SUVH9_ARATH
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 03-AUG-2022, entry version 146.
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}.
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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.AT4G13460.2; -.
DR PaxDb; Q9T0G7; -.
DR PRIDE; Q9T0G7; -.
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; locus:2140827; AT4G13460.
DR eggNOG; KOG1082; Eukaryota.
DR HOGENOM; CLU_004556_4_0_1; -.
DR InParanoid; Q9T0G7; -.
DR OMA; IGCYCAQ; -.
DR OrthoDB; 541949at2759; -.
DR PhylomeDB; Q9T0G7; -.
DR PRO; PR:Q9T0G7; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9T0G7; baseline and differential.
DR Genevisible; Q9T0G7; AT.
DR GO; GO:0000775; C:chromosome, centromeric region; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003690; F:double-stranded DNA binding; IBA:GO_Central.
DR GO; GO:0042054; F:histone methyltransferase activity; IBA:GO_Central.
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:0009294; P:DNA-mediated transformation; IMP:TAIR.
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; IBA:GO_Central.
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 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
