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Q8GZB6

- SUVH4_ARATH

UniProt

Q8GZB6 - SUVH4_ARATH

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Protein
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4
Gene
SUVH4, KYP, SDG33, SET33, At5g13960, MAC12.7
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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].

Sites

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

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
Complete GO annotation...

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 SUVH4
PRO_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.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini149 – 302154YDG
Add
BLAST
Domaini381 – 44363Pre-SET
Add
BLAST
Domaini446 – 594149SET
Add
BLAST
Domaini608 – 62417Post-SET
Add
BLAST

Region

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

Contains 1 post-SET domain.
Contains 1 pre-SET domain.
Contains 1 SET domain.
Contains 1 YDG domain.

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti189 – 1891E → D in AAO17392. 1 Publication
Sequence conflicti548 – 5481R → T in AAK28969. 1 Publication
Sequence conflicti576 – 5761V → A in AAK28969. 1 Publication

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

« Hide 'large scale' publications
  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: June 11, 2014
This is version 103 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

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