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Protein

DNA (cytosine-5)-methyltransferase CMT3

Gene

CMT3

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

Functioni

Involved in the CpXpG methylation and in gene silencing. Methylates preferentially transposon-related sequences. Functionally redundant to DRM1/DRM2 to maintain non-CpG methylation. Involved in RNA-directed DNA methylation.4 Publications

Catalytic activityi

S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine.PROSITE-ProRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei460PROSITE-ProRule annotation1

GO - Molecular functioni

  • chromatin binding Source: InterPro
  • DNA (cytosine-5-)-methyltransferase activity Source: TAIR
  • DNA binding Source: UniProtKB-KW

GO - Biological processi

  • chromatin silencing Source: TAIR
  • DNA methylation Source: TAIR
  • DNA methylation on cytosine within a CNG sequence Source: TAIR
  • histone H3-K9 methylation Source: TAIR
  • negative regulation of gene expression, epigenetic Source: TAIR
  • transcription, DNA-templated Source: UniProtKB-KW
  • zygote asymmetric cytokinesis in embryo sac Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Methyltransferase, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BRENDAi2.1.1.37. 399.

Protein family/group databases

REBASEi4853. M.AthCMT3.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA (cytosine-5)-methyltransferase CMT3 (EC:2.1.1.37)
Alternative name(s):
Chromomethylase 3
Protein CHROMOMETHYLASE 3
Gene namesi
Name:CMT3
Ordered Locus Names:At1g69770
ORF Names:T6C23.3
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G69770.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi279G → E: Loss of activity. 1 Publication1
Mutagenesisi382F → A: Loss of binding to H3. 1 Publication1
Mutagenesisi456G → D: Loss of activity. 1 Publication1
Mutagenesisi465G → D: Loss of activity. 1 Publication1
Mutagenesisi470R → K in cmt3-10; partial loss of activity. 1 Publication1
Mutagenesisi541G → E in cmt3-6; loss of activity. 1 Publication1
Mutagenesisi542L → F: Loss of activity. 1 Publication1
Mutagenesisi683R → K: Loss of activity. 1 Publication1
Mutagenesisi724G → E in cmt3-4; loss of activity. 1 Publication1
Mutagenesisi733L → F: Loss of activity. 1 Publication1
Mutagenesisi748P → L: Loss of activity. 1 Publication1
Mutagenesisi763S → F in cmt3-8; partial loss of activity. 1 Publication1
Mutagenesisi769R → K in cmt3-3; loss of activity. 1 Publication1
Mutagenesisi807G → R: Loss of activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002466931 – 839DNA (cytosine-5)-methyltransferase CMT3Add BLAST839

Proteomic databases

PaxDbiQ94F88.
PRIDEiQ94F88.

Expressioni

Gene expression databases

GenevisibleiQ94F88. AT.

Interactioni

Subunit structurei

Homodimer. Interacts with HP1 and, through its chromodomain, with the N-terminal tail of histone H3 doubly methylated at 'Lys-9' and 'Lys-27'.2 Publications

Protein-protein interaction databases

BioGridi28534. 3 interactors.
DIPiDIP-60719N.
STRINGi3702.AT1G69770.1.

Structurei

3D structure databases

ProteinModelPortaliQ94F88.
SMRiQ94F88.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini108 – 227BAHPROSITE-ProRule annotationAdd BLAST120
Domaini269 – 813SAM-dependent MTase C5-typePROSITE-ProRule annotationAdd BLAST545
Domaini382 – 447ChromoPROSITE-ProRule annotationAdd BLAST66

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.PROSITE-ProRule annotation
Contains 1 BAH domain.PROSITE-ProRule annotation
Contains 1 chromo domain.PROSITE-ProRule annotation
Contains 1 SAM-dependent MTase C5-type domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG410IH5K. Eukaryota.
COG0270. LUCA.
HOGENOMiHOG000082844.
InParanoidiQ94F88.
KOiK00558.
OMAiHRPLELN.
OrthoDBiEOG0936054M.
PhylomeDBiQ94F88.

