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Q9T0G7

- SUVH9_ARATH

UniProt

Q9T0G7 - SUVH9_ARATH

Protein

Histone-lysine N-methyltransferase family member SUVH9

Gene

SUVH9

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 106 (01 Oct 2014)
      Sequence version 1 (01 May 2000)
      Previous versions | rss
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    Functioni

    Histone methyltransferase family member that plays a role in gene silencing. According to PubMed:19043555, the protein does not bind S-adenosyl-L-methionine and lacks methyltransferase activity. Instead, it may function downstream of DRM2 in RNA-directed DNA methylation, binding to methylated DNA and recruiting DNA-directed RNA polymerase V to chromatin (PubMed:24463519).2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi434 – 4341Zinc 1
    Metal bindingi434 – 4341Zinc 2
    Metal bindingi436 – 4361Zinc 1
    Metal bindingi440 – 4401Zinc 1
    Metal bindingi440 – 4401Zinc 3
    Metal bindingi444 – 4441Zinc 1
    Metal bindingi446 – 4461Zinc 2
    Metal bindingi472 – 4721Zinc 2
    Metal bindingi472 – 4721Zinc 3
    Metal bindingi476 – 4761Zinc 2
    Metal bindingi478 – 4781Zinc 3
    Metal bindingi482 – 4821Zinc 3

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. histone-lysine N-methyltransferase activity Source: InterPro
    3. zinc ion binding Source: InterPro

    GO - Biological processi

    1. DNA mediated transformation Source: TAIR

    Keywords - Molecular functioni

    Chromatin regulator

    Keywords - Ligandi

    DNA-binding, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciARA:AT4G13460-MONOMER.
    ARA:GQT-2273-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone-lysine N-methyltransferase family member SUVH9
    Alternative name(s):
    Histone H3-K9 methyltransferase 9
    Short name:
    H3-K9-HMTase 9
    Protein SET DOMAIN GROUP 22
    Suppressor of variegation 3-9 homolog protein 9
    Short name:
    Su(var)3-9 homolog protein 9
    Gene namesi
    Name:SUVH9
    Synonyms:SDG22, SET22
    Ordered Locus Names:At4g13460
    ORF Names:T6G15.10
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 4

    Organism-specific databases

    TAIRiAT4G13460.

    Subcellular locationi

    Nucleus 1 Publication. Chromosomecentromere By similarity
    Note: Associates with centromeric constitutive heterochromatin.Curated

    GO - Cellular componenti

    1. chromosome, centromeric region Source: UniProtKB-SubCell
    2. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Centromere, Chromosome, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 650650Histone-lysine N-methyltransferase family member SUVH9PRO_0000186080Add
    BLAST

    Proteomic databases

    PaxDbiQ9T0G7.
    PRIDEiQ9T0G7.

    Expressioni

    Gene expression databases

    GenevestigatoriQ9T0G7.

    Structurei

    Secondary structure

    1
    650
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi140 – 16728
    Helixi178 – 19215
    Beta strandi215 – 2173
    Helixi219 – 2246
    Beta strandi234 – 2385
    Beta strandi242 – 2465
    Beta strandi249 – 2568
    Beta strandi268 – 2725
    Helixi291 – 30111
    Beta strandi306 – 3127
    Beta strandi322 – 33817
    Beta strandi344 – 3529
    Helixi360 – 37213
    Helixi374 – 3763
    Beta strandi382 – 3854
    Beta strandi391 – 3944
    Beta strandi396 – 3994
    Helixi407 – 4104
    Beta strandi411 – 4133
    Helixi445 – 4495
    Turni450 – 4523
    Helixi487 – 4893
    Beta strandi495 – 4995
    Beta strandi501 – 51111
    Beta strandi518 – 5214
    Beta strandi525 – 5273
    Helixi529 – 5379
    Helixi545 – 5473
    Helixi551 – 5533
    Turni554 – 5574
    Turni560 – 5623
    Beta strandi580 – 5823
    Beta strandi584 – 5874
    Helixi589 – 5924
    Beta strandi600 – 60910
    Beta strandi617 – 6248
    Beta strandi633 – 6353

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4NJ5X-ray2.40A134-650[»]
    ProteinModelPortaliQ9T0G7.
    SMRiQ9T0G7. Positions 138-637.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini205 – 352148YDGPROSITE-ProRule annotationAdd
    BLAST
    Domaini432 – 49059Pre-SETPROSITE-ProRule annotationAdd
    BLAST
    Domaini493 – 637145SETPROSITE-ProRule annotationAdd
    BLAST

    Domaini

    Although both SET and pre-SET domains are present, the absence of the post-SET domain may explain the lack of methyltransferase activity. Besides, the Cys residues in the SET domain that normally bind a zinc ion are not conserved.
    In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster; some of these Cys residues contribute to the binding of two zinc ions within the cluster.

