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Q8GZB6

- SUVH4_ARATH

UniProt

Q8GZB6 - SUVH4_ARATH

Protein

Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4

Gene

SUVH4

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 2 (09 May 2003)
      Previous versions | rss
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    Functioni

    Histone methyltransferase. Methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. The silencing mechanism via DNA CpNpG methylation requires the targeting of chromomethylase CMT3 to methylated histones, probably through an interaction with an HP1-like adapter. By its function, KYP is directly required for the maintenance of the DNA CpNpG and asymmetric methylation. Involved in the silencing of transposable elements.5 Publications

    Catalytic activityi

    S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].PROSITE-ProRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi383 – 3831Zinc 1By similarity
    Metal bindingi383 – 3831Zinc 2By similarity
    Metal bindingi385 – 3851Zinc 1By similarity
    Metal bindingi389 – 3891Zinc 1By similarity
    Metal bindingi389 – 3891Zinc 3By similarity
    Metal bindingi395 – 3951Zinc 1By similarity
    Metal bindingi397 – 3971Zinc 2By similarity
    Metal bindingi425 – 4251Zinc 2By similarity
    Metal bindingi425 – 4251Zinc 3By similarity
    Metal bindingi429 – 4291Zinc 2By similarity
    Metal bindingi431 – 4311Zinc 3By similarity
    Metal bindingi435 – 4351Zinc 3By similarity
    Binding sitei493 – 4931S-adenosyl-L-methioninePROSITE-ProRule annotation
    Binding sitei548 – 5481S-adenosyl-L-methioninePROSITE-ProRule annotation
    Metal bindingi554 – 5541Zinc 4By similarity
    Metal bindingi612 – 6121Zinc 4By similarity
    Metal bindingi614 – 6141Zinc 4By similarity
    Metal bindingi619 – 6191Zinc 4By similarity

    GO - Molecular functioni

    1. double-stranded methylated DNA binding Source: TAIR
    2. histone methyltransferase activity (H3-K9 specific) Source: TAIR
    3. methyl-CpG binding Source: TAIR
    4. methyl-CpNpG binding Source: TAIR
    5. methyl-CpNpN binding Source: TAIR
    6. zinc ion binding Source: InterPro

    GO - Biological processi

    1. histone H3-K9 methylation Source: TAIR
    2. histone methylation Source: TAIR
    3. maintenance of DNA methylation Source: TAIR
    4. peptidyl-lysine methylation Source: TAIR

    Keywords - Molecular functioni

    Chromatin regulator, Methyltransferase, Transferase

    Keywords - Ligandi

    Metal-binding, S-adenosyl-L-methionine, Zinc

    Enzyme and pathway databases

    BioCyciARA:AT5G13960-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 (EC:2.1.1.43)
    Alternative name(s):
    Histone H3-K9 methyltransferase 4
    Short name:
    H3-K9-HMTase 4
    Protein KRYPTONITE
    Protein SET DOMAIN GROUP 33
    Suppressor of variegation 3-9 homolog protein 4
    Short name:
    Su(var)3-9 homolog protein 4
    Gene namesi
    Name:SUVH4
    Synonyms:KYP, SDG33, SET33
    Ordered Locus Names:At5g13960
    ORF Names:MAC12.7
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 5

    Organism-specific databases

    TAIRiAT5G13960.

    Subcellular locationi

    Nucleus. Chromosome. Chromosomecentromere
    Note: Associates with centromeric constitutive heterochromatin and at a lower level with regions of euchromatin.

    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 – 624624Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4PRO_0000186075Add
    BLAST

    Proteomic databases

    PaxDbiQ8GZB6.
    PRIDEiQ8GZB6.

    Expressioni

    Tissue specificityi

    Expressed in leaves stems and flowers.1 Publication

    Gene expression databases

    GenevestigatoriQ8GZB6.

    Interactioni

    Subunit structurei

    Interacts with H3 histone.

