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Protein

Histone-lysine N-methyltransferase family member SUVH9

Gene

SUVH9

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Histone methyltransferase family member that plays a role in gene silencing (PubMed:19043555, PubMed:24463519, PubMed:27171427). Together with MORC6 and SUVH2, regulates the silencing of some transposable elements (TEs) (PubMed:27171427). According to PubMed:19043555, the protein does not bind S-adenosyl-L-methionine and lacks methyltransferase activity. Instead, it may function downstream of DRM2 in RNA-directed DNA methylation, binding to methylated DNA and recruiting DNA-directed RNA polymerase V to chromatin (PubMed:24463519, PubMed:27171427).3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi434Zinc 11
Metal bindingi434Zinc 21
Metal bindingi436Zinc 11
Metal bindingi440Zinc 11
Metal bindingi440Zinc 31
Metal bindingi444Zinc 11
Metal bindingi446Zinc 21
Metal bindingi472Zinc 21
Metal bindingi472Zinc 31
Metal bindingi476Zinc 21
Metal bindingi478Zinc 31
Metal bindingi482Zinc 31

GO - Molecular functioni

GO - Biological processi

  • DNA mediated transformation Source: TAIR
  • RNA-directed DNA methylation Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Histone-lysine N-methyltransferase family member SUVH9
Alternative name(s):
Histone H3-K9 methyltransferase 9
Short name:
H3-K9-HMTase 9
Protein SET DOMAIN GROUP 22
Suppressor of variegation 3-9 homolog protein 9
Short name:
Su(var)3-9 homolog protein 9
Gene namesi
Name:SUVH9
Synonyms:SDG22, SET22
Ordered Locus Names:At4g13460
ORF Names:T6G15.10
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G13460.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Nucleus

Pathology & Biotechi

Disruption phenotypei

Impaired gene silencing due to decondensation of chromocenters leading to the derepression of DNA-methylated genes and transposable elements (TEs).1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001860801 – 650Histone-lysine N-methyltransferase family member SUVH9Add BLAST650

Proteomic databases

PaxDbiQ9T0G7.

Expressioni

Gene expression databases

ExpressionAtlasiQ9T0G7. baseline and differential.
GenevisibleiQ9T0G7. AT.

Interactioni

Subunit structurei

Component of an RNA-directed DNA methylation (RdDM) complex that contains at least MORC6, MORC1/CRT1, MORC2, SWI3D and SUVH9. Interacts directly with MORC6, MORC2 and MORC1/CRT1. Interacts with SWI3B, SWI3C and SWI3D (PubMed:27171427).2 Publications

Protein-protein interaction databases

STRINGi3702.AT4G13460.1.

Structurei

Secondary structure

1650
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi140 – 167Combined sources28
Helixi178 – 192Combined sources15
Beta strandi215 – 217Combined sources3
Helixi219 – 224Combined sources6
Beta strandi234 – 238Combined sources5
Beta strandi242 – 246Combined sources5
Beta strandi249 – 256Combined sources8
Beta strandi268 – 272Combined sources5
Helixi291 – 301Combined sources11
Beta strandi306 – 312Combined sources7
Beta strandi322 – 338Combined sources17
Beta strandi344 – 352Combined sources9
Helixi360 – 372Combined sources13
Helixi374 – 376Combined sources3
Beta strandi382 – 385Combined sources4
Beta strandi391 – 394Combined sources4
Beta strandi396 – 399Combined sources4
Helixi407 – 410Combined sources4
Beta strandi411 – 413Combined sources3
Helixi445 – 449Combined sources5
Turni450 – 452Combined sources3
Helixi487 – 489Combined sources3
Beta strandi495 – 499Combined sources5
Beta strandi501 – 511Combined sources11
Beta strandi518 – 521Combined sources4
Beta strandi525 – 527Combined sources3
Helixi529 – 537Combined sources9
Helixi545 – 547Combined sources3
Helixi551 – 553Combined sources3
Turni554 – 557Combined sources4
Turni560 – 562Combined sources3
Beta strandi580 – 582Combined sources3
Beta strandi584 – 587Combined sources4
Helixi589 – 592Combined sources4
Beta strandi600 – 609Combined sources10
Beta strandi617 – 624Combined sources8
Beta strandi633 – 635Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4NJ5X-ray2.40A134-650[»]
ProteinModelPortaliQ9T0G7.
SMRiQ9T0G7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini205 – 352YDGPROSITE-ProRule annotationAdd BLAST148
Domaini432 – 490Pre-SETPROSITE-ProRule annotationAdd BLAST59
Domaini493 – 637SETPROSITE-ProRule annotationAdd BLAST145

Domaini

Although both SET and pre-SET domains are present, the absence of the post-SET domain may explain the lack of methyltransferase activity. Besides, the Cys residues in the SET domain that normally bind a zinc ion are not conserved.
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.

Sequence similaritiesi

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

eggNOGiENOG410IN61. Eukaryota.
COG3440. LUCA.
HOGENOMiHOG000238382.
InParanoidiQ9T0G7.
KOiK11420.
OMAiYCAQRNG.
OrthoDBiEOG093603OW.
PhylomeDBiQ9T0G7.