    Sequence similaritiesi

    Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. Suvar3-9 subfamily.PROSITE-ProRule annotation
    Contains 1 pre-SET domain.PROSITE-ProRule annotation
    Contains 1 SET domain.PROSITE-ProRule annotation
    Contains 1 YDG domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG3440.
    HOGENOMiHOG000238382.
    InParanoidiQ9T0G7.
    KOiK11420.
    OMAiSWFDVGK.
    PhylomeDBiQ9T0G7.

    Family and domain databases

    Gene3Di2.30.280.10. 1 hit.
    InterProiIPR025794. Hist-Lys_N-MeTrfase_plant.
    IPR007728. Pre-SET_dom.
    IPR003606. Pre-SET_Zn-bd_sub.
    IPR015947. PUA-like_domain.
    IPR001214. SET_dom.
    IPR003105. SRA_YDG.
    [Graphical view]
    PfamiPF05033. Pre-SET. 1 hit.
    PF02182. SAD_SRA. 1 hit.
    PF00856. SET. 1 hit.
    [Graphical view]
    SMARTiSM00468. PreSET. 1 hit.
    SM00317. SET. 1 hit.
    SM00466. SRA. 1 hit.
    [Graphical view]
    SUPFAMiSSF88697. SSF88697. 1 hit.
    PROSITEiPS50867. PRE_SET. 1 hit.
    PS51575. SAM_MT43_SUVAR39_2. 1 hit.
    PS50280. SET. 1 hit.
    PS51015. YDG. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9T0G7-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGSSHIPLDP SLNPSPSLIP KLEPVTESTQ NLAFQLPNTN PQALISSAVS    50
    DFNEATDFSS DYNTVAESAR SAFAQRLQRH DDVAVLDSLT GAIVPVEENP 100
    EPEPNPYSTS DSSPSVATQR PRPQPRSSEL VRITDVGPES ERQFREHVRK 150
    TRMIYDSLRM FLMMEEAKRN GVGGRRARAD GKAGKAGSMM RDCMLWMNRD 200
    KRIVGSIPGV QVGDIFFFRF ELCVMGLHGH PQSGIDFLTG SLSSNGEPIA 250
    TSVIVSGGYE DDDDQGDVIM YTGQGGQDRL GRQAEHQRLE GGNLAMERSM 300
    YYGIEVRVIR GLKYENEVSS RVYVYDGLFR IVDSWFDVGK SGFGVFKYRL 350
    ERIEGQAEMG SSVLKFARTL KTNPLSVRPR GYINFDISNG KENVPVYLFN 400
    DIDSDQEPLY YEYLAQTSFP PGLFVQQSGN ASGCDCVNGC GSGCLCEAKN 450
    SGEIAYDYNG TLIRQKPLIH ECGSACQCPP SCRNRVTQKG LRNRLEVFRS 500
    LETGWGVRSL DVLHAGAFIC EYAGVALTRE QANILTMNGD TLVYPARFSS 550
    ARWEDWGDLS QVLADFERPS YPDIPPVDFA MDVSKMRNVA CYISHSTDPN 600
    VIVQFVLHDH NSLMFPRVML FAAENIPPMT ELSLDYGVVD DWNAKLAICN 650
    Length:650
    Mass (Da):72,174
    Last modified:May 1, 2000 - v1
    Checksum:iB2F291C5FA18A6E9
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF344452 mRNA. Translation: AAK28974.1.
    AL049656 Genomic DNA. Translation: CAB41104.1.
    AL161536 Genomic DNA. Translation: CAB78388.1.
    CP002687 Genomic DNA. Translation: AEE83282.1.
    CP002687 Genomic DNA. Translation: AEE83283.1.
    PIRiT06648.
    RefSeqiNP_001031625.1. NM_001036548.1.
    NP_193082.1. NM_117420.2.
    UniGeneiAt.3118.

