Reviewed, UniProtKB/Swiss-Prot O88509 (DNM3B_MOUSE)

Names and origin

Protein names

Recommended name:
    DNA (cytosine-5)-methyltransferase 3B
      Short name=Dnmt3b
    EC=2.1.1.37
Alternative name(s):
    DNA methyltransferase MmuIIIB
      Short name=DNA MTase MmuIIIB
      Short name=M.MmuIIIB

Gene names

Name:

Dnmt3b

Organism

Mus musculus (Mouse)

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus

Protein attributes

Sequence length	859 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Required for genome wide de novo methylation and is essential for development. DNA methylation is coordinated with methylation of histones. Ref.3 Ref.7
Catalytic activity	S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine.
Subunit structure	Interacts with SETDB1, UBL1 and UBE2I9. Interacts with DNMT1 and DNMT3A By similarity. Interacts with SUV39H1. Interacts with the PRC2/EED-EZH2 complex.
Subcellular location	Nucleus Probable.
Developmental stage	Highly expressed, at E7.5, in the embryonic ectoderm, neural ectoderm, and chorionic ectoderm; a weak expression is also detected in mesodermal and endodermal cells. At later stages, the expression is detected predominantly in the forebrain and eyes but weakly throughout the embryo. Ref.3
Sequence similarities	Belongs to the C5-methyltransferase family. Contains 1 ADD-type zinc finger. Contains 1 PWWP domain.

Ontologies

Keywords
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Zinc-finger
Ligand	DNA-binding Metal-binding S-adenosyl-L-methionine Zinc
Molecular function	Methyltransferase Transferase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	DNA methylation Inferred from genetic interaction. Source: MGI genetic imprinting Inferred from mutant phenotype. Source: MGI methylation-dependent chromatin silencing Inferred from genetic interaction. Source: MGI protein complex localization Inferred from direct assay. Source: MGI
Cellular component	nuclear heterochromatin Inferred from direct assay. Source: MGI
Molecular function	DNA (cytosine-5-)-methyltransferase activity Inferred from direct assay. Source: MGI DNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: MGI zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: O88509-1)

Also known as: 5;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: O88509-2)

Also known as: 6;

The sequence of this isoform differs from the canonical sequence as follows:
     363-382: Missing.

Isoform 3 (identifier: O88509-3)

Also known as: 8;

The sequence of this isoform differs from the canonical sequence as follows:
     363-382: Missing.
     750-812: Missing.

Isoform 4 (identifier: O88509-4)

Also known as: 7;

The sequence of this isoform differs from the canonical sequence as follows:
     750-812: Missing.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 859

859

DNA (cytosine-5)-methyltransferase 3B

PRO_0000088046

Regions

Domain

232 – 290

59

PWWP

Zinc finger

440 – 532

93

ADD-type

Region

1 – 305

305

Interaction with DNMT1 and DNMT3A By similarity

Region

440 – 532

93

Interaction with the PRC2/EED-EZH2 complex

Compositional bias

160 – 165

6

Poly-Arg

Sites

Active site

657

1

By similarity

Natural variations

Alternative sequence

363 – 382

20

Missing in isoform 2 and isoform 3.

VSP_005642

Alternative sequence

750 – 812

63

Missing in isoform 3 and isoform 4.

VSP_005643

Experimental info

Sequence conflict

217 – 218

2

RD → IY in AAF74515. Ref.2

Sequence conflict

217 – 218

2

RD → IY in AAF74516. Ref.2

Secondary structure

1

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859

Helix Strand Turn

Details...

