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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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei460 – 4601PROSITE-ProRule annotation

GO - Molecular functioni

  1. chromatin binding Source: InterPro
  2. DNA (cytosine-5-)-methyltransferase activity Source: TAIR
  3. DNA binding Source: UniProtKB-KW

GO - Biological processi

  1. C-5 methylation of cytosine Source: GOC
  2. chromatin silencing Source: TAIR
  3. DNA methylation Source: TAIR
  4. DNA methylation on cytosine within a CNG sequence Source: TAIR
  5. histone H3-K9 methylation Source: TAIR
  6. negative regulation of gene expression, epigenetic Source: TAIR
  7. transcription, DNA-templated Source: UniProtKB-KW
  8. 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

BioCyciARA:AT1G69770-MONOMER.
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
ProteomesiUP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G69770.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi279 – 2791G → E: Loss of activity. 1 Publication
Mutagenesisi382 – 3821F → A: Loss of binding to H3. 1 Publication
Mutagenesisi456 – 4561G → D: Loss of activity. 1 Publication
Mutagenesisi465 – 4651G → D: Loss of activity. 1 Publication
Mutagenesisi470 – 4701R → K in cmt3-10; partial loss of activity. 1 Publication
Mutagenesisi541 – 5411G → E in cmt3-6; loss of activity. 1 Publication
Mutagenesisi542 – 5421L → F: Loss of activity. 1 Publication
Mutagenesisi683 – 6831R → K: Loss of activity. 1 Publication
Mutagenesisi724 – 7241G → E in cmt3-4; loss of activity. 1 Publication
Mutagenesisi733 – 7331L → F: Loss of activity. 1 Publication
Mutagenesisi748 – 7481P → L: Loss of activity. 1 Publication
Mutagenesisi763 – 7631S → F in cmt3-8; partial loss of activity. 1 Publication
Mutagenesisi769 – 7691R → K in cmt3-3; loss of activity. 1 Publication
Mutagenesisi807 – 8071G → R: Loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 839839DNA (cytosine-5)-methyltransferase CMT3PRO_0000246693Add
BLAST

Proteomic databases

PaxDbiQ94F88.
PRIDEiQ94F88.

Expressioni

Gene expression databases

ExpressionAtlasiQ94F88. baseline and differential.
GenevestigatoriQ94F88.

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. 1 interaction.
DIPiDIP-60719N.

Structurei

3D structure databases

ProteinModelPortaliQ94F88.
SMRiQ94F88. Positions 46-827.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini108 – 227120BAHPROSITE-ProRule annotationAdd
BLAST
Domaini269 – 813545SAM-dependent MTase C5-typePROSITE-ProRule annotationAdd
BLAST
Domaini382 – 44766ChromoPROSITE-ProRule annotationAdd
BLAST

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

eggNOGiCOG0270.
HOGENOMiHOG000082844.
InParanoidiQ94F88.
KOiK00558.
OMAiHRPLELN.
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.
[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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti138 – 1381A → V in AAK71870 (PubMed:11349138).Curated
Sequence conflicti165 – 1651K → N in AAK71870 (PubMed:11349138).Curated
Sequence conflicti166 – 1661K → E in AAK69756 (PubMed:11459824).Curated
Sequence conflicti266 – 2683HKK → QKE in AAK71870 (PubMed:11349138).Curated
Sequence conflicti433 – 4331E → G in AAK71870 (PubMed:11349138).Curated
Sequence conflicti821 – 8222LT → II in AAK71870 (PubMed:11349138).Curated

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_105645.3.
UniGeneiAt.35376.

Genome annotation databases

EnsemblPlantsiAT1G69770.1; AT1G69770.1; AT1G69770.
GeneIDi843313.
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_105645.3.
UniGeneiAt.35376.

3D structure databases

ProteinModelPortaliQ94F88.
SMRiQ94F88. Positions 46-827.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi28534. 1 interaction.
DIPiDIP-60719N.

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.
KEGGiath:AT1G69770.

Organism-specific databases

TAIRiAT1G69770.

Phylogenomic databases

eggNOGiCOG0270.
HOGENOMiHOG000082844.
InParanoidiQ94F88.
KOiK00558.
OMAiHRPLELN.
PhylomeDBiQ94F88.

Enzyme and pathway databases

BioCyciARA:AT1G69770-MONOMER.
BRENDAi2.1.1.37. 399.

Gene expression databases

ExpressionAtlasiQ94F88. baseline and differential.
GenevestigatoriQ94F88.

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.
[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...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene."
    Bartee L., Malagnac F., Bender J.
    Genes Dev. 15:1753-1758(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF GLY-279; GLY-456; GLY-465; LEU-542; ARG-683; LEU-733; PRO-748 AND GLY-807, FUNCTION.
    Strain: cv. Wassilewskija.
  4. "Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation."
    Lindroth A.M., Cao X., Jackson J.P., Zilberman D., McCallum C.M., Henikoff S., Jacobsen S.E.
    Science 292:2077-2080(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF ARG-470; GLY-541; GLY-724; SER-763 AND ARG-769, FUNCTION.
    Strain: cv. Landsberg erecta.
  5. "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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH H3, MUTAGENESIS OF PHE-382.
  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(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HP1.
  7. "Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3."
    Tompa R., McCallum C.M., Delrow J., Henikoff J.G., van Steensel B., Henikoff S.
    Curr. Biol. 12:65-68(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation."
    Cao X., Aufsatz W., Zilberman D., Mette M.F., Huang M.S., Matzke M., Jacobsen S.E.
    Curr. Biol. 13:2212-2217(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

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: April 1, 2015
This is version 97 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

External Data

Dasty 3

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 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.