Reviewed, UniProtKB/Swiss-Prot Q94F88 (CMT3_ARATH)

Names and origin

Protein names

Recommended name:
    DNA (cytosine-5)-methyltransferase CMT3
    EC=2.1.1.37
Alternative name(s):
    Chromomethylase 3
    Protein CHROMOMETHYLASE 3

Gene names

Name:	CMT3
Ordered Locus Names:	At1g69770
ORF Names:	T6C23.3

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	839 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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. Ref.2 Ref.3 Ref.6 Ref.7
Catalytic activity	S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine.
Subunit structure	Homodimer. Interacts with HP1 and, through its chromodomain, with the N-terminal tail of histone H3 doubly methylated at 'Lys-9' and 'Lys-27'. Ref.4 Ref.5
Subcellular location	Nucleus By similarity.
Sequence similarities	Belongs to the C5-methyltransferase family. Contains 1 BAH domain. Contains 1 chromo domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Ligand	DNA-binding S-adenosyl-L-methionine
Molecular function	Chromatin regulator Methyltransferase Transferase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	DNA methylation on cytosine within a CNG sequence Ref.3 Inferred from mutant phenotype. Source: TAIR chromatin assembly or disassembly Inferred from electronic annotation. Source: InterPro chromatin silencing Ref.3 Inferred from genetic interaction. Source: TAIR histone H3-K9 methylation Inferred from genetic interaction. Source: TAIR transcription Inferred from electronic annotation. Source: UniProtKB-KW zygote asymmetric cytokinesis in the embryo sac Inferred from mutant phenotype. Source: TAIR
Cellular component	chromatin Inferred from electronic annotation. Source: InterPro nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	DNA (cytosine-5-)-methyltransferase activity Ref.2 Inferred from mutant phenotype. Source: TAIR DNA binding Inferred from electronic annotation. Source: UniProtKB-KW chromatin binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 839	839	DNA (cytosine-5)-methyltransferase CMT3		PRO_0000246693
Regions
	Domain	108 – 227	120	BAH
	Domain	382 – 447	66	Chromo
Experimental info
	Mutagenesis	279	1	G → E: Loss of activity. Ref.2
	Mutagenesis	382	1	F → A: Loss of binding to H3. Ref.4
	Mutagenesis	456	1	G → D: Loss of activity. Ref.2
	Mutagenesis	465	1	G → D: Loss of activity. Ref.2
	Mutagenesis	470	1	R → K in cmt3-10; partial loss of activity. Ref.3
	Mutagenesis	541	1	G → E in cmt3-6; loss of activity. Ref.3
	Mutagenesis	542	1	L → F: Loss of activity. Ref.2
	Mutagenesis	683	1	R → K: Loss of activity. Ref.2
	Mutagenesis	724	1	G → E in cmt3-4; loss of activity. Ref.3
	Mutagenesis	733	1	L → F: Loss of activity. Ref.2
	Mutagenesis	748	1	P → L: Loss of activity. Ref.2
	Mutagenesis	763	1	S → F in cmt3-8; partial loss of activity. Ref.3
	Mutagenesis	769	1	R → K in cmt3-3; loss of activity. Ref.3
	Mutagenesis	807	1	G → R: Loss of activity. Ref.2
	Sequence conflict	138	1	A → V in AAK71870. Ref.3
	Sequence conflict	165	1	K → N in AAK71870. Ref.3
	Sequence conflict	166	1	K → E in AAK69756. Ref.2
	Sequence conflict	266 – 268	3	HKK → QKE in AAK71870. Ref.3
	Sequence conflict	433	1	E → G in AAK71870. Ref.3
	Sequence conflict	821 – 822	2	LT → II in AAK71870. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	Q94F88-1 [UniParc]. Last modified July 25, 2006. Version 2. Checksum: B1B4D5F7AE0A3AAC	FASTA	839	94,905
