H3-K27-HMTase 2;
DE   AltName: Full=H4-K20-HMTase 2;
DE   AltName: Full=Histone H3-K9 methyltransferase 2;
DE            Short=H3-K9-HMTase 2;
DE   AltName: Full=Protein SET DOMAIN GROUP 3;
DE   AltName: Full=Suppressor of variegation 3-9 homolog protein 2;
DE            Short=Su(var)3-9 homolog protein 2;
GN   Name=SUVH2; Synonyms=SDG3, SET3; OrderedLocusNames=At2g33290;
GN   ORFNames=F4P9.6;
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], SUBCELLULAR LOCATION, NOMENCLATURE, AND TISSUE
RP   SPECIFICITY.
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   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=10617197; DOI=10.1038/45471;
RA   Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA   Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA   Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA   Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA   Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA   Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA   Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT   "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL   Nature 402:761-768(1999).
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   FUNCTION, SUBCELLULAR LOCATION, AND MUTAGENESIS OF GLU-143; ARG-351;
RP   VAL-385; ARG-411; VAL-584; MET-620; LEU-630 AND GLY-645.
RX   PubMed=15775980; DOI=10.1038/sj.emboj.7600604;
RA   Naumann K., Fischer A., Hofmann I., Krauss V., Phalke S., Irmler K.,
RA   Hause G., Aurich A.-C., Dorn R., Jenuwein T., Reuter G.;
RT   "Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene
RT   silencing in Arabidopsis.";
RL   EMBO J. 24:1418-1429(2005).
RN   [5]
RP   FUNCTION, AND GENE FAMILY.
RX   PubMed=16384625; DOI=10.1016/j.jplph.2005.10.015;
RA   Fischer A., Hofmann I., Naumann K., Reuter G.;
RT   "Heterochromatin proteins and the control of heterochromatic gene silencing
RT   in Arabidopsis.";
RL   J. Plant Physiol. 163:358-368(2006).
RN   [6]
RP   FUNCTION, DNA-BINDING, LACK OF METHYLTRANSFERASE ACTIVITY, AND LACK OF
RP   S-ADENOSYL-L-METHIONINE BINDING.
RX   PubMed=19043555; DOI=10.1371/journal.pgen.1000280;
RA   Johnson L.M., Law J.A., Khattar A., Henderson I.R., Jacobsen S.E.;
RT   "SRA-domain proteins required for DRM2-mediated de novo DNA methylation.";
RL   PLoS Genet. 4:E1000280-E1000280(2008).
RN   [7]
RP   FUNCTION, AND INTERACTION WITH NRPE1 AND DRD1.
RX   PubMed=24463519; DOI=10.1038/nature12931;
RA   Johnson L.M., Du J., Hale C.J., Bischof S., Feng S., Chodavarapu R.K.,
RA   Zhong X., Marson G., Pellegrini M., Segal D.J., Patel D.J., Jacobsen S.E.;
RT   "SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to
RT   DNA methylation.";
RL   Nature 507:124-128(2014).
RN   [8]
RP   INTERACTION WITH MORC1/CRT1; DRD1 AND DMS3, AND SELF-INTERACTION.
RC   STRAIN=cv. Columbia;
RX   PubMed=24465213; DOI=10.1371/journal.pgen.1003948;
RA   Liu Z.-W., Shao C.-R., Zhang C.-J., Zhou J.-X., Zhang S.-W., Li L.,
RA   Chen S., Huang H.-W., Cai T., He X.-J.;
RT   "The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy
RT   at RNA-directed DNA methylation loci.";
RL   PLoS Genet. 10:E1003948-E1003948(2014).
RN   [9]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=27171427; DOI=10.1371/journal.pgen.1006026;
RA   Liu Z.-W., Zhou J.-X., Huang H.-W., Li Y.-Q., Shao C.-R., Li L., Cai T.,
RA   Chen S., He X.-J.;
RT   "Two components of the RNA-Directed DNA methylation pathway associate with
RT   MORC6 and silence loci targeted by MORC6 in Arabidopsis.";
RL   PLoS Genet. 12:E1006026-E1006026(2016).
