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Protein

Histone-lysine N-methyltransferase family member SUVH2

Gene

SUVH2

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 central role in gene silencing (PubMed:15775980, PubMed:16384625, PubMed:19043555, PubMed:24463519, PubMed:27171427). Together with MORC6 and SUVH9, regulates the silencing of some transposable elements (TEs) (PubMed:27171427). According to PubMed:15775980, it is required for normal methylation of 'Lys-9' and 'Lys-27' of histone H3, 'Lys-20' of H4, and cytosine, but PubMed:19043555 see no significant effect on histone methylation when the gene is mutated. 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).5 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi436Zinc 1By similarity1
Metal bindingi436Zinc 2By similarity1
Metal bindingi438Zinc 1By similarity1
Metal bindingi442Zinc 1By similarity1
Metal bindingi442Zinc 3By similarity1
Metal bindingi446Zinc 1By similarity1
Metal bindingi448Zinc 2By similarity1
Metal bindingi474Zinc 2By similarity1
Metal bindingi474Zinc 3By similarity1
Metal bindingi478Zinc 2By similarity1
Metal bindingi480Zinc 3By similarity1
Metal bindingi484Zinc 3By similarity1

GO - Molecular functioni

GO - Biological processi

  • histone methylation Source: TAIR
  • regulation of gene expression, epigenetic 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 SUVH2
Alternative name(s):
Cytosine-HMTase 2
H3-K27-HMTase 2
H4-K20-HMTase 2
Histone H3-K9 methyltransferase 2
Short name:
H3-K9-HMTase 2
Protein SET DOMAIN GROUP 3
Suppressor of variegation 3-9 homolog protein 2
Short name:
Su(var)3-9 homolog protein 2
Gene namesi
Name:SUVH2
Synonyms:SDG3, SET3
Ordered Locus Names:At2g33290
ORF Names:F4P9.6
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G33290.

Subcellular locationi

GO - Cellular componenti

  • chromosome, centromeric region Source: UniProtKB-SubCell
  • nuclear heterochromatin Source: TAIR
  • nucleus Source: TAIR
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

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi143E → D in 5-1; ectopic nuclear localization. 1 Publication1
Mutagenesisi351R → K in 5-2; loss of 5-methylcytosine, H3K9 dimethylation and H4K20 monomethylation. 1 Publication1
Mutagenesisi385V → A in 5-3; loss of 5-methylcytosine, H3K9 dimethylation and H4K20 monomethylation. 1 Publication1
Mutagenesisi411R → I in 5-4; loss of H3K9 and H4K20 methylation. 1 Publication1
Mutagenesisi584V → G in 5-5; loss of H3K9 and H4K20 methylation. 1 Publication1
Mutagenesisi620M → T in 5-6; loss of H3K9 and H4K20 methylation; when associated with T-630. 1 Publication1
Mutagenesisi630L → V in 5-6; loss of H3K9 and H4K20 methylation; when associated with V-620. 1 Publication1
Mutagenesisi645G → S in 5-7; loss of H3K9 and H4K20 methylation. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001860731 – 651Histone-lysine N-methyltransferase family member SUVH2Add BLAST651

Proteomic databases

PaxDbiO22781.

Expressioni

Tissue specificityi

Expressed at low levels in leaves stems and flowers.1 Publication

Gene expression databases

GenevisibleiO22781. AT.

Interactioni

Subunit structurei

Self-interacts (PubMed:24465213). Interacts with DNA-directed RNA polymerase V subunit NRPE1 and with DRD1 and DMS3 (PubMed:24463519, PubMed:24465213). Binds to MORC1/CRT1 (PubMed:24465213).2 Publications

Protein-protein interaction databases

DIPiDIP-62059N.
STRINGi3702.AT2G33290.1.

Structurei

3D structure databases

ProteinModelPortaliO22781.
SMRiO22781.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini202 – 358YDGPROSITE-ProRule annotationAdd BLAST157
Domaini434 – 492Pre-SETPROSITE-ProRule annotationAdd BLAST59
Domaini495 – 638SETPROSITE-ProRule annotationAdd BLAST144

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.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 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.
InParanoidiO22781.
KOiK11420.
OrthoDBiEOG093603OW.
PhylomeDBiO22781.

