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Q9UBC3 (DNM3B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 140. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA (cytosine-5)-methyltransferase 3B

Short name=Dnmt3b
EC=2.1.1.37
Alternative name(s):
DNA methyltransferase HsaIIIB
Short name=DNA MTase HsaIIIB
Short name=M.HsaIIIB
Gene names
Name:DNMT3B
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length853 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing By similarity. In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two conserved methyltransferase motifs. Function as transcriptional corepressor by associating with ZHX1. Ref.11 Ref.13 Ref.15 Ref.16

Catalytic activity

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

Enzyme regulation

Activated by binding to the regulatory factor DNMT3L By similarity.

Subunit structure

Interacts with BAZ2A/TIP5, SUV39H1 and CBX4. Interacts with UHRF1 By similarity. Interacts with DNMT1 and DNMT3A, SETDB1, UBL1, UBE2I9 and ZHX1. Interacts with the PRC2/EED-EZH2 complex. Ref.8 Ref.9 Ref.10 Ref.11 Ref.13

Subcellular location

Nucleus Ref.8 Ref.9.

Tissue specificity

Ubiquitous; highly expressed in fetal liver, heart, kidney, placenta, and at lower levels in spleen, colon, brain, liver, small intestine, lung, peripheral blood mononuclear cells, and skeletal muscle. Isoform 1 is expressed in all tissues except brain, skeletal muscle and PBMC, 3 is ubiquitous, 4 is expressed in all tissues except brain, skeletal muscle, lung and prostate and 5 is detectable only in testis and at very low level in brain and prostate.

Domain

The PWWP domain is essential for targeting to pericentric heterochromatin.

Post-translational modification

Sumoylated. Ref.8

Citrullinated by PADI4 By similarity.

Involvement in disease

Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1) [MIM:242860]: A rare disorder characterized by a variable immunodeficiency resulting in recurrent infections, facial anomalies, and branching of chromosomes 1, 9, and 16. Other variable symptoms include growth retardation, failure to thrive, and psychomotor retardation. Laboratory studies show limited hypomethylation of DNA in a small fraction of the genome in some, but not all, patients.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.2 Ref.21 Ref.22 Ref.23 Ref.24

Sequence similarities

Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.

Contains 1 ADD domain.

Contains 1 GATA-type zinc finger.

Contains 1 PHD-type zinc finger.

Contains 1 PWWP domain.

Contains 1 SAM-dependent MTase C5-type domain.

Ontologies

Keywords
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   DiseaseDisease mutation
   DomainZinc-finger
   LigandDNA-binding
Metal-binding
S-adenosyl-L-methionine
Zinc
   Molecular functionActivator
Methyltransferase
Repressor
Transferase
   PTMCitrullination
Phosphoprotein
Ubl conjugation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA methylation

Non-traceable author statement Ref.21Ref.23. Source: UniProtKB

DNA methylation on cytosine within a CG sequence

Inferred from electronic annotation. Source: Ensembl

S-adenosylhomocysteine metabolic process

Inferred from electronic annotation. Source: Ensembl

S-adenosylmethioninamine metabolic process

Inferred from electronic annotation. Source: Ensembl

cellular response to amino acid stimulus

Inferred from electronic annotation. Source: Ensembl

methylation-dependent chromatin silencing

Inferred from electronic annotation. Source: Ensembl

negative regulation of histone H3-K9 methylation

Inferred from mutant phenotype Ref.15. Source: UniProtKB

negative regulation of transcription from RNA polymerase II promoter

Inferred from direct assay Ref.13. Source: UniProtKB

positive regulation of gene expression

Inferred from mutant phenotype Ref.15. Source: UniProtKB

positive regulation of histone H3-K4 methylation

Inferred from mutant phenotype Ref.15. Source: UniProtKB

positive regulation of neuron differentiation

Inferred from electronic annotation. Source: Ensembl

protein complex localization

Inferred from electronic annotation. Source: Ensembl

regulation of gene expression by genetic imprinting

Inferred from electronic annotation. Source: Ensembl

response to drug

Inferred from electronic annotation. Source: Ensembl

response to ionizing radiation

Inferred from electronic annotation. Source: Ensembl

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: Ensembl

intracellular membrane-bounded organelle

Inferred from direct assay. Source: HPA

nuclear heterochromatin

Inferred from electronic annotation. Source: Ensembl

nucleus

Inferred from direct assay Ref.13. Source: UniProtKB

   Molecular_functionDNA (cytosine-5-)-methyltransferase activity

Non-traceable author statement Ref.2. Source: UniProtKB

DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates

Inferred from electronic annotation. Source: Ensembl

DNA-methyltransferase activity

Non-traceable author statement Ref.7Ref.21Ref.23. Source: UniProtKB

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

transcription corepressor activity

Inferred from direct assay Ref.13. Source: UniProtKB

unmethylated CpG binding

Inferred from electronic annotation. Source: Ensembl

Complete GO annotation...

