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Q8GZB6 (SUVH4_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 101. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:SUVH4
Synonyms:KYP, SDG33, SET33
Ordered Locus Names:At5g13960
ORF Names:MAC12.7
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length624 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.6 Ref.8 Ref.9 Ref.10 Ref.11

Catalytic activity

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

Subunit structure

Interacts with H3 histone.

Subcellular location

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

Tissue specificity

Expressed in leaves stems and flowers. Ref.1

Domain

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

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.

Sequence similarities

Belongs to the class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. Suvar3-9 subfamily.

Contains 1 post-SET domain.

Contains 1 pre-SET domain.

Contains 1 SET domain.

Contains 1 YDG domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 624624Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4
PRO_0000186075

Regions

Domain149 – 302154YDG
Domain381 – 44363Pre-SET
Domain446 – 594149SET
Domain608 – 62417Post-SET

Experimental info

Sequence conflict1891E → D in AAO17392. Ref.2
Sequence conflict5481R → T in AAK28969. Ref.1
Sequence conflict5761V → A in AAK28969. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Q8GZB6 [UniParc].

Last modified May 9, 2003. Version 2.
Checksum: 67B5CF6606F16B07

FASTA62470,056
        10         20         30         40         50         60 
MAGKRKRANA PDQTERRSSV RVQKVRQKAL DEKARLVQER VKLLSDRKSE ICVDDTELHE 

        70         80         90        100        110        120 
KEEENVDGSP KRRSPPKLTA MQKGKQKLSV SLNGKDVNLE PHLKVTKCLR LFNKQYLLCV 

       130        140        150        160        170        180 
QAKLSRPDLK GVTEMIKAKA ILYPRKIIGD LPGIDVGHRF FSRAEMCAVG FHNHWLNGID 

       190        200        210        220        230        240 
YMSMEYEKEY SNYKLPLAVS IVMSGQYEDD LDNADTVTYT GQGGHNLTGN KRQIKDQLLE 

       250        260        270        280        290        300 
RGNLALKHCC EYNVPVRVTR GHNCKSSYTK RVYTYDGLYK VEKFWAQKGV SGFTVYKYRL 

       310        320        330        340        350        360 
KRLEGQPELT TDQVNFVAGR IPTSTSEIEG LVCEDISGGL EFKGIPATNR VDDSPVSPTS 

       370        380        390        400        410        420 
GFTYIKSLII EPNVIIPKSS TGCNCRGSCT DSKKCACAKL NGGNFPYVDL NDGRLIESRD 

       430        440        450        460        470        480 
VVFECGPHCG CGPKCVNRTS QKRLRFNLEV FRSAKKGWAV RSWEYIPAGS PVCEYIGVVR 

       490        500        510        520        530        540 
RTADVDTISD NEYIFEIDCQ QTMQGLGGRQ RRLRDVAVPM NNGVSQSSED ENAPEFCIDA 

       550        560        570        580        590        600 
GSTGNFARFI NHSCEPNLFV QCVLSSHQDI RLARVVLFAA DNISPMQELT YDYGYALDSV 

       610        620 
HGPDGKVKQL ACYCGALNCR KRLY 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_196900.1. NM_121399.2.
UniGeneAt.8330.

3D structure databases

ProteinModelPortalQ8GZB6.
SMRQ8GZB6. Positions 143-623.
ModBaseSearch...
MobiDBSearch...

Proteomic databases

PaxDbQ8GZB6.
PRIDEQ8GZB6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT5G13960.1; AT5G13960.1; AT5G13960.
GeneID831244.
KEGGath:AT5G13960.

Organism-specific databases

TAIRAT5G13960.

Phylogenomic databases

eggNOGCOG3440.
HOGENOMHOG000238382.
InParanoidQ8GZB6.
KOK11420.
OMADCEGDCA.
PhylomeDBQ8GZB6.
ProtClustDBCLSN2916622.

Enzyme and pathway databases

BioCycARA:AT5G13960-MONOMER.

Gene expression databases

GenevestigatorQ8GZB6.

Family and domain databases

Gene3D2.30.280.10. 1 hit.
InterProIPR025794. 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]
PfamPF05033. Pre-SET. 1 hit.
PF02182. SAD_SRA. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]
SMARTSM00508. PostSET. 1 hit.
SM00317. SET. 1 hit.
[Graphical view]
SUPFAMSSF88697. SSF88697. 1 hit.
PROSITEPS50868. 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]
ProtoNetSearch...

Entry information

Entry nameSUVH4_ARATH
AccessionPrimary (citable) accession number: Q8GZB6
Secondary accession number(s): Q9C5P3, Q9FFX9
Entry history
Integrated into UniProtKB/Swiss-Prot: May 9, 2003
Last sequence update: May 9, 2003
Last modified: April 16, 2014
This is version 101 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names