Reviewed, UniProtKB/Swiss-Prot Q8GZB6 (SUVH4_ARATH)

Names and origin

Protein names

Recommended name:
    Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4
    EC=2.1.1.43
Alternative name(s):
    Histone H3-K9 methyltransferase 4
    H3-K9-HMTase 4
    Suppressor of variegation 3-9 homolog protein 4
      Short name=Su(var)3-9 homolog protein 4
    Protein KRYPTONITE
    Protein SET DOMAIN GROUP 33

Gene names

Name:	SUVH4
Synonyms:	KYP, SDG33, SET33
Ordered Locus Names:	At5g13960
ORF Names:	MAC12.7

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	624 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence 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 tranposable elements.
Catalytic activity	S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N(6)-methyl-L-lysine.
Subunit structure	Interacts with H3 histone.
Subcellular location	Nucleus. Centromere. Note= Associates with centromeric constitutive heterochromatin and at a lower level with regions of euchromatin.
Tissue specificity	Expressed in leaves stems and flowers.
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 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.

Ontologies

Keywords
Cellular component	Centromere Nucleus
Ligand	S-adenosyl-L-methionine
Molecular function	Chromatin regulator Methyltransferase Transferase
Technical term	Complete proteome
Gene Ontology (GO)
None. [Check GOA]

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view
Molecule processing
	Chain	1 – 624	624	Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4
Regions
	Domain	149 – 302	154	YDG
	Domain	381 – 443	63	Pre-SET
	Domain	445 – 598	154	SET
	Domain	608 – 624	17	Post-SET
Experimental info
	Sequence conflict	189	1	E → D in AAO17392. Ref.2
	Sequence conflict	548	1	R → T in AAK28969. Ref.1
	Sequence conflict	576	1	V → A in AAK28969. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q8GZB6-1 [UniParc]. Last modified May 9, 2003. Version 2. Checksum: 67B5CF6606F16B07	FASTA	624	70,056
	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

References

	« Hide 'large scale' referencesShow '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: 11691919] [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: 12486005] [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: 9330910] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[4]	"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: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"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: 11898023] [Abstract] Cited for: FUNCTION, MUTANTS KYP-1; KYP-2 AND KYP-3.
[6]	"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: 12194816] [Abstract] Cited for: EPIGENETIC METHYLATION.
[7]	"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: 15457214] [Abstract] Cited for: FUNCTION.
[8]	"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: 15598823] [Abstract] Cited for: FUNCTION.
[9]	"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:RESEARCH90.1-RESEARCH90.11(2005) [PubMed: 16277745] [Abstract] Cited for: FUNCTION.
[10]	"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: 16287862] [Abstract] Cited for: FUNCTION.
[11]	"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: 16384625] [Abstract] Cited for: GENE FAMILY.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF344447 mRNA. Translation: AAK28969.1. AF538715 Genomic DNA. Translation: AAO17392.1. AB005230 Genomic DNA. Translation: BAB11124.1. BT002313 mRNA. Translation: AAN86146.1.
RefSeq	NP_196900.1.
UniGene	At.8330
3D structure databases
HSSP	HSSP built from PDB template 1MVH based on UniProtKB O60016.
ModBase	Search...
Genome annotation databases
GeneID	831244.
GenomeReviews	Gene locus AT5G13960 in contig BA000015_GR.
KEGG	ath:AT5G13960.
NMPDR	fig|3702.1.peg.23524.
Organism-specific databases
TAIR	At5g13960.
Gene expression databases
ArrayExpress	Q8GZB6.
GermOnline	AT5G13960. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR003616. Post-SET_Zn_bd. IPR007728. Pre-SET_Zn_bd. IPR001214. SET. IPR003105. SRA_YDG. [Graphical view]
Pfam	PF05033. Pre-SET. 1 hit. PF00856. SET. 1 hit. PF02182. YDG_SRA. 1 hit. [Graphical view]
SMART	SM00508. PostSET. 1 hit. SM00317. SET. 1 hit. [Graphical view]
PROSITE	PS50868. POST_SET. 1 hit. PS50867. PRE_SET. 1 hit. PS50280. SET. 1 hit. PS51015. YDG. 1 hit. [Graphical view]
ProDom	Q8GZB6. [Graphical view] [Entries sharing at least one domain]
BLOCKS	Search...
Other Resources
ProtoNet	Search...

Entry information

Entry name

SUVH4_ARATH

Accession

Primary (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:	July 22, 2008
This is version 54 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)