GenomeNet

Database: UniProt/SWISS-PROT
Entry: SUVH9_ARATH
LinkDB: SUVH9_ARATH
Original site: 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   23-MAY-2018, entry version 129.
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; Magnoliophyta; eudicotyledons; Gunneridae;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   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
RT   encoding SET domain proteins that can be assigned to four
RT   evolutionarily conserved 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.,
RA   Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N.,
RA   Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M.,
RA   Weichselgartner M., de Simone V., Obermaier B., Mache R., Mueller M.,
RA   Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T.,
RA   Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I.,
RA   Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P.,
RA   Langham S.-A., McCullagh B., Bilham L., Robben J.,
RA   van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F.,
RA   Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
RA   Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA   Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W.,
RA   Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P.,
RA   Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H.,
RA   De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R.,
RA   van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S.,
RA   Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R.,
RA   Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S.,
RA   Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H.,
RA   Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S.,
RA   Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
RA   Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA   Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R.,
RA   Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S.,
RA   Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E.,
RA   Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A.,
RA   Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T.,
RA   Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C.,
RA   Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S.,
RA   Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K.,
RA   Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L.,
RA   Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J.,
RA   Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J.,
RA   Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D.,
RA   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.,
RA   Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C.,
RA   Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C.,
RA   Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R.,
RA   Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S.,
RA   Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A.,
RA   Chen E., Marra M.A., Martienssen R., McCombie W.R.;
RT   "Sequence and analysis of chromosome 4 of the plant Arabidopsis
RT   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
RT   reference 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
RT   silencing 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
RT   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
RT   occupancy 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.,
RA   Cai T., Chen S., He X.-J.;
RT   "Two components of the RNA-Directed DNA methylation pathway associate
RT   with 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.,
RA   Jacobsen S.E.;
RT   "SRA- and SET-domain-containing proteins link RNA polymerase V
RT   occupancy to DNA methylation.";
RL   Nature 507:124-128(2014).
CC   -!- FUNCTION: Histone methyltransferase family member that plays a
CC       role in gene silencing (PubMed:19043555, PubMed:24463519,
CC       PubMed:27171427). Together with MORC6 and SUVH2, regulates the
CC       silencing of some transposable elements (TEs) (PubMed:27171427).
CC       According to PubMed:19043555, the protein does not bind S-
CC       adenosyl-L-methionine and lacks methyltransferase activity.
CC       Instead, it may function downstream of DRM2 in RNA-directed DNA
CC       methylation, binding to methylated DNA and recruiting DNA-directed
CC       RNA polymerase V to chromatin (PubMed:24463519, PubMed:27171427).
CC       {ECO:0000269|PubMed:19043555, ECO:0000269|PubMed:24463519,
CC       ECO:0000269|PubMed:27171427}.
CC   -!- SUBUNIT: Component of an RNA-directed DNA methylation (RdDM)
CC       complex that contains at least MORC6, MORC1/CRT1, MORC2, SWI3D and
CC       SUVH9. Interacts directly with MORC6, MORC2 and MORC1/CRT1.
CC       Interacts with SWI3B, SWI3C and SWI3D (PubMed:27171427).
CC       {ECO:0000269|PubMed:24465213, ECO:0000269|PubMed:27171427}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:24463519}.
CC       Chromosome, centromere {ECO:0000250}. Note=Associates with
CC       centromeric constitutive heterochromatin. {ECO:0000305}.
CC   -!- DOMAIN: Although both SET and pre-SET domains are present, the
CC       absence of the post-SET domain may explain the lack of
CC       methyltransferase activity. Besides, the Cys residues in the SET
CC       domain that normally bind a zinc ion are not conserved.
CC   -!- DOMAIN: In the pre-SET domain, Cys residues bind 3 zinc ions that
CC       are arranged in a triangular cluster; some of these Cys residues
CC       contribute to the binding of two zinc ions within the cluster.
CC   -!- DISRUPTION PHENOTYPE: Impaired gene silencing due to
CC       decondensation of chromocenters leading to the derepression of
CC       DNA-methylated genes and transposable elements (TEs).
CC       {ECO:0000269|PubMed:27171427}.