Beta strand

226 – 229

4

Beta strand

235 – 240

6

Turn

241 – 243

3

Beta strand

244 – 251

8

Helix

253 – 255

3

Beta strand

265 – 270

6

Turn

271 – 273

3

Beta strand

276 – 280

5

Helix

281 – 283

3

Helix

290 – 293

4

Helix

296 – 301

6

Helix

303 – 320

18

Helix

332 – 344

13

Turn

348 – 350

3

Helix

351 – 355

5

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 (5) [UniParc]. Last modified May 1, 2000. Version 2. Checksum: 93E334D9FBCC590E	FASTA	859	97,228
	10 20 30 40 50 60 MKGDSRHLNE EEGASGYEEC IIVNGNFSDQ SSDTKDAPSP PVLEAICTEP VCTPETRGRR 70 80 90 100 110 120 SSSRLSKREV SSLLNYTQDM TGDGDRDDEV DDGNGSDILM PKLTRETKDT RTRSESPAVR 130 140 150 160 170 180 TRHSNGTSSL ERQRASPRIT RGRQGRHHVQ EYPVEFPATR SRRRRASSSA STPWSSPASV 190 200 210 220 230 240 DFMEEVTPKS VSTPSVDLSQ DGDQEGMDTT QVDAESRDGD STEYQDDKEF GIGDLVWGKI 250 260 270 280 290 300 KGFSWWPAMV VSWKATSKRQ AMPGMRWVQW FGDGKFSEIS ADKLVALGLF SQHFNLATFN 310 320 330 340 350 360 KLVSYRKAMY HTLEKARVRA GKTFSSSPGE SLEDQLKPML EWAHGGFKPT GIEGLKPNKK 370 380 390 400 410 420 QPVVNKSKVR RSDSRNLEPR RRENKSRRRT TNDSAASESP PPKRLKTNSY GGKDRGEDEE 430 440 450 460 470 480 SRERMASEVT NNKGNLEDRC LSCGKKNPVS FHPLFEGGLC QSCRDRFLEL FYMYDEDGYQ 490 500 510 520 530 540 SYCTVCCEGR ELLLCSNTSC CRCFCVECLE VLVGAGTAED AKLQEPWSCY MCLPQRCHGV 550 560 570 580 590 600 LRRRKDWNMR LQDFFTTDPD LEEFEPPKLY PAIPAAKRRP IRVLSLFDGI ATGYLVLKEL 610 620 630 640 650 660 GIKVEKYIAS EVCAESIAVG TVKHEGQIKY VNDVRKITKK NIEEWGPFDL VIGGSPCNDL 670 680 690 700 710 720 SNVNPARKGL YEGTGRLFFE FYHLLNYTRP KEGDNRPFFW MFENVVAMKV NDKKDISRFL 730 740 750 760 770 780 ACNPVMIDAI KVSAAHRARY FWGNLPGMNR PVMASKNDKL ELQDCLEFSR TAKLKKVQTI 790 800 810 820 830 840 TTKSNSIRQG KNQLFPVVMN GKDDVLWCTE LERIFGFPAH YTDVSNMGRG ARQKLLGRSW 850 SVPVIRHLFA PLKDYFACE
	Isoform 2 (6). Checksum: 59BF48AB459A1298	FASTA	839	94,793
	10 20 30 40 50 60 MKGDSRHLNE EEGASGYEEC IIVNGNFSDQ SSDTKDAPSP PVLEAICTEP VCTPETRGRR 70 80 90 100 110 120 SSSRLSKREV SSLLNYTQDM TGDGDRDDEV DDGNGSDILM PKLTRETKDT RTRSESPAVR 130 140 150 160 170 180 TRHSNGTSSL ERQRASPRIT RGRQGRHHVQ EYPVEFPATR SRRRRASSSA STPWSSPASV 190 200 210 220 230 240 DFMEEVTPKS VSTPSVDLSQ DGDQEGMDTT QVDAESRDGD STEYQDDKEF GIGDLVWGKI 250 260 270 280 290 300 KGFSWWPAMV VSWKATSKRQ AMPGMRWVQW FGDGKFSEIS ADKLVALGLF SQHFNLATFN 310 320 330 340 350 360 KLVSYRKAMY HTLEKARVRA GKTFSSSPGE SLEDQLKPML EWAHGGFKPT GIEGLKPNKK 370 380 390 400 410 420 QPENKSRRRT TNDSAASESP PPKRLKTNSY GGKDRGEDEE SRERMASEVT NNKGNLEDRC 430 440 450 460 470 480 LSCGKKNPVS FHPLFEGGLC QSCRDRFLEL FYMYDEDGYQ SYCTVCCEGR ELLLCSNTSC 490 500 510 520 530 540 CRCFCVECLE VLVGAGTAED AKLQEPWSCY MCLPQRCHGV LRRRKDWNMR LQDFFTTDPD 550 560 570 580 590 600 LEEFEPPKLY PAIPAAKRRP IRVLSLFDGI ATGYLVLKEL GIKVEKYIAS EVCAESIAVG 610 620 630 640 650 660 TVKHEGQIKY VNDVRKITKK NIEEWGPFDL VIGGSPCNDL SNVNPARKGL YEGTGRLFFE 670 680 690 700 710 720 FYHLLNYTRP KEGDNRPFFW MFENVVAMKV NDKKDISRFL ACNPVMIDAI KVSAAHRARY 730 740 750 760 770 780 FWGNLPGMNR PVMASKNDKL ELQDCLEFSR TAKLKKVQTI TTKSNSIRQG KNQLFPVVMN 790 800 810 820 830 GKDDVLWCTE LERIFGFPAH YTDVSNMGRG ARQKLLGRSW SVPVIRHLFA PLKDYFACE
