ID   SUVH3_ARATH             Reviewed;         669 AA.
AC   Q9C5P4; Q9SSL7;
DT   09-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT   09-MAY-2003, sequence version 2.
DT   27-MAR-2024, entry version 159.
DE   RecName: Full=Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH3;
DE            EC=2.1.1.367 {ECO:0000250|UniProtKB:Q5QD03};
DE   AltName: Full=Histone H3-K9 methyltransferase 3;
DE            Short=H3-K9-HMTase 3;
DE   AltName: Full=Protein SET DOMAIN GROUP 19;
DE   AltName: Full=Suppressor of variegation 3-9 homolog protein 3;
DE            Short=Su(var)3-9 homolog protein 3;
GN   Name=SUVH3; Synonyms=SDG19, SET19; OrderedLocusNames=At1g73100;
GN   ORFNames=F3N23.30;
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=11130712; DOI=10.1038/35048500;
RA   Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA   Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA   Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA   Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA   Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA   Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA   Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA   Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA   Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA   Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA   Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA   Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA   Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA   Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA   Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT   "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL   Nature 408:816-820(2000).
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;
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   [5]
RP   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).
CC   -!- FUNCTION: Histone methyltransferase. Methylates 'Lys-9' of histone H3.
CC       H3 'Lys-9' methylation represents a specific tag for epigenetic
CC       transcriptional repression. {ECO:0000250|UniProtKB:Q5QD03}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=L-lysyl(9)-[histone H3] + S-adenosyl-L-methionine = H(+) +
CC         N(6)-methyl-L-lysyl(9)-[histone H3] + S-adenosyl-L-homocysteine;
CC         Xref=Rhea:RHEA:60280, Rhea:RHEA-COMP:15542, Rhea:RHEA-COMP:15546,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC         ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; EC=2.1.1.367;
CC         Evidence={ECO:0000250|UniProtKB:Q5QD03};
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00358,
CC       ECO:0000269|PubMed:11691919}. Chromosome, centromere
CC       {ECO:0000269|PubMed:11691919}. Note=Associates with centromeric
CC       constitutive heterochromatin.
CC   -!- TISSUE SPECIFICITY: Expressed in leaves stems and flowers.
CC       {ECO:0000269|PubMed:11691919}.
CC   -!- DOMAIN: Although the SET domain contains the active site of enzymatic
CC       activity, both pre-SET and post-SET domains are required for
CC       methyltransferase activity.
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   -!- 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; AF344446; AAK28968.1; -; mRNA.
DR   EMBL; AC008017; AAD55657.1; -; Genomic_DNA.
DR   EMBL; CP002684; AEE35414.1; -; Genomic_DNA.
DR   EMBL; AY099620; AAM20471.1; -; mRNA.
DR   EMBL; BT002137; AAN72148.1; -; mRNA.
DR   PIR; F96756; F96756.
DR   RefSeq; NP_565056.1; NM_105968.3.
DR   AlphaFoldDB; Q9C5P4; -.
DR   SMR; Q9C5P4; -.
DR   BioGRID; 28860; 10.
DR   IntAct; Q9C5P4; 6.
DR   STRING; 3702.Q9C5P4; -.
DR   PaxDb; 3702-AT1G73100-1; -.
DR   ProteomicsDB; 226571; -.
DR   EnsemblPlants; AT1G73100.1; AT1G73100.1; AT1G73100.
DR   GeneID; 843641; -.
DR   Gramene; AT1G73100.1; AT1G73100.1; AT1G73100.
DR   KEGG; ath:AT1G73100; -.
DR   Araport; AT1G73100; -.
DR   TAIR; AT1G73100; SUVH3.
DR   eggNOG; KOG1082; Eukaryota.
DR   HOGENOM; CLU_004556_2_1_1; -.
DR   InParanoid; Q9C5P4; -.
DR   OMA; SISESWV; -.
DR   OrthoDB; 5481936at2759; -.
DR   PhylomeDB; Q9C5P4; -.
DR   BRENDA; 2.1.1.367; 399.
DR   PRO; PR:Q9C5P4; -.
DR   Proteomes; UP000006548; Chromosome 1.
DR   ExpressionAtlas; Q9C5P4; baseline and differential.