CC   -!- SIMILARITY: Belongs to the class V-like SAM-binding
CC       methyltransferase superfamily. Histone-lysine methyltransferase
CC       family. Suvar3-9 subfamily. {ECO:0000255|PROSITE-
CC       ProRule:PRU00908}.
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   UniGene; At.3118; -.
DR   PDB; 4NJ5; X-ray; 2.40 A; A=134-650.
DR   PDBsum; 4NJ5; -.
DR   ProteinModelPortal; Q9T0G7; -.
DR   SMR; Q9T0G7; -.
DR   BioGrid; 12275; 1.
DR   STRING; 3702.AT4G13460.1; -.
DR   PaxDb; Q9T0G7; -.
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; ENOG410IN61; Eukaryota.
DR   eggNOG; COG3440; LUCA.
DR   HOGENOM; HOG000238382; -.
DR   InParanoid; Q9T0G7; -.
DR   KO; K11420; -.
DR   OMA; VYKYKML; -.
DR   OrthoDB; EOG093603OW; -.
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:0003677; F:DNA binding; IEA:UniProtKB-KW.
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:RNA-directed DNA methylation; IMP:UniProtKB.
DR   Gene3D; 2.30.280.10; -; 1.
DR   InterPro; IPR025794; Hist-Lys_N-MeTrfase_plant.
DR   InterPro; IPR007728; Pre-SET_dom.
DR   InterPro; IPR015947; PUA-like_sf.
DR   InterPro; IPR001214; SET_dom.
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; 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;
KW   Complete proteome; DNA-binding; Metal-binding; Nucleus;
KW   Reference proteome; Zinc.
FT   CHAIN         1    650       Histone-lysine N-methyltransferase family
FT                                member SUVH9.
FT                                /FTId=PRO_0000186080.
FT   DOMAIN      205    352       YDG. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00358}.
FT   DOMAIN      432    490       Pre-SET. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00157}.
FT   DOMAIN      493    637       SET. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00190}.
FT   METAL       434    434       Zinc 1.
FT   METAL       434    434       Zinc 2.
FT   METAL       436    436       Zinc 1.
FT   METAL       440    440       Zinc 1.
FT   METAL       440    440       Zinc 3.
FT   METAL       444    444       Zinc 1.
FT   METAL       446    446       Zinc 2.
FT   METAL       472    472       Zinc 2.
FT   METAL       472    472       Zinc 3.
FT   METAL       476    476       Zinc 2.
FT   METAL       478    478       Zinc 3.
FT   METAL       482    482       Zinc 3.
FT   HELIX       140    167       {ECO:0000244|PDB:4NJ5}.
FT   HELIX       178    192       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      215    217       {ECO:0000244|PDB:4NJ5}.
FT   HELIX       219    224       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      234    238       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      242    246       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      249    256       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      268    272       {ECO:0000244|PDB:4NJ5}.
FT   HELIX       291    301       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      306    312       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      322    338       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      344    352       {ECO:0000244|PDB:4NJ5}.
FT   HELIX       360    372       {ECO:0000244|PDB:4NJ5}.
FT   HELIX       374    376       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      382    385       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      391    394       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      396    399       {ECO:0000244|PDB:4NJ5}.
FT   HELIX       407    410       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      411    413       {ECO:0000244|PDB:4NJ5}.
FT   HELIX       445    449       {ECO:0000244|PDB:4NJ5}.
FT   TURN        450    452       {ECO:0000244|PDB:4NJ5}.
FT   HELIX       487    489       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      495    499       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      501    511       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      518    521       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      525    527       {ECO:0000244|PDB:4NJ5}.
FT   HELIX       529    537       {ECO:0000244|PDB:4NJ5}.
FT   HELIX       545    547       {ECO:0000244|PDB:4NJ5}.
FT   HELIX       551    553       {ECO:0000244|PDB:4NJ5}.
FT   TURN        554    557       {ECO:0000244|PDB:4NJ5}.
FT   TURN        560    562       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      580    582       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      584    587       {ECO:0000244|PDB:4NJ5}.
FT   HELIX       589    592       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      600    609       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      617    624       {ECO:0000244|PDB:4NJ5}.
FT   STRAND      633    635       {ECO:0000244|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
//
DBGET integrated database retrieval system