CC   -!- FUNCTION: Histone methyltransferase family member that plays a central
CC       role in gene silencing (PubMed:15775980, PubMed:16384625,
CC       PubMed:19043555, PubMed:24463519, PubMed:27171427). Together with MORC6
CC       and SUVH9, regulates the silencing of some transposable elements (TEs)
CC       (PubMed:27171427). According to PubMed:15775980, it is required for
CC       normal methylation of 'Lys-9' and 'Lys-27' of histone H3, 'Lys-20' of
CC       H4, and cytosine, but PubMed:19043555 see no significant effect on
CC       histone methylation when the gene is mutated. According to
CC       PubMed:19043555, the protein does not bind S-adenosyl-L-methionine and
CC       lacks methyltransferase activity. Instead, it may function downstream
CC       of DRM2 in RNA-directed DNA methylation, binding to methylated DNA and
CC       recruiting DNA-directed RNA polymerase V to chromatin (PubMed:24463519,
CC       PubMed:27171427). {ECO:0000269|PubMed:15775980,
CC       ECO:0000269|PubMed:16384625, ECO:0000269|PubMed:19043555,
CC       ECO:0000269|PubMed:24463519, ECO:0000269|PubMed:27171427}.
CC   -!- SUBUNIT: Self-interacts (PubMed:24465213). Interacts with DNA-directed
CC       RNA polymerase V subunit NRPE1 and with DRD1 and DMS3 (PubMed:24463519,
CC       PubMed:24465213). Binds to MORC1/CRT1 (PubMed:24465213).
CC       {ECO:0000269|PubMed:24463519, ECO:0000269|PubMed:24465213}.
CC   -!- SUBCELLULAR LOCATION: Nucleus. Chromosome, centromere. Note=Associates
CC       with centromeric constitutive heterochromatin.
CC   -!- TISSUE SPECIFICITY: Expressed at low levels in leaves stems and
CC       flowers. {ECO:0000269|PubMed:11691919}.
CC   -!- DOMAIN: Although both SET and pre-SET domains are present, the absence
CC       of the post-SET domain may explain the lack of methyltransferase
CC       activity. Besides, the Cys residues in the SET domain that normally
CC       bind a zinc ion are not conserved.
CC   -!- DOMAIN: In the pre-SET domain, Cys residues bind 3 zinc ions that are
CC       arranged in a triangular cluster; some of these Cys residues contribute
CC       to the binding of two zinc ions within the cluster. {ECO:0000250}.
CC   -!- DISRUPTION PHENOTYPE: Impaired gene silencing due to decondensation of
CC       chromocenters leading to the derepression of DNA-methylated genes and
CC       transposable elements (TEs). {ECO:0000269|PubMed:27171427}.
CC   -!- SIMILARITY: Belongs to the class V-like SAM-binding methyltransferase
CC       superfamily. Histone-lysine methyltransferase family. Suvar3-9
CC       subfamily. {ECO:0000255|PROSITE-ProRule:PRU00908}.
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DR   EMBL; AF344445; AAK28967.1; -; mRNA.
DR   EMBL; AC002332; AAB80647.1; -; Genomic_DNA.
DR   EMBL; CP002685; AEC08810.1; -; Genomic_DNA.
DR   EMBL; CP002685; ANM61886.1; -; Genomic_DNA.
DR   EMBL; CP002685; ANM61887.1; -; Genomic_DNA.
DR   EMBL; CP002685; ANM61888.1; -; Genomic_DNA.
DR   PIR; F84743; F84743.
DR   RefSeq; NP_001318341.1; NM_001336444.1.
DR   RefSeq; NP_001324077.1; NM_001336445.1.
DR   RefSeq; NP_001324078.1; NM_001336446.1.
DR   RefSeq; NP_180887.1; NM_128889.3.
DR   AlphaFoldDB; O22781; -.
DR   SMR; O22781; -.
DR   BioGRID; 3239; 36.
DR   DIP; DIP-62059N; -.
