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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

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].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
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-KW
  2. nucleus Source: UniProtKB-KW
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 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

Secondary structure

1
624
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi101 – 12121Combined sources
Helixi127 – 13711Combined sources
Beta strandi159 – 1624Combined sources
Helixi163 – 1686Combined sources
Beta strandi170 – 1723Combined sources
Beta strandi178 – 1825Combined sources
Helixi184 – 1863Combined sources
Turni187 – 1926Combined sources
Beta strandi197 – 2037Combined sources
Beta strandi211 – 2133Combined sources
Beta strandi216 – 2205Combined sources
Beta strandi222 – 2254Combined sources
Beta strandi227 – 2304Combined sources
Beta strandi239 – 2413Combined sources
Helixi242 – 25211Combined sources
Beta strandi256 – 2638Combined sources
Beta strandi271 – 28818Combined sources
Beta strandi292 – 30211Combined sources
Beta strandi304 – 3063Combined sources
Beta strandi331 – 3344Combined sources
Beta strandi336 – 3394Combined sources
Beta strandi341 – 3433Combined sources
Turni358 – 3614Combined sources
Beta strandi386 – 3883Combined sources
Turni392 – 3943Combined sources
Helixi396 – 4005Combined sources
Beta strandi406 – 4105Combined sources
Beta strandi420 – 4234Combined sources
Helixi436 – 4416Combined sources
Beta strandi448 – 4525Combined sources
Beta strandi454 – 4563Combined sources
Beta strandi458 – 4647Combined sources
Beta strandi471 – 4744Combined sources
Beta strandi477 – 4815Combined sources
Helixi482 – 4843Combined sources
Beta strandi494 – 4963Combined sources
Beta strandi536 – 5394Combined sources
Beta strandi541 – 5444Combined sources
Helixi546 – 5494Combined sources
Beta strandi557 – 56711Combined sources
Helixi570 – 5723Combined sources
Beta strandi574 – 5818Combined sources
Beta strandi603 – 6053Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4QENX-ray2.00A93-624[»]
4QEOX-ray2.00A93-624[»]
4QEPX-ray3.10A93-624[»]
ProteinModelPortaliQ8GZB6.
SMRiQ8GZB6. Positions 99-624.
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

        10         20         30         40         50
MAGKRKRANA PDQTERRSSV RVQKVRQKAL DEKARLVQER VKLLSDRKSE
60 70 80 90 100
ICVDDTELHE KEEENVDGSP KRRSPPKLTA MQKGKQKLSV SLNGKDVNLE
110 120 130 140 150
PHLKVTKCLR LFNKQYLLCV QAKLSRPDLK GVTEMIKAKA ILYPRKIIGD
160 170 180 190 200
LPGIDVGHRF FSRAEMCAVG FHNHWLNGID YMSMEYEKEY SNYKLPLAVS
210 220 230 240 250
IVMSGQYEDD LDNADTVTYT GQGGHNLTGN KRQIKDQLLE RGNLALKHCC
260 270 280 290 300
EYNVPVRVTR GHNCKSSYTK RVYTYDGLYK VEKFWAQKGV SGFTVYKYRL
310 320 330 340 350
KRLEGQPELT TDQVNFVAGR IPTSTSEIEG LVCEDISGGL EFKGIPATNR
360 370 380 390 400
VDDSPVSPTS GFTYIKSLII EPNVIIPKSS TGCNCRGSCT DSKKCACAKL
410 420 430 440 450
NGGNFPYVDL NDGRLIESRD VVFECGPHCG CGPKCVNRTS QKRLRFNLEV
460 470 480 490 500
FRSAKKGWAV RSWEYIPAGS PVCEYIGVVR RTADVDTISD NEYIFEIDCQ
510 520 530 540 550
QTMQGLGGRQ RRLRDVAVPM NNGVSQSSED ENAPEFCIDA GSTGNFARFI
560 570 580 590 600
NHSCEPNLFV QCVLSSHQDI RLARVVLFAA DNISPMQELT YDYGYALDSV
610 620
HGPDGKVKQL ACYCGALNCR KRLY
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4QEN X-ray 2.00 A 93-624 [» ]
4QEO X-ray 2.00 A 93-624 [» ]
4QEP X-ray 3.10 A 93-624 [» ]
ProteinModelPortali Q8GZB6.
SMRi Q8GZB6. Positions 99-624.
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: November 26, 2014
This is version 106 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

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