Family and domain databases

Gene3Di2.30.280.10. 1 hit.
InterProiIPR025794. Hist-Lys_N-MeTrfase_plant.
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.
PROSITEiPS50867. 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.

Q9T0G7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGSSHIPLDP SLNPSPSLIP KLEPVTESTQ NLAFQLPNTN PQALISSAVS
60 70 80 90 100
DFNEATDFSS DYNTVAESAR SAFAQRLQRH DDVAVLDSLT GAIVPVEENP
110 120 130 140 150
EPEPNPYSTS DSSPSVATQR PRPQPRSSEL VRITDVGPES ERQFREHVRK
160 170 180 190 200
TRMIYDSLRM FLMMEEAKRN GVGGRRARAD GKAGKAGSMM RDCMLWMNRD
210 220 230 240 250
KRIVGSIPGV QVGDIFFFRF ELCVMGLHGH PQSGIDFLTG SLSSNGEPIA
260 270 280 290 300
TSVIVSGGYE DDDDQGDVIM YTGQGGQDRL GRQAEHQRLE GGNLAMERSM
310 320 330 340 350
YYGIEVRVIR GLKYENEVSS RVYVYDGLFR IVDSWFDVGK SGFGVFKYRL
360 370 380 390 400
ERIEGQAEMG SSVLKFARTL KTNPLSVRPR GYINFDISNG KENVPVYLFN
410 420 430 440 450
DIDSDQEPLY YEYLAQTSFP PGLFVQQSGN ASGCDCVNGC GSGCLCEAKN
460 470 480 490 500
SGEIAYDYNG TLIRQKPLIH ECGSACQCPP SCRNRVTQKG LRNRLEVFRS
510 520 530 540 550
LETGWGVRSL DVLHAGAFIC EYAGVALTRE QANILTMNGD TLVYPARFSS
560 570 580 590 600
ARWEDWGDLS QVLADFERPS YPDIPPVDFA MDVSKMRNVA CYISHSTDPN
610 620 630 640 650
VIVQFVLHDH NSLMFPRVML FAAENIPPMT ELSLDYGVVD DWNAKLAICN
Length:650
Mass (Da):72,174
Last modified:May 1, 2000 - v1
Checksum:iB2F291C5FA18A6E9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF344452 mRNA. Translation: AAK28974.1.
AL049656 Genomic DNA. Translation: CAB41104.1.
AL161536 Genomic DNA. Translation: CAB78388.1.
CP002687 Genomic DNA. Translation: AEE83282.1.
CP002687 Genomic DNA. Translation: AEE83283.1.
PIRiT06648.
RefSeqiNP_001031625.1. NM_001036548.2.
NP_193082.1. NM_117420.3.
UniGeneiAt.3118.

Genome annotation databases

EnsemblPlantsiAT4G13460.1; AT4G13460.1; AT4G13460.
AT4G13460.2; AT4G13460.2; AT4G13460.
GeneIDi826978.
GrameneiAT4G13460.1; AT4G13460.1; AT4G13460.
AT4G13460.2; AT4G13460.2; AT4G13460.
KEGGiath:AT4G13460.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF344452 mRNA. Translation: AAK28974.1.
AL049656 Genomic DNA. Translation: CAB41104.1.
AL161536 Genomic DNA. Translation: CAB78388.1.
CP002687 Genomic DNA. Translation: AEE83282.1.
CP002687 Genomic DNA. Translation: AEE83283.1.
PIRiT06648.
RefSeqiNP_001031625.1. NM_001036548.2.
NP_193082.1. NM_117420.3.
UniGeneiAt.3118.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4NJ5X-ray2.40A134-650[»]
ProteinModelPortaliQ9T0G7.
SMRiQ9T0G7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT4G13460.1.

Proteomic databases

PaxDbiQ9T0G7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G13460.1; AT4G13460.1; AT4G13460.
AT4G13460.2; AT4G13460.2; AT4G13460.
GeneIDi826978.
GrameneiAT4G13460.1; AT4G13460.1; AT4G13460.
AT4G13460.2; AT4G13460.2; AT4G13460.
KEGGiath:AT4G13460.

Organism-specific databases

TAIRiAT4G13460.

Phylogenomic databases

eggNOGiENOG410IN61. Eukaryota.
COG3440. LUCA.
HOGENOMiHOG000238382.
InParanoidiQ9T0G7.
KOiK11420.
OMAiYCAQRNG.
OrthoDBiEOG093603OW.
PhylomeDBiQ9T0G7.

Miscellaneous databases

PROiQ9T0G7.

Gene expression databases

ExpressionAtlasiQ9T0G7. baseline and differential.
GenevisibleiQ9T0G7. AT.

Family and domain databases

Gene3Di2.30.280.10. 1 hit.
InterProiIPR025794. Hist-Lys_N-MeTrfase_plant.
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.
PROSITEiPS50867. 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 nameiSUVH9_ARATH
AccessioniPrimary (citable) accession number: Q9T0G7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 9, 2003
Last sequence update: May 1, 2000
Last modified: November 30, 2016
This is version 119 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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.