    Structurei

    3D structure databases

    ProteinModelPortaliQ8GZB6.
    SMRiQ8GZB6. Positions 97-623.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini149 – 302154YDGPROSITE-ProRule annotationAdd
    BLAST
    Domaini381 – 44363Pre-SETPROSITE-ProRule annotationAdd
    BLAST
    Domaini446 – 594149SETPROSITE-ProRule annotationAdd
    BLAST
    Domaini608 – 62417Post-SETPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni456 – 4583S-adenosyl-L-methionine bindingBy similarity
    Regioni551 – 5522S-adenosyl-L-methionine bindingBy similarity

    Domaini

    Although the SET domain contains the active site of enzymatic activity, both pre-SET and post-SET domains are required for methyltransferase activity.
    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.By similarity

    Sequence similaritiesi

    Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. Suvar3-9 subfamily.PROSITE-ProRule annotation
    Contains 1 post-SET domain.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.
    InParanoidiQ8GZB6.
    KOiK11420.
    OMAiVNRTSQK.
    PhylomeDBiQ8GZB6.

    Family and domain databases

    Gene3Di2.30.280.10. 1 hit.
    InterProiIPR025794. Hist-Lys_N-MeTrfase_plant.
    IPR003616. Post-SET_dom.
    IPR007728. Pre-SET_dom.
    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]
    SMARTiSM00508. PostSET. 1 hit.
    SM00317. SET. 1 hit.
    [Graphical view]
    SUPFAMiSSF88697. SSF88697. 1 hit.
    PROSITEiPS50868. POST_SET. 1 hit.
    PS50867. 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.

    Q8GZB6-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAGKRKRANA PDQTERRSSV RVQKVRQKAL DEKARLVQER VKLLSDRKSE    50
    ICVDDTELHE KEEENVDGSP KRRSPPKLTA MQKGKQKLSV SLNGKDVNLE 100
    PHLKVTKCLR LFNKQYLLCV QAKLSRPDLK GVTEMIKAKA ILYPRKIIGD 150
    LPGIDVGHRF FSRAEMCAVG FHNHWLNGID YMSMEYEKEY SNYKLPLAVS 200
    IVMSGQYEDD LDNADTVTYT GQGGHNLTGN KRQIKDQLLE RGNLALKHCC 250
    EYNVPVRVTR GHNCKSSYTK RVYTYDGLYK VEKFWAQKGV SGFTVYKYRL 300
    KRLEGQPELT TDQVNFVAGR IPTSTSEIEG LVCEDISGGL EFKGIPATNR 350
    VDDSPVSPTS GFTYIKSLII EPNVIIPKSS TGCNCRGSCT DSKKCACAKL 400
    NGGNFPYVDL NDGRLIESRD VVFECGPHCG CGPKCVNRTS QKRLRFNLEV 450
    FRSAKKGWAV RSWEYIPAGS PVCEYIGVVR RTADVDTISD NEYIFEIDCQ 500
    QTMQGLGGRQ RRLRDVAVPM NNGVSQSSED ENAPEFCIDA GSTGNFARFI 550
    NHSCEPNLFV QCVLSSHQDI RLARVVLFAA DNISPMQELT YDYGYALDSV 600
    HGPDGKVKQL ACYCGALNCR KRLY 624
    Length:624
    Mass (Da):70,056
    Last modified:May 9, 2003 - v2
    Checksum:i67B5CF6606F16B07
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti189 – 1891E → D in AAO17392. (PubMed:12486005)Curated
    Sequence conflicti548 – 5481R → T in AAK28969. (PubMed:11691919)Curated
    Sequence conflicti576 – 5761V → A in AAK28969. (PubMed:11691919)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF344447 mRNA. Translation: AAK28969.1.
    AF538715 Genomic DNA. Translation: AAO17392.1.
    AB005230 Genomic DNA. Translation: BAB11124.1.
    CP002688 Genomic DNA. Translation: AED91966.1.
    BT002313 mRNA. Translation: AAN86146.1.
    RefSeqiNP_196900.1. NM_121399.2.
    UniGeneiAt.8330.

    Genome annotation databases

    EnsemblPlantsiAT5G13960.1; AT5G13960.1; AT5G13960.
    GeneIDi831244.
    KEGGiath:AT5G13960.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF344447 mRNA. Translation: AAK28969.1 .
    AF538715 Genomic DNA. Translation: AAO17392.1 .
    AB005230 Genomic DNA. Translation: BAB11124.1 .
    CP002688 Genomic DNA. Translation: AED91966.1 .
    BT002313 mRNA. Translation: AAN86146.1 .
    RefSeqi NP_196900.1. NM_121399.2.
    UniGenei At.8330.