DR   IntAct; O22781; 37.
DR   STRING; 3702.O22781; -.
DR   PaxDb; 3702-AT2G33290-1; -.
DR   ProteomicsDB; 226519; -.
DR   EnsemblPlants; AT2G33290.1; AT2G33290.1; AT2G33290.
DR   EnsemblPlants; AT2G33290.2; AT2G33290.2; AT2G33290.
DR   EnsemblPlants; AT2G33290.3; AT2G33290.3; AT2G33290.
DR   EnsemblPlants; AT2G33290.4; AT2G33290.4; AT2G33290.
DR   GeneID; 817892; -.
DR   Gramene; AT2G33290.1; AT2G33290.1; AT2G33290.
DR   Gramene; AT2G33290.2; AT2G33290.2; AT2G33290.
DR   Gramene; AT2G33290.3; AT2G33290.3; AT2G33290.
DR   Gramene; AT2G33290.4; AT2G33290.4; AT2G33290.
DR   KEGG; ath:AT2G33290; -.
DR   Araport; AT2G33290; -.
DR   TAIR; AT2G33290; SUVH2.
DR   eggNOG; KOG1082; Eukaryota.
DR   HOGENOM; CLU_004556_4_0_1; -.
DR   InParanoid; O22781; -.
DR   OMA; HYEYIAK; -.
DR   OrthoDB; 5481936at2759; -.
DR   PhylomeDB; O22781; -.
DR   BRENDA; 2.1.1.368; 399.
DR   PRO; PR:O22781; -.
DR   Proteomes; UP000006548; Chromosome 2.
DR   ExpressionAtlas; O22781; baseline and differential.
DR   GO; GO:0000775; C:chromosome, centromeric region; IEA:UniProtKB-SubCell.
DR   GO; GO:0000792; C:heterochromatin; IDA:TAIR.
DR   GO; GO:0005634; C:nucleus; IDA:TAIR.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0042054; F:histone methyltransferase activity; ISS:TAIR.
DR   GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR   GO; GO:0040029; P:epigenetic regulation of gene expression; IMP:TAIR.
DR   GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IMP:UniProtKB.
DR   GO; GO:0016571; P:histone methylation; IDA:TAIR.
DR   Gene3D; 2.170.270.10; SET domain; 1.
DR   Gene3D; 2.30.280.10; SRA-YDG; 1.
DR   InterPro; IPR025794; H3-K9-MeTrfase_plant.
DR   InterPro; IPR007728; Pre-SET_dom.
DR   InterPro; IPR015947; PUA-like_sf.
DR   InterPro; IPR001214; SET_dom.
DR   InterPro; IPR046341; SET_dom_sf.
DR   InterPro; IPR036987; SRA-YDG_sf.
DR   InterPro; IPR003105; SRA_YDG.
DR   PANTHER; PTHR45660:SF81; HISTONE-LYSINE N-METHYLTRANSFERASE FAMILY MEMBER SUVH2; 1.
DR   PANTHER; PTHR45660; HISTONE-LYSINE N-METHYLTRANSFERASE SETMAR; 1.
DR   Pfam; PF05033; Pre-SET; 1.
DR   Pfam; PF02182; SAD_SRA; 1.
DR   Pfam; PF00856; SET; 1.
DR   SMART; SM00468; PreSET; 1.
DR   SMART; SM00317; SET; 1.
DR   SMART; SM00466; SRA; 1.
DR   SUPFAM; SSF88697; PUA domain-like; 1.
DR   SUPFAM; SSF82199; SET domain; 1.
DR   PROSITE; PS50867; PRE_SET; 1.
DR   PROSITE; PS51575; SAM_MT43_SUVAR39_2; 1.
DR   PROSITE; PS50280; SET; 1.
DR   PROSITE; PS51015; YDG; 1.
DR   Genevisible; O22781; AT.
PE   1: Evidence at protein level;
KW   Centromere; Chromatin regulator; Chromosome; DNA-binding; Metal-binding;
KW   Nucleus; Reference proteome; Zinc.
