ID SUVH9_ARATH Reviewed; 650 AA. AC Q9T0G7; DT 09-MAY-2003, integrated into UniProtKB/Swiss-Prot. DT 01-MAY-2000, sequence version 1. DT 24-JAN-2024, entry version 153. DE RecName: Full=Histone-lysine N-methyltransferase family member SUVH9; DE AltName: Full=Histone H3-K9 methyltransferase 9; DE Short=H3-K9-HMTase 9; DE AltName: Full=Protein SET DOMAIN GROUP 22; DE AltName: Full=Suppressor of variegation 3-9 homolog protein 9; DE Short=Su(var)3-9 homolog protein 9; GN Name=SUVH9; Synonyms=SDG22, SET22; OrderedLocusNames=At4g13460; GN ORFNames=T6G15.10; 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], AND 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 [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=cv. Columbia; RX PubMed=10617198; DOI=10.1038/47134; RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M., RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., RA Martienssen R., McCombie W.R.; RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."; RL Nature 402:769-777(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 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 [5] 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 [6] RP SUBUNIT, AND INTERACTION WITH MORC6; MORC2 AND MORC1/CRT1. 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 [7] RP FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH SWI3B; SWI3C AND RP SWI3D. 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). RN [8] RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 134-650 IN COMPLEX WITH ZINC RP IONS, SUBCELLULAR LOCATION, AND FUNCTION. 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). CC -!- FUNCTION: Histone methyltransferase family member that plays a role in CC gene silencing (PubMed:19043555, PubMed:24463519, PubMed:27171427). CC Together with MORC6 and SUVH2, regulates the silencing of some CC transposable elements (TEs) (PubMed:27171427). 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:19043555, CC ECO:0000269|PubMed:24463519, ECO:0000269|PubMed:27171427}. CC -!- SUBUNIT: Component of an RNA-directed DNA methylation (RdDM) complex CC that contains at least MORC6, MORC1/CRT1, MORC2, SWI3D and SUVH9. CC Interacts directly with MORC6, MORC2 and MORC1/CRT1. Interacts with CC SWI3B, SWI3C and SWI3D (PubMed:27171427). {ECO:0000269|PubMed:24465213, CC ECO:0000269|PubMed:27171427}. CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:24463519}. CC Chromosome, centromere {ECO:0000250}. Note=Associates with centromeric CC constitutive heterochromatin. {ECO:0000305}. 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. 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AF344452; AAK28974.1; -; mRNA. DR EMBL; AL049656; CAB41104.1; -; Genomic_DNA. DR EMBL; AL161536; CAB78388.1; -; Genomic_DNA. DR EMBL; CP002687; AEE83282.1; -; Genomic_DNA. DR EMBL; CP002687; AEE83283.1; -; Genomic_DNA. DR PIR; T06648; T06648. DR RefSeq; NP_001031625.1; NM_001036548.2. DR RefSeq; NP_193082.1; NM_117420.3. DR PDB; 4NJ5; X-ray; 2.40 A; A=134-650. DR PDBsum; 4NJ5; -. DR AlphaFoldDB; Q9T0G7; -. DR SMR; Q9T0G7; -. DR BioGRID; 12275; 1. DR STRING; 3702.Q9T0G7; -. DR PaxDb; 3702-AT4G13460-2; -. DR ProteomicsDB; 226525; -. DR EnsemblPlants; AT4G13460.1; AT4G13460.1; AT4G13460. DR EnsemblPlants; AT4G13460.2; AT4G13460.2; AT4G13460. DR GeneID; 826978; -. DR Gramene; AT4G13460.1; AT4G13460.1; AT4G13460. DR Gramene; AT4G13460.2; AT4G13460.2; AT4G13460. DR KEGG; ath:AT4G13460; -. DR Araport; AT4G13460; -. DR TAIR; AT4G13460; SUVH9. DR eggNOG; KOG1082; Eukaryota. DR HOGENOM; CLU_004556_4_0_1; -. DR InParanoid; Q9T0G7; -. DR OMA; IGCYCAQ; -. DR OrthoDB; 5481936at2759; -. DR PhylomeDB; Q9T0G7; -. DR PRO; PR:Q9T0G7; -. DR Proteomes; UP000006548; Chromosome 4. DR ExpressionAtlas; Q9T0G7; baseline and differential. DR GO; GO:0000775; C:chromosome, centromeric region; IEA:UniProtKB-SubCell. DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell. DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW. DR GO; GO:0042054; F:histone methyltransferase activity; IEA:InterPro. DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro. DR GO; GO:0009294; P:DNA-mediated transformation; IMP:TAIR. DR GO; GO:0080188; P:gene silencing by RNA-directed DNA methylation; IMP:UniProtKB. DR CDD; cd10545; SET_AtSUVH-like; 1. 