SUVH2_ARATH
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 03-AUG-2022, entry version 152.
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.AT2G33290.1; -.
DR PaxDb; O22781; -.
DR PRIDE; O22781; -.
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; locus:2051083; AT2G33290.
DR eggNOG; KOG1082; Eukaryota.
DR HOGENOM; CLU_004556_4_0_1; -.
DR InParanoid; O22781; -.
DR OMA; SGCECTD; -.
DR OrthoDB; 541949at2759; -.
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 Genevisible; O22781; AT.
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:0003690; F:double-stranded DNA binding; IBA:GO_Central.
DR GO; GO:0042054; F:histone methyltransferase activity; ISS:TAIR.
DR GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IMP:UniProtKB.
DR GO; GO:0034968; P:histone lysine methylation; IEA:InterPro.
DR GO; GO:0016571; P:histone methylation; IDA:TAIR.
DR GO; GO:0040029; P:regulation of gene expression, epigenetic; IMP:TAIR.
DR Gene3D; 2.170.270.10; -; 1.
DR Gene3D; 2.30.280.10; -; 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 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; SSF82199; SSF82199; 1.
DR SUPFAM; SSF88697; SSF88697; 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.
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