    Genome annotation databases

    EnsemblPlantsiAT4G13460.1; AT4G13460.1; AT4G13460.
    AT4G13460.2; AT4G13460.2; AT4G13460.
    GeneIDi826978.
    KEGGiath:AT4G13460.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF344452 mRNA. Translation: AAK28974.1 .
    AL049656 Genomic DNA. Translation: CAB41104.1 .
    AL161536 Genomic DNA. Translation: CAB78388.1 .
    CP002687 Genomic DNA. Translation: AEE83282.1 .
    CP002687 Genomic DNA. Translation: AEE83283.1 .
    PIRi T06648.
    RefSeqi NP_001031625.1. NM_001036548.1.
    NP_193082.1. NM_117420.2.
    UniGenei At.3118.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4NJ5 X-ray 2.40 A 134-650 [» ]
    ProteinModelPortali Q9T0G7.
    SMRi Q9T0G7. Positions 138-637.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PaxDbi Q9T0G7.
    PRIDEi Q9T0G7.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT4G13460.1 ; AT4G13460.1 ; AT4G13460 .
    AT4G13460.2 ; AT4G13460.2 ; AT4G13460 .
    GeneIDi 826978.
    KEGGi ath:AT4G13460.

    Organism-specific databases

    TAIRi AT4G13460.

    Phylogenomic databases

    eggNOGi COG3440.
    HOGENOMi HOG000238382.
    InParanoidi Q9T0G7.
    KOi K11420.
    OMAi SWFDVGK.
    PhylomeDBi Q9T0G7.

    Enzyme and pathway databases

    BioCyci ARA:AT4G13460-MONOMER.
    ARA:GQT-2273-MONOMER.

    Gene expression databases

    Genevestigatori Q9T0G7.

    Family and domain databases

    Gene3Di 2.30.280.10. 1 hit.
    InterProi IPR025794. Hist-Lys_N-MeTrfase_plant.
    IPR007728. Pre-SET_dom.
    IPR003606. Pre-SET_Zn-bd_sub.
    IPR015947. PUA-like_domain.
    IPR001214. SET_dom.
    IPR003105. SRA_YDG.
    [Graphical view ]
    Pfami PF05033. Pre-SET. 1 hit.
    PF02182. SAD_SRA. 1 hit.
    PF00856. SET. 1 hit.
    [Graphical view ]
    SMARTi SM00468. PreSET. 1 hit.
    SM00317. SET. 1 hit.
    SM00466. SRA. 1 hit.
    [Graphical view ]
    SUPFAMi SSF88697. SSF88697. 1 hit.
    PROSITEi PS50867. PRE_SET. 1 hit.
    PS51575. SAM_MT43_SUVAR39_2. 1 hit.
    PS50280. SET. 1 hit.
    PS51015. YDG. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes."
      Baumbusch L.O., Thorstensen T., Krauss V., Fischer A., Naumann K., Assalkhou R., Schulz I., Reuter G., Aalen R.B.
      Nucleic Acids Res. 29:4319-4333(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], NOMENCLATURE.
    2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
      Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
      , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
      Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Heterochromatin proteins and the control of heterochromatic gene silencing in Arabidopsis."
      Fischer A., Hofmann I., Naumann K., Reuter G.
      J. Plant Physiol. 163:358-368(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE FAMILY.
    5. "SRA-domain proteins required for DRM2-mediated de novo DNA methylation."
      Johnson L.M., Law J.A., Khattar A., Henderson I.R., Jacobsen S.E.
      PLoS Genet. 4:E1000280-E1000280(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DNA-BINDING, LACK OF METHYLTRANSFERASE ACTIVITY, LACK OF S-ADENOSYL-L-METHIONINE BINDING.
    6. "SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation."
      Johnson L.M., Du J., Hale C.J., Bischof S., Feng S., Chodavarapu R.K., Zhong X., Marson G., Pellegrini M., Segal D.J., Patel D.J., Jacobsen S.E.
      Nature 507:124-128(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) OF 134-650 IN COMPLEX WITH ZINC IONS, SUBCELLULAR LOCATION, FUNCTION.

    Entry informationi

    Entry nameiSUVH9_ARATH
    AccessioniPrimary (citable) accession number: Q9T0G7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 9, 2003
    Last sequence update: May 1, 2000
    Last modified: October 1, 2014
    This is version 106 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3