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:SF3; HISTONE-LYSINE N-METHYLTRANSFERASE FAMILY MEMBER SUVH9; 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; Q9T0G7; AT. PE 1: Evidence at protein level; KW 3D-structure; Centromere; Chromatin regulator; Chromosome; DNA-binding; KW Metal-binding; Nucleus; Reference proteome; Zinc. FT CHAIN 1..650 FT /note="Histone-lysine N-methyltransferase family member FT SUVH9" FT /id="PRO_0000186080" FT DOMAIN 205..352 FT /note="YDG" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00358" FT DOMAIN 432..490 FT /note="Pre-SET" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00157" FT DOMAIN 493..637 FT /note="SET" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00190" FT REGION 1..24 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 95..129 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 103..125 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT BINDING 434 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="1" FT BINDING 434 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="2" FT BINDING 436 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="1" FT BINDING 440 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="1" FT BINDING 440 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="3" FT BINDING 444 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="1" FT BINDING 446 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="2" FT BINDING 472 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="2" FT BINDING 472 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="3" FT BINDING 476 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="2" FT BINDING 478 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="3" FT BINDING 482 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /ligand_label="3" FT HELIX 140..167 FT /evidence="ECO:0007829|PDB:4NJ5" FT HELIX 178..192 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 215..217 FT /evidence="ECO:0007829|PDB:4NJ5" FT HELIX 219..224 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 234..238 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 242..246 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 249..256 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 268..272 FT /evidence="ECO:0007829|PDB:4NJ5" FT HELIX 291..301 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 306..312 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 322..338 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 344..352 FT /evidence="ECO:0007829|PDB:4NJ5" FT HELIX 360..372 FT /evidence="ECO:0007829|PDB:4NJ5" FT HELIX 374..376 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 382..385 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 391..394 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 396..399 FT /evidence="ECO:0007829|PDB:4NJ5" FT HELIX 407..410 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 411..413 FT /evidence="ECO:0007829|PDB:4NJ5" FT HELIX 445..449 FT /evidence="ECO:0007829|PDB:4NJ5" FT TURN 450..452 FT /evidence="ECO:0007829|PDB:4NJ5" FT HELIX 487..489 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 495..499 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 501..511 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 518..521 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 525..527 FT /evidence="ECO:0007829|PDB:4NJ5" FT HELIX 529..537 FT /evidence="ECO:0007829|PDB:4NJ5" FT HELIX 545..547 FT /evidence="ECO:0007829|PDB:4NJ5" FT HELIX 551..553 FT /evidence="ECO:0007829|PDB:4NJ5" FT TURN 554..557 FT /evidence="ECO:0007829|PDB:4NJ5" FT TURN 560..562 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 580..582 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 584..587 FT /evidence="ECO:0007829|PDB:4NJ5" FT HELIX 589..592 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 600..609 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 617..624 FT /evidence="ECO:0007829|PDB:4NJ5" FT STRAND 633..635 FT /evidence="ECO:0007829|PDB:4NJ5" SQ SEQUENCE 650 AA; 72174 MW; B2F291C5FA18A6E9 CRC64; MGSSHIPLDP SLNPSPSLIP KLEPVTESTQ NLAFQLPNTN PQALISSAVS DFNEATDFSS DYNTVAESAR SAFAQRLQRH DDVAVLDSLT GAIVPVEENP EPEPNPYSTS DSSPSVATQR PRPQPRSSEL VRITDVGPES ERQFREHVRK TRMIYDSLRM FLMMEEAKRN GVGGRRARAD GKAGKAGSMM RDCMLWMNRD KRIVGSIPGV QVGDIFFFRF ELCVMGLHGH PQSGIDFLTG SLSSNGEPIA TSVIVSGGYE DDDDQGDVIM YTGQGGQDRL GRQAEHQRLE GGNLAMERSM YYGIEVRVIR GLKYENEVSS RVYVYDGLFR IVDSWFDVGK SGFGVFKYRL ERIEGQAEMG SSVLKFARTL KTNPLSVRPR GYINFDISNG KENVPVYLFN DIDSDQEPLY YEYLAQTSFP PGLFVQQSGN ASGCDCVNGC GSGCLCEAKN SGEIAYDYNG TLIRQKPLIH ECGSACQCPP SCRNRVTQKG LRNRLEVFRS LETGWGVRSL DVLHAGAFIC EYAGVALTRE QANILTMNGD TLVYPARFSS ARWEDWGDLS QVLADFERPS YPDIPPVDFA MDVSKMRNVA CYISHSTDPN VIVQFVLHDH NSLMFPRVML FAAENIPPMT ELSLDYGVVD DWNAKLAICN //