FT   CHAIN           1..651
FT                   /note="Histone-lysine N-methyltransferase family member
FT                   SUVH2"
FT                   /id="PRO_0000186073"
FT   DOMAIN          202..358
FT                   /note="YDG"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00358"
FT   DOMAIN          434..492
FT                   /note="Pre-SET"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00157"
FT   DOMAIN          495..638
FT                   /note="SET"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT   REGION          1..28
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..27
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         436
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         436
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         438
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         442
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         442
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250"
FT   BINDING         446
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         448
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         474
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         474
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250"
FT   BINDING         478
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         480
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250"
FT   BINDING         484
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250"
FT   MUTAGEN         143
FT                   /note="E->D: In 5-1; ectopic nuclear localization."
FT                   /evidence="ECO:0000269|PubMed:15775980"
FT   MUTAGEN         351
FT                   /note="R->K: In 5-2; loss of 5-methylcytosine, H3K9
FT                   dimethylation and H4K20 monomethylation."
FT                   /evidence="ECO:0000269|PubMed:15775980"
FT   MUTAGEN         385
FT                   /note="V->A: In 5-3; loss of 5-methylcytosine, H3K9
FT                   dimethylation and H4K20 monomethylation."
FT                   /evidence="ECO:0000269|PubMed:15775980"
FT   MUTAGEN         411
FT                   /note="R->I: In 5-4; loss of H3K9 and H4K20 methylation."
FT                   /evidence="ECO:0000269|PubMed:15775980"
FT   MUTAGEN         584
FT                   /note="V->G: In 5-5; loss of H3K9 and H4K20 methylation."
FT                   /evidence="ECO:0000269|PubMed:15775980"
FT   MUTAGEN         620
FT                   /note="M->T: In 5-6; loss of H3K9 and H4K20 methylation;
FT                   when associated with T-630."
FT                   /evidence="ECO:0000269|PubMed:15775980"
FT   MUTAGEN         630
FT                   /note="L->V: In 5-6; loss of H3K9 and H4K20 methylation;
FT                   when associated with V-620."
FT                   /evidence="ECO:0000269|PubMed:15775980"
FT   MUTAGEN         645
FT                   /note="G->S: In 5-7; loss of H3K9 and H4K20 methylation."
FT                   /evidence="ECO:0000269|PubMed:15775980"
SQ   SEQUENCE   651 AA;  72848 MW;  412AD76C8869ACF9 CRC64;
     MSTLLPFPDL NLMPDSQSST AGTTAGDTVV TGKLEVKSEP IEEWQTPPSS TSDQSANTDL
     IAEFIRISEL FRSAFKPLQV KGLDGVSVYG LDSGAIVAVP EKENRELIEP PPGFKDNRVS
     TVVVSPKFER PRELARIAIL GHEQRKELRQ VMKRTRMTYE SLRIHLMAES MKNHVLGQGR
     RRRSDMAAAY IMRDRGLWLN YDKHIVGPVT GVEVGDIFFY RMELCVLGLH GQTQAGIDCL
     TAERSATGEP IATSIVVSGG YEDDEDTGDV LVYTGHGGQD HQHKQCDNQR LVGGNLGMER
     SMHYGIEVRV IRGIKYENSI SSKVYVYDGL YKIVDWWFAV GKSGFGVFKF RLVRIEGQPM
     MGSAVMRFAQ TLRNKPSMVR PTGYVSFDLS NKKENVPVFL YNDVDGDQEP RHYEYIAKAV
     FPPGIFGQGG ISRTGCECKL SCTDDCLCAR KNGGEFAYDD NGHLLKGKHV VFECGEFCTC
     GPSCKSRVTQ KGLRNRLEVF RSKETGWGVR TLDLIEAGAF ICEYAGVVVT RLQAEILSMN
     GDVMVYPGRF TDQWRNWGDL SQVYPDFVRP NYPSLPPLDF SMDVSRMRNV ACYISHSKEP
     NVMVQFVLHD HNHLMFPRVM LFALENISPL AELSLDYGLA DEVNGKLAIC N
//