	10 20 30 40 50 60 MAPKRKRPAT KDDTTKSIPK PKKRAPKRAK TVKEEPVTVV EEGEKHVARF LDEPIPESEA 70 80 90 100 110 120 KSTWPDRYKP IEVQPPKASS RKKTKDDEKV EIIRARCHYR RAIVDERQIY ELNDDAYVQS 130 140 150 160 170 180 GEGKDPFICK IIEMFEGANG KLYFTARWFY RPSDTVMKEF EILIKKKRVF FSEIQDTNEL 190 200 210 220 230 240 GLLEKKLNIL MIPLNENTKE TIPATENCDF FCDMNYFLPY DTFEAIQQET MMAISESSTI 250 260 270 280 290 300 SSDTDIREGA AAISEIGECS QETEGHKKAT LLDLYSGCGA MSTGLCMGAQ LSGLNLVTKW 310 320 330 340 350 360 AVDMNAHACK SLQHNHPETN VRNMTAEDFL FLLKEWEKLC IHFSLRNSPN SEEYANLHGL 370 380 390 400 410 420 NNVEDNEDVS EESENEDDGE VFTVDKIVGI SFGVPKKLLK RGLYLKVRWL NYDDSHDTWE 430 440 450 460 470 480 PIEGLSNCRG KIEEFVKLGY KSGILPLPGG VDVVCGGPPC QGISGHNRFR NLLDPLEDQK 490 500 510 520 530 540 NKQLLVYMNI VEYLKPKFVL MENVVDMLKM AKGYLARFAV GRLLQMNYQV RNGMMAAGAY 550 560 570 580 590 600 GLAQFRLRFF LWGALPSEII PQFPLPTHDL VHRGNIVKEF QGNIVAYDEG HTVKLADKLL 610 620 630 640 650 660 LKDVISDLPA VANSEKRDEI TYDKDPTTPF QKFIRLRKDE ASGSQSKSKS KKHVLYDHHP 670 680 690 700 710 720 LNLNINDYER VCQVPKRKGA NFRDFPGVIV GPGNVVKLEE GKERVKLESG KTLVPDYALT 730 740 750 760 770 780 YVDGKSCKPF GRLWWDEIVP TVVTRAEPHN QVIIHPEQNR VLSIRENARL QGFPDDYKLF 790 800 810 820 830 GPPKQKYIQV GNAVAVPVAK ALGYALGTAF QGLAVGKDPL LTLPEGFAFM KPTLPSELA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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(2000) [PubMed: 11130712] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[2]	"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(2001) [PubMed: 11459824] [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.
[3]	"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(2001) [PubMed: 11349138] [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.
[4]	"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(2004) [PubMed: 15457214] [Abstract] Cited for: INTERACTION WITH H3, MUTAGENESIS OF PHE-382.
[5]	"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(2002) [PubMed: 11898023] [Abstract] Cited for: INTERACTION WITH HP1.
[6]	"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(2002) [PubMed: 11790305] [Abstract] Cited for: FUNCTION.
[7]	"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(2003) [PubMed: 14680640] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AC013289 Genomic DNA. Translation: AAG52543.1. AF383170 Genomic DNA. Translation: AAK69756.1. AF364174 Genomic DNA. Translation: AAK71870.1.
IPI	IPI00534552.
PIR	G96719.
RefSeq	NP_177135.1.
UniGene	At.35376
3D structure databases
HSSP	HSSP built from PDB template 1G55 based on UniProtKB O14717.
ModBase	Search...
Protein-protein interaction databases
STRING	Q94F88.
Proteomic databases
PRIDE	Q94F88.
Genome annotation databases
GeneID	843313.
GenomeReviews	Gene locus AT1G69770 in contig CT485782_GR.
KEGG	ath:AT1G69770.
NMPDR	fig|3702.1.peg.6449.
Organism-specific databases
TAIR	At1g69770.
Phylogenomic databases
OMA	HRPLELN.
Enzyme and pathway databases
BRENDA	2.1.1.37. 302.
Gene expression databases
Genevestigator	Q94F88.
GermOnline	AT1G69770. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR001025. BAH. IPR001525. C5_DNA_meth. IPR018117. C5_DNA_meth_AS. IPR000953. Chromodomain. [Graphical view]
PANTHER	PTHR10629. C5_DNA_meth. 1 hit.
Pfam	PF01426. BAH. 1 hit. PF00385. Chromo. 1 hit. PF00145. DNA_methylase. 1 hit. [Graphical view]
PRINTS	PR00105. C5METTRFRASE.
SMART	SM00439. BAH. 1 hit. SM00298. CHROMO. 1 hit. [Graphical view]
TIGRFAMs	TIGR00675. dcm. 1 hit.
PROSITE	PS51038. BAH. 1 hit. PS00094. C5_MTASE_1. 1 hit. PS00598. CHROMO_1. 1 hit. PS50013. CHROMO_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

CMT3_ARATH

Accession

Primary (citable) accession number: Q94F88
Secondary accession number(s): Q94FN4, Q9C9L8

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 25, 2006
Last sequence update:	July 25, 2006
Last modified:	November 3, 2009
This is version 54 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)