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.

O22781-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTLLPFPDL NLMPDSQSST AGTTAGDTVV TGKLEVKSEP IEEWQTPPSS
60 70 80 90 100
TSDQSANTDL IAEFIRISEL FRSAFKPLQV KGLDGVSVYG LDSGAIVAVP
110 120 130 140 150
EKENRELIEP PPGFKDNRVS TVVVSPKFER PRELARIAIL GHEQRKELRQ
160 170 180 190 200
VMKRTRMTYE SLRIHLMAES MKNHVLGQGR RRRSDMAAAY IMRDRGLWLN
210 220 230 240 250
YDKHIVGPVT GVEVGDIFFY RMELCVLGLH GQTQAGIDCL TAERSATGEP
260 270 280 290 300
IATSIVVSGG YEDDEDTGDV LVYTGHGGQD HQHKQCDNQR LVGGNLGMER
310 320 330 340 350
SMHYGIEVRV IRGIKYENSI SSKVYVYDGL YKIVDWWFAV GKSGFGVFKF
360 370 380 390 400
RLVRIEGQPM MGSAVMRFAQ TLRNKPSMVR PTGYVSFDLS NKKENVPVFL
410 420 430 440 450
YNDVDGDQEP RHYEYIAKAV FPPGIFGQGG ISRTGCECKL SCTDDCLCAR
460 470 480 490 500
KNGGEFAYDD NGHLLKGKHV VFECGEFCTC GPSCKSRVTQ KGLRNRLEVF
510 520 530 540 550
RSKETGWGVR TLDLIEAGAF ICEYAGVVVT RLQAEILSMN GDVMVYPGRF
560 570 580 590 600
TDQWRNWGDL SQVYPDFVRP NYPSLPPLDF SMDVSRMRNV ACYISHSKEP
610 620 630 640 650
NVMVQFVLHD HNHLMFPRVM LFALENISPL AELSLDYGLA DEVNGKLAIC

N
Length:651
Mass (Da):72,848
Last modified:January 1, 1998 - v1
Checksum:i412AD76C8869ACF9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF344445 mRNA. Translation: AAK28967.1.
AC002332 Genomic DNA. Translation: AAB80647.1.
CP002685 Genomic DNA. Translation: AEC08810.1.
PIRiF84743.
RefSeqiNP_180887.1. NM_128889.3.
UniGeneiAt.12115.

Genome annotation databases

EnsemblPlantsiAT2G33290.1; AT2G33290.1; AT2G33290.
GeneIDi817892.
GrameneiAT2G33290.1; AT2G33290.1; AT2G33290.
KEGGiath:AT2G33290.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF344445 mRNA. Translation: AAK28967.1.
AC002332 Genomic DNA. Translation: AAB80647.1.
CP002685 Genomic DNA. Translation: AEC08810.1.
PIRiF84743.
RefSeqiNP_180887.1. NM_128889.3.
UniGeneiAt.12115.

3D structure databases

ProteinModelPortaliO22781.
SMRiO22781.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-62059N.
STRINGi3702.AT2G33290.1.

Proteomic databases

PaxDbiO22781.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G33290.1; AT2G33290.1; AT2G33290.
GeneIDi817892.
GrameneiAT2G33290.1; AT2G33290.1; AT2G33290.
KEGGiath:AT2G33290.

Organism-specific databases

TAIRiAT2G33290.

Phylogenomic databases

eggNOGiKOG1082. Eukaryota.
COG2940. LUCA.
COG3440. LUCA.
HOGENOMiHOG000238382.
InParanoidiO22781.
KOiK11420.
OrthoDBiEOG093603OW.
PhylomeDBiO22781.

Miscellaneous databases

PROiO22781.

Gene expression databases

GenevisibleiO22781. 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 nameiSUVH2_ARATH
AccessioniPrimary (citable) accession number: O22781
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 9, 2003
Last sequence update: January 1, 1998
Last modified: November 30, 2016
This is version 124 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

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. 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.