    3D structure databases

    ProteinModelPortali Q8GZB6.
    SMRi Q8GZB6. Positions 97-623.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PaxDbi Q8GZB6.
    PRIDEi Q8GZB6.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT5G13960.1 ; AT5G13960.1 ; AT5G13960 .
    GeneIDi 831244.
    KEGGi ath:AT5G13960.

    Organism-specific databases

    TAIRi AT5G13960.

    Phylogenomic databases

    eggNOGi COG3440.
    HOGENOMi HOG000238382.
    InParanoidi Q8GZB6.
    KOi K11420.
    OMAi VNRTSQK.
    PhylomeDBi Q8GZB6.

    Enzyme and pathway databases

    BioCyci ARA:AT5G13960-MONOMER.

    Gene expression databases

    Genevestigatori Q8GZB6.

    Family and domain databases

    Gene3Di 2.30.280.10. 1 hit.
    InterProi IPR025794. Hist-Lys_N-MeTrfase_plant.
    IPR003616. Post-SET_dom.
    IPR007728. Pre-SET_dom.
    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 SM00508. PostSET. 1 hit.
    SM00317. SET. 1 hit.
    [Graphical view ]
    SUPFAMi SSF88697. SSF88697. 1 hit.
    PROSITEi PS50868. POST_SET. 1 hit.
    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, TISSUE SPECIFICITY.
    2. "An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation."
      Malagnac F., Bartee L., Bender J.
      EMBO J. 21:6842-6852(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: cv. Wassilewskija.
    3. "Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones."
      Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M., Miyajima N., Tabata S.
      DNA Res. 4:215-230(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    4. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    6. "Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase."
      Jackson J.P., Lindroth A.M., Cao X., Jacobsen S.E.
      Nature 416:556-560(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTANTS KYP-1; KYP-2 AND KYP-3.
    7. "Interplay between two epigenetic marks: DNA methylation and histone H3 lysine 9 methylation."
      Johnson L.M., Cao X., Jacobsen S.E.
      Curr. Biol. 12:1360-1367(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: EPIGENETIC METHYLATION.
    8. "Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3."
      Lindroth A.M., Shultis D., Jasencakova Z., Fuchs J., Johnson L., Schubert D., Patnaik D., Pradhan S., Goodrich J., Schubert I., Jenuwein T., Khorasanizadeh S., Jacobsen S.E.
      EMBO J. 23:4286-4296(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications."
      Johnson L., Mollah S., Garcia B.A., Muratore T.L., Shabanowitz J., Hunt D.F., Jacobsen S.E.
      Nucleic Acids Res. 32:6511-6518(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    10. "Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis."
      Tran R.K., Zilberman D., de Bustos C., Ditt R.F., Henikoff J.G., Lindroth A.M., Delrow J., Boyle T., Kwong S., Bryson T.D., Jacobsen S.E., Henikoff S.
      Genome Biol. 6:R90.1-R90.11(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    11. "H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases."
      Ebbs M.L., Bartee L., Bender J.
      Mol. Cell. Biol. 25:10507-10515(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    12. "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.

    Entry informationi

    Entry nameiSUVH4_ARATH
    AccessioniPrimary (citable) accession number: Q8GZB6
    Secondary accession number(s): Q9C5P3, Q9FFX9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 9, 2003
    Last sequence update: May 9, 2003
    Last modified: October 1, 2014
    This is version 104 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Mutations in the KYP/SUVH4 gene decrease the level of histone H3-K9 dimethylated, trimethylated or dimethylated in association with H3-K14Ac by factors of 4,3 and 3, respectively. The level of monomethylated H3-K9 is unchanged. Such mutations lead to a drastic decrease of cytosine methylation at CpNpG sites, causing the reactivation of endogenous retrotransposons. The KRYPTONYTE methyltransferase name was given according to its involvement in SUPERMAN gene silencing.

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3