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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: 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)DescriptionActionsGraphical viewLength
Metal bindingi383Zinc 1By similarity1
Metal bindingi383Zinc 2By similarity1
Metal bindingi385Zinc 1By similarity1
Metal bindingi389Zinc 1By similarity1
Metal bindingi389Zinc 3By similarity1
Metal bindingi395Zinc 1By similarity1
Metal bindingi397Zinc 2By similarity1
Metal bindingi425Zinc 2By similarity1
Metal bindingi425Zinc 3By similarity1
Metal bindingi429Zinc 2By similarity1
Metal bindingi431Zinc 3By similarity1
Metal bindingi435Zinc 3By similarity1
Binding sitei493S-adenosyl-L-methioninePROSITE-ProRule annotation1
Binding sitei548S-adenosyl-L-methioninePROSITE-ProRule annotation1
Metal bindingi554Zinc 4By similarity1
Metal bindingi612Zinc 4By similarity1
Metal bindingi614Zinc 4By similarity1
Metal bindingi619Zinc 4By similarity1

GO - Molecular functioni

  • double-stranded methylated DNA binding Source: TAIR
  • histone methyltransferase activity (H3-K9 specific) Source: TAIR
  • methyl-CpG binding Source: TAIR
  • methyl-CpNpG binding Source: TAIR
  • methyl-CpNpN binding Source: TAIR
  • zinc ion binding Source: InterPro

GO - Biological processi

  • histone H3-K9 methylation Source: TAIR
  • histone methylation Source: TAIR
  • maintenance of DNA methylation Source: TAIR
  • 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
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G13960.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001860751 – 624Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4Add BLAST624

Proteomic databases

PaxDbiQ8GZB6.

PTM databases

iPTMnetiQ8GZB6.

Expressioni

Tissue specificityi

Expressed in leaves stems and flowers.1 Publication

Gene expression databases

GenevisibleiQ8GZB6. AT.

Interactioni

Subunit structurei

Interacts with H3 histone.

Protein-protein interaction databases

BioGridi16522. 1 interactor.
DIPiDIP-62058N.
STRINGi3702.AT5G13960.1.

Structurei

Secondary structure

1624
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi101 – 121Combined sources21
Helixi127 – 137Combined sources11
Beta strandi159 – 162Combined sources4
Helixi163 – 168Combined sources6
Beta strandi170 – 172Combined sources3
Beta strandi178 – 182Combined sources5
Helixi184 – 186Combined sources3
Turni187 – 192Combined sources6
Beta strandi197 – 203Combined sources7
Beta strandi211 – 213Combined sources3
Beta strandi216 – 220Combined sources5
Beta strandi222 – 225Combined sources4
Beta strandi227 – 230Combined sources4
Beta strandi239 – 241Combined sources3
Helixi242 – 252Combined sources11
Beta strandi256 – 263Combined sources8
Beta strandi271 – 288Combined sources18
Beta strandi292 – 302Combined sources11
Beta strandi304 – 306Combined sources3
Beta strandi331 – 334Combined sources4
Beta strandi336 – 339Combined sources4
Beta strandi341 – 343Combined sources3
Turni358 – 361Combined sources4
Beta strandi386 – 388Combined sources3
Turni392 – 394Combined sources3
Helixi396 – 400Combined sources5
Beta strandi406 – 410Combined sources5
Beta strandi420 – 423Combined sources4
Helixi436 – 441Combined sources6
Beta strandi448 – 452Combined sources5
Beta strandi454 – 456Combined sources3
Beta strandi458 – 464Combined sources7
Beta strandi471 – 474Combined sources4
Beta strandi477 – 481Combined sources5
Helixi482 – 484Combined sources3
Beta strandi494 – 496Combined sources3
Beta strandi536 – 539Combined sources4
Beta strandi541 – 544Combined sources4
Helixi546 – 549Combined sources4
Beta strandi557 – 567Combined sources11
Helixi570 – 572Combined sources3
Beta strandi574 – 581Combined sources8
Beta strandi603 – 605Combined sources3

3D structure databases

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

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini149 – 302YDGPROSITE-ProRule annotationAdd BLAST154
Domaini381 – 443Pre-SETPROSITE-ProRule annotationAdd BLAST63
Domaini446 – 594SETPROSITE-ProRule annotationAdd BLAST149
Domaini608 – 624Post-SETPROSITE-ProRule annotationAdd BLAST17

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni456 – 458S-adenosyl-L-methionine bindingBy similarity3
Regioni551 – 552S-adenosyl-L-methionine bindingBy similarity2

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

eggNOGiKOG1082. Eukaryota.
COG2940. LUCA.
COG3440. LUCA.
HOGENOMiHOG000238382.
InParanoidiQ8GZB6.
KOiK11420.
OMAiDTELHEK.
OrthoDBiEOG09360A66.
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]
SMARTiSM00468. PreSET. 1 hit.
SM00317. SET. 1 hit.
SM00466. SRA. 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)DescriptionActionsGraphical viewLength
Sequence conflicti189E → D in AAO17392 (PubMed:12486005).Curated1
Sequence conflicti548R → T in AAK28969 (PubMed:11691919).Curated1
Sequence conflicti576V → A in AAK28969 (PubMed:11691919).Curated1

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_121399.3.
UniGeneiAt.8330.

Genome annotation databases

EnsemblPlantsiAT5G13960.1; AT5G13960.1; AT5G13960.
GeneIDi831244.
GrameneiAT5G13960.1; AT5G13960.1; AT5G13960.
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.
RefSeqiNP_196900.1. NM_121399.3.
UniGeneiAt.8330.

3D structure databases

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

Protein-protein interaction databases

BioGridi16522. 1 interactor.
DIPiDIP-62058N.
STRINGi3702.AT5G13960.1.

PTM databases

iPTMnetiQ8GZB6.

Proteomic databases

PaxDbiQ8GZB6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G13960.1; AT5G13960.1; AT5G13960.
GeneIDi831244.
GrameneiAT5G13960.1; AT5G13960.1; AT5G13960.
KEGGiath:AT5G13960.

Organism-specific databases

TAIRiAT5G13960.

Phylogenomic databases

eggNOGiKOG1082. Eukaryota.
COG2940. LUCA.
COG3440. LUCA.
HOGENOMiHOG000238382.
InParanoidiQ8GZB6.
KOiK11420.
OMAiDTELHEK.
OrthoDBiEOG09360A66.
PhylomeDBiQ8GZB6.

Enzyme and pathway databases

BioCyciARA:AT5G13960-MONOMER.

Miscellaneous databases

PROiQ8GZB6.

Gene expression databases

GenevisibleiQ8GZB6. AT.

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]
SMARTiSM00468. PreSET. 1 hit.
SM00317. SET. 1 hit.
SM00466. SRA. 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]
ProtoNetiSearch...

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 30, 2016
This is version 120 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.