Family and domain databases

Gene3Di3.40.50.150. 2 hits.
InterProiIPR001025. BAH_dom.
IPR018117. C5_DNA_meth_AS.
IPR001525. C5_MeTfrase.
IPR000953. Chromo/shadow_dom.
IPR023780. Chromo_domain.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01426. BAH. 1 hit.
PF00385. Chromo. 1 hit.
PF00145. DNA_methylase. 1 hit.
[Graphical view]
PRINTSiPR00105. C5METTRFRASE.
SMARTiSM00439. BAH. 1 hit.
SM00298. CHROMO. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 4 hits.
SSF54160. SSF54160. 1 hit.
TIGRFAMsiTIGR00675. dcm. 1 hit.
PROSITEiPS51038. BAH. 1 hit.
PS00094. C5_MTASE_1. 1 hit.
PS00598. CHROMO_1. 1 hit.
PS50013. CHROMO_2. 1 hit.
PS51679. SAM_MT_C5. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q94F88-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAPKRKRPAT KDDTTKSIPK PKKRAPKRAK TVKEEPVTVV EEGEKHVARF
60 70 80 90 100
LDEPIPESEA KSTWPDRYKP IEVQPPKASS RKKTKDDEKV EIIRARCHYR
110 120 130 140 150
RAIVDERQIY ELNDDAYVQS GEGKDPFICK IIEMFEGANG KLYFTARWFY
160 170 180 190 200
RPSDTVMKEF EILIKKKRVF FSEIQDTNEL GLLEKKLNIL MIPLNENTKE
210 220 230 240 250
TIPATENCDF FCDMNYFLPY DTFEAIQQET MMAISESSTI SSDTDIREGA
260 270 280 290 300
AAISEIGECS QETEGHKKAT LLDLYSGCGA MSTGLCMGAQ LSGLNLVTKW
310 320 330 340 350
AVDMNAHACK SLQHNHPETN VRNMTAEDFL FLLKEWEKLC IHFSLRNSPN
360 370 380 390 400
SEEYANLHGL NNVEDNEDVS EESENEDDGE VFTVDKIVGI SFGVPKKLLK
410 420 430 440 450
RGLYLKVRWL NYDDSHDTWE PIEGLSNCRG KIEEFVKLGY KSGILPLPGG
460 470 480 490 500
VDVVCGGPPC QGISGHNRFR NLLDPLEDQK NKQLLVYMNI VEYLKPKFVL
510 520 530 540 550
MENVVDMLKM AKGYLARFAV GRLLQMNYQV RNGMMAAGAY GLAQFRLRFF
560 570 580 590 600
LWGALPSEII PQFPLPTHDL VHRGNIVKEF QGNIVAYDEG HTVKLADKLL
610 620 630 640 650
LKDVISDLPA VANSEKRDEI TYDKDPTTPF QKFIRLRKDE ASGSQSKSKS
660 670 680 690 700
KKHVLYDHHP LNLNINDYER VCQVPKRKGA NFRDFPGVIV GPGNVVKLEE
710 720 730 740 750
GKERVKLESG KTLVPDYALT YVDGKSCKPF GRLWWDEIVP TVVTRAEPHN
760 770 780 790 800
QVIIHPEQNR VLSIRENARL QGFPDDYKLF GPPKQKYIQV GNAVAVPVAK
810 820 830
ALGYALGTAF QGLAVGKDPL LTLPEGFAFM KPTLPSELA
Length:839
Mass (Da):94,905
Last modified:July 25, 2006 - v2
Checksum:iB1B4D5F7AE0A3AAC
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti138A → V in AAK71870 (PubMed:11349138).Curated1
Sequence conflicti165K → N in AAK71870 (PubMed:11349138).Curated1
Sequence conflicti166K → E in AAK69756 (PubMed:11459824).Curated1
Sequence conflicti266 – 268HKK → QKE in AAK71870 (PubMed:11349138).Curated3
Sequence conflicti433E → G in AAK71870 (PubMed:11349138).Curated1
Sequence conflicti821 – 822LT → II in AAK71870 (PubMed:11349138).Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC013289 Genomic DNA. Translation: AAG52543.1.
CP002684 Genomic DNA. Translation: AEE34973.1.
AF383170 Genomic DNA. Translation: AAK69756.1.
AF364174 Genomic DNA. Translation: AAK71870.1.
PIRiG96719.
RefSeqiNP_177135.1. NM_105645.4.
UniGeneiAt.35376.

Genome annotation databases

EnsemblPlantsiAT1G69770.1; AT1G69770.1; AT1G69770.
GeneIDi843313.
GrameneiAT1G69770.1; AT1G69770.1; AT1G69770.
KEGGiath:AT1G69770.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC013289 Genomic DNA. Translation: AAG52543.1.
CP002684 Genomic DNA. Translation: AEE34973.1.
AF383170 Genomic DNA. Translation: AAK69756.1.
AF364174 Genomic DNA. Translation: AAK71870.1.
PIRiG96719.
RefSeqiNP_177135.1. NM_105645.4.
UniGeneiAt.35376.

3D structure databases

ProteinModelPortaliQ94F88.
SMRiQ94F88.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi28534. 3 interactors.
DIPiDIP-60719N.
STRINGi3702.AT1G69770.1.

Protein family/group databases

REBASEi4853. M.AthCMT3.

Proteomic databases

PaxDbiQ94F88.
PRIDEiQ94F88.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G69770.1; AT1G69770.1; AT1G69770.
GeneIDi843313.
GrameneiAT1G69770.1; AT1G69770.1; AT1G69770.
KEGGiath:AT1G69770.

Organism-specific databases

TAIRiAT1G69770.

Phylogenomic databases

eggNOGiENOG410IH5K. Eukaryota.
COG0270. LUCA.
HOGENOMiHOG000082844.
InParanoidiQ94F88.
KOiK00558.
OMAiHRPLELN.
OrthoDBiEOG0936054M.
PhylomeDBiQ94F88.

Enzyme and pathway databases

BRENDAi2.1.1.37. 399.

Miscellaneous databases

PROiQ94F88.

Gene expression databases

GenevisibleiQ94F88. AT.

Family and domain databases

Gene3Di3.40.50.150. 2 hits.
InterProiIPR001025. BAH_dom.
IPR018117. C5_DNA_meth_AS.
IPR001525. C5_MeTfrase.
IPR000953. Chromo/shadow_dom.
IPR023780. Chromo_domain.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01426. BAH. 1 hit.
PF00385. Chromo. 1 hit.
PF00145. DNA_methylase. 1 hit.
[Graphical view]
PRINTSiPR00105. C5METTRFRASE.
SMARTiSM00439. BAH. 1 hit.
SM00298. CHROMO. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 4 hits.
SSF54160. SSF54160. 1 hit.
TIGRFAMsiTIGR00675. dcm. 1 hit.
PROSITEiPS51038. BAH. 1 hit.
PS00094. C5_MTASE_1. 1 hit.
PS00598. CHROMO_1. 1 hit.
PS50013. CHROMO_2. 1 hit.
PS51679. SAM_MT_C5. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCMT3_ARATH
AccessioniPrimary (citable) accession number: Q94F88
Secondary accession number(s): Q94FN4, Q9C9L8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 25, 2006
Last sequence update: July 25, 2006
Last modified: November 30, 2016
This is version 109 of the entry and version 2 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.