	Isoform 3 (8). Checksum: 211E2DE8BF06C48E	FASTA	776	87,586
	10 20 30 40 50 60 MKGDSRHLNE EEGASGYEEC IIVNGNFSDQ SSDTKDAPSP PVLEAICTEP VCTPETRGRR 70 80 90 100 110 120 SSSRLSKREV SSLLNYTQDM TGDGDRDDEV DDGNGSDILM PKLTRETKDT RTRSESPAVR 130 140 150 160 170 180 TRHSNGTSSL ERQRASPRIT RGRQGRHHVQ EYPVEFPATR SRRRRASSSA STPWSSPASV 190 200 210 220 230 240 DFMEEVTPKS VSTPSVDLSQ DGDQEGMDTT QVDAESRDGD STEYQDDKEF GIGDLVWGKI 250 260 270 280 290 300 KGFSWWPAMV VSWKATSKRQ AMPGMRWVQW FGDGKFSEIS ADKLVALGLF SQHFNLATFN 310 320 330 340 350 360 KLVSYRKAMY HTLEKARVRA GKTFSSSPGE SLEDQLKPML EWAHGGFKPT GIEGLKPNKK 370 380 390 400 410 420 QPENKSRRRT TNDSAASESP PPKRLKTNSY GGKDRGEDEE SRERMASEVT NNKGNLEDRC 430 440 450 460 470 480 LSCGKKNPVS FHPLFEGGLC QSCRDRFLEL FYMYDEDGYQ SYCTVCCEGR ELLLCSNTSC 490 500 510 520 530 540 CRCFCVECLE VLVGAGTAED AKLQEPWSCY MCLPQRCHGV LRRRKDWNMR LQDFFTTDPD 550 560 570 580 590 600 LEEFEPPKLY PAIPAAKRRP IRVLSLFDGI ATGYLVLKEL GIKVEKYIAS EVCAESIAVG 610 620 630 640 650 660 TVKHEGQIKY VNDVRKITKK NIEEWGPFDL VIGGSPCNDL SNVNPARKGL YEGTGRLFFE 670 680 690 700 710 720 FYHLLNYTRP KEGDNRPFFW MFENVVAMKV NDKKDISRFL ACNPVMIDAI KVSAAHRARY 730 740 750 760 770 FWGNLPGMNR IFGFPAHYTD VSNMGRGARQ KLLGRSWSVP VIRHLFAPLK DYFACE
	Isoform 4 (7). Checksum: 0B7D93B4D802744E	FASTA	796	90,021
	10 20 30 40 50 60 MKGDSRHLNE EEGASGYEEC IIVNGNFSDQ SSDTKDAPSP PVLEAICTEP VCTPETRGRR 70 80 90 100 110 120 SSSRLSKREV SSLLNYTQDM TGDGDRDDEV DDGNGSDILM PKLTRETKDT RTRSESPAVR 130 140 150 160 170 180 TRHSNGTSSL ERQRASPRIT RGRQGRHHVQ EYPVEFPATR SRRRRASSSA STPWSSPASV 190 200 210 220 230 240 DFMEEVTPKS VSTPSVDLSQ DGDQEGMDTT QVDAESRDGD STEYQDDKEF GIGDLVWGKI 250 260 270 280 290 300 KGFSWWPAMV VSWKATSKRQ AMPGMRWVQW FGDGKFSEIS ADKLVALGLF SQHFNLATFN 310 320 330 340 350 360 KLVSYRKAMY HTLEKARVRA GKTFSSSPGE SLEDQLKPML EWAHGGFKPT GIEGLKPNKK 370 380 390 400 410 420 QPVVNKSKVR RSDSRNLEPR RRENKSRRRT TNDSAASESP PPKRLKTNSY GGKDRGEDEE 430 440 450 460 470 480 SRERMASEVT NNKGNLEDRC LSCGKKNPVS FHPLFEGGLC QSCRDRFLEL FYMYDEDGYQ 490 500 510 520 530 540 SYCTVCCEGR ELLLCSNTSC CRCFCVECLE VLVGAGTAED AKLQEPWSCY MCLPQRCHGV 550 560 570 580 590 600 LRRRKDWNMR LQDFFTTDPD LEEFEPPKLY PAIPAAKRRP IRVLSLFDGI ATGYLVLKEL 610 620 630 640 650 660 GIKVEKYIAS EVCAESIAVG TVKHEGQIKY VNDVRKITKK NIEEWGPFDL VIGGSPCNDL 670 680 690 700 710 720 SNVNPARKGL YEGTGRLFFE FYHLLNYTRP KEGDNRPFFW MFENVVAMKV NDKKDISRFL 730 740 750 760 770 780 ACNPVMIDAI KVSAAHRARY FWGNLPGMNR IFGFPAHYTD VSNMGRGARQ KLLGRSWSVP 790 VIRHLFAPLK DYFACE