DR   GO; GO:0005694; C:chromosome; IDA:TAIR.
DR   GO; GO:0000775; C:chromosome, centromeric region; IEA:UniProtKB-SubCell.
DR   GO; GO:0005634; C:nucleus; IDA:TAIR.
DR   GO; GO:0010385; F:double-stranded methylated DNA binding; IDA:TAIR.
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; TAS:TAIR.
DR   GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
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; IPR003616; Post-SET_dom.
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; HISTONE-LYSINE N-METHYLTRANSFERASE SETMAR; 1.
DR   PANTHER; PTHR45660:SF24; HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC SUVH3-RELATED; 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; PS50868; POST_SET; 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; Q9C5P4; AT.
PE   2: Evidence at transcript level;
KW   Centromere; Chromatin regulator; Chromosome; DNA-binding; Metal-binding;
KW   Methyltransferase; Nucleus; Reference proteome; S-adenosyl-L-methionine;
KW   Transferase; Zinc.
FT   CHAIN           1..669
FT                   /note="Histone-lysine N-methyltransferase, H3 lysine-9
FT                   specific SUVH3"
FT                   /id="PRO_0000186074"
FT   DOMAIN          208..355
FT                   /note="YDG"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00358"
FT   DOMAIN          430..491
FT                   /note="Pre-SET"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00157"
FT   DOMAIN          494..638
FT                   /note="SET"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT   DOMAIN          653..669
FT                   /note="Post-SET"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00155"
FT   DNA_BIND        108..120
FT                   /note="A.T hook"
FT   REGION          56..127
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          270..290
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        56..112
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         432
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         432
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         434
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
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         438
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250"
FT   BINDING         445
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         447
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         473
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         473
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250"
FT   BINDING         477
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         479
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250"
FT   BINDING         483
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250"
FT   BINDING         504..506
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         540
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT   BINDING         542
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT   BINDING         592
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00190"
FT   BINDING         595..596
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         598
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="4"
FT                   /evidence="ECO:0000250"
FT   BINDING         657
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="4"
FT                   /evidence="ECO:0000250"
FT   BINDING         659
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="4"
FT                   /evidence="ECO:0000250"
FT   BINDING         664
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="4"
FT                   /evidence="ECO:0000250"
FT   CONFLICT        416
FT                   /note="S -> P (in Ref. 1; AAK28968)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   669 AA;  73439 MW;  8878E000747FD1AB CRC64;
     MQGVPGFNTV PNPNHYDKSI VLDIKPLRSL KPVFPNGNQG PPFVGCPPFG PSSSEYSSFF
     PFGAQQPTHD TPDLNQTQNT PIPSFVPPLR SYRTPTKTNG PSSSSGTKRG VGRPKGTTSV
     KKKEKKTVAN EPNLDVQVVK KFSSDFDSGI SAAEREDGNA YLVSSVLMRF DAVRRRLSQV
     EFTKSATSKA AGTLMSNGVR TNMKKRVGTV PGIEVGDIFF SRIEMCLVGL HMQTMAGIDY
     IISKAGSDEE SLATSIVSSG RYEGEAQDPE SLIYSGQGGN ADKNRQASDQ KLERGNLALE
     NSLRKGNGVR VVRGEEDAAS KTGKIYIYDG LYSISESWVE KGKSGCNTFK YKLVRQPGQP
     PAFGFWKSVQ KWKEGLTTRP GLILPDLTSG AESKPVSLVN DVDEDKGPAY FTYTSSLKYS
     ETFKLTQPVI GCSCSGSCSP GNHNCSCIRK NDGDLPYLNG VILVSRRPVI YECGPTCPCH
     ASCKNRVIQT GLKSRLEVFK TRNRGWGLRS WDSLRAGSFI CEYAGEVKDN GNLRGNQEED
     AYVFDTSRVF NSFKWNYEPE LVDEDPSTEV PEEFNLPSPL LISAKKFGNV ARFMNHSCSP
     NVFWQPVIRE GNGESVIHIA FFAMRHIPPM AELTYDYGIS PTSEARDESL LHGQRTCLCG
     SEQCRGSFG
//