References

[1]	"Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases." Okano M., Xie S., Li E. Nat. Genet. 19:219-220(1998) [PubMed: 9662389] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2 AND 3).
[2]	"Cloning of full-length Dnmt3b cDNA and its alternative splicing isoforms in mouse embryo." Yin B., Chen Y., Zhu N., Wu G., Shen Y. Zhongguo Yi Xue Ke Xue Yuan Xue Bao 21:431-438(1999) [PubMed: 12567489] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2; 3 AND 4). Strain: KM. Tissue: Embryo.
[3]	"DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development." Okano M., Bell D.W., Haber D.A., Li E. Cell 99:247-257(1999) [PubMed: 10555141] [Abstract] Cited for: FUNCTION, DEVELOPMENTAL STAGE.
[4]	"Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin." Lehnertz B., Ueda Y., Derijck A.A.H.A., Braunschweig U., Perez-Burgos L., Kubicek S., Chen T., Li E., Jenuwein T., Peters A.H.F.M. Curr. Biol. 13:1192-1200(2003) [PubMed: 12867029] [Abstract] Cited for: INTERACTION WITH SUV39H1.
[5]	"The Polycomb group protein EZH2 directly controls DNA methylation." Vire E., Brenner C., Deplus R., Blanchon L., Fraga M., Didelot C., Morey L., Van Eynde A., Bernard D., Vanderwinden J.-M., Bollen M., Esteller M., Di Croce L., de Launoit Y., Fuks F. Nature 439:871-874(2006) [PubMed: 16357870] [Abstract] Cited for: INTERACTION WITH EED AND EZH2.
[6]	Erratum Vire E., Brenner C., Deplus R., Blanchon L., Fraga M., Didelot C., Morey L., Van Eynde A., Bernard D., Vanderwinden J.-M., Bollen M., Esteller M., Di Croce L., de Launoit Y., Fuks F. Nature 446:824-824(2006)
[7]	"The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds." Qiu C., Sawada K., Zhang X., Cheng X. Nat. Struct. Biol. 9:217-224(2002) [PubMed: 11836534] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 219-362, FUNCTION, INTERACTION WITH DNA.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AF068626 mRNA. Translation: AAC40178.2.
AF068627 mRNA. Translation: AAC40179.2.
AF068628 mRNA. Translation: AAC40180.2.
AF151969 mRNA. Translation: AAF74515.1.
AF151970 mRNA. Translation: AAF74516.1.
AF151971 mRNA. Translation: AAF74517.1.
AF151972 mRNA. Translation: AAF74518.1.
AF151973 mRNA. Translation: AAF74519.1.
AF151974 mRNA. Translation: AAF74520.1.
AF151975 mRNA. Translation: AAF74521.1.
AF151976 mRNA. Translation: AAF74522.1.

IPI

IPI00228733.
IPI00268106.
IPI00276159.
IPI00331143.

RefSeq

NP_001003960.2.
NP_001003961.2.
NP_001003963.2.
NP_034198.3.

UniGene

Mm.89772

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1KHC	X-ray	1.80	A	219-362	[»]

ModBase

Search...

Protein family/group databases

REBASE

3748. M.MmuDnmt3B.

PTM databases

PhosphoSite

O88509.

Genome annotation databases

Ensembl

ENSMUSG00000027478. Mus musculus. [Contig view]

GeneID

13436.

KEGG

mmu:13436.

Organism-specific databases

MGI

MGI:1261819. Dnmt3b.

Phylogenomic databases

HOVERGEN

O88509.

Enzyme and pathway databases

BRENDA

2.1.1.37. 244.

Gene expression databases

ArrayExpress

O88509.

Bgee

O88509.

CleanEx

MM_DNMT3B.

GermOnline

ENSMUSG00000027478. Mus musculus.

Family and domain databases

InterPro

IPR001525. C5_DNA_meth.
IPR018117. C5_DNA_meth_AS.
IPR000313. PWWP.
[Graphical view]

Pfam

PF00145. DNA_methylase. 1 hit.
PF00855. PWWP. 1 hit.
[Graphical view]

SMART

SM00293. PWWP. 1 hit.
[Graphical view]

PROSITE

PS00094. C5_MTASE_1. 1 hit.
PS00095. C5_MTASE_2. False negative.
PS50812. PWWP. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

283873.

SOURCE

Search...

Entry information

Entry name

DNM3B_MOUSE

Accession

Primary (citable) accession number: O88509
Secondary accession number(s): O88510, O88511

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 26, 2001
Last sequence update:	May 1, 2000
Last modified:	June 16, 2009
This is version 79 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)