Alternative products

This entry describes 8 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9UBC3-1)

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: Q9UBC3-2)

The sequence of this isoform differs from the canonical sequence as follows:
     356-375: Missing.
Isoform 3 (identifier: Q9UBC3-3)

The sequence of this isoform differs from the canonical sequence as follows:
     356-375: Missing.
     745-807: Missing.
Isoform 4 (identifier: Q9UBC3-4)

The sequence of this isoform differs from the canonical sequence as follows:
     356-375: Missing.
     744-744: R → S
     745-853: Missing.
Isoform 5 (identifier: Q9UBC3-5)

The sequence of this isoform differs from the canonical sequence as follows:
     356-375: Missing.
     768-853: LKKVQTITTK...APLKDYFACE → DLWLSCALHR...LRPSEGLLCM
Isoform 6 (identifier: Q9UBC3-6)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MEPSPEPPSLESM
     356-375: Missing.
Isoform 7 (identifier: Q9UBC3-7)

The sequence of this isoform differs from the canonical sequence as follows:
     69-144: Missing.
     356-375: Missing.
     744-806: Missing.
Note: No experimental confirmation available.
Isoform 8 (identifier: Q9UBC3-8)

The sequence of this isoform differs from the canonical sequence as follows:
     103-144: Missing.
     356-375: Missing.
     744-806: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 853853DNA (cytosine-5)-methyltransferase 3B
PRO_0000088045

Regions

Domain225 – 28359PWWP
Domain423 – 555133ADD
Domain575 – 853279SAM-dependent MTase C5-type
Zinc finger434 – 46431GATA-type; atypical
Zinc finger475 – 53157PHD-type; atypical
Region1 – 298298Interaction with DNMT1 and DNMT3A
Region435 – 52793Interaction with the PRC2/EED-EZH2 complex By similarity
Region582 – 5865S-adenosyl-L-methionine binding By similarity
Region627 – 6293S-adenosyl-L-methionine binding By similarity
Region832 – 8343S-adenosyl-L-methionine binding By similarity

Sites

Active site6511 By similarity
Binding site6051S-adenosyl-L-methionine By similarity

Amino acid modifications

Modified residue821Phosphoserine Ref.18
Modified residue961Phosphothreonine Ref.18
Modified residue1001Phosphoserine Ref.18
Modified residue1101Phosphoserine Ref.18
Modified residue1361Phosphoserine Ref.17 Ref.18
Modified residue1951Phosphoserine Ref.18
Modified residue2021Phosphoserine Ref.18
Modified residue2091Phosphoserine Ref.18
Modified residue4101Citrulline By similarity

Natural variations

Alternative sequence11M → MEPSPEPPSLESM in isoform 6.
VSP_005636
Alternative sequence69 – 14476Missing in isoform 7.
VSP_045874
Alternative sequence103 – 14442Missing in isoform 8.
VSP_045875
Alternative sequence356 – 37520Missing in isoform 2, isoform 3, isoform 4, isoform 5, isoform 6, isoform 7 and isoform 8.
VSP_005637
Alternative sequence744 – 80663Missing in isoform 7 and isoform 8.
VSP_045876
Alternative sequence7441R → S in isoform 4.
VSP_005639
Alternative sequence745 – 853109Missing in isoform 4.
VSP_005640
Alternative sequence745 – 80763Missing in isoform 3.
VSP_005638
Alternative sequence768 – 85386LKKVQ…YFACE → DLWLSCALHRRVQHGPWCPP EAAGKVLERACHPTPLRPSE GLLCM in isoform 5.
VSP_005641
Natural variant541R → P.
Corresponds to variant rs17123590 [ dbSNP | Ensembl ].
VAR_033885
Natural variant2701S → P in ICF1. Ref.24
Corresponds to variant rs121908947 [ dbSNP | Ensembl ].
VAR_022579
Natural variant5851A → V in ICF1. Ref.23 Ref.24
VAR_011506
Natural variant6031A → T in ICF1. Ref.21 Ref.22 Ref.23 Ref.24
Corresponds to variant rs121908943 [ dbSNP | Ensembl ].
VAR_011499
Natural variant6061V → A in ICF1. Ref.23 Ref.24
Corresponds to variant rs146981624 [ dbSNP | Ensembl ].
VAR_011507
Natural variant6631G → S in ICF1. Ref.2 Ref.24
Corresponds to variant rs121908942 [ dbSNP | Ensembl ].
VAR_011500
Natural variant6641L → P in ICF1. Ref.24
VAR_022580
Natural variant6991V → G in ICF1. Ref.23 Ref.24
VAR_011508
Natural variant7261V → G in ICF1. Ref.2 Ref.22 Ref.23 Ref.24
Corresponds to variant rs121908941 [ dbSNP | Ensembl ].
VAR_011501
Natural variant7661A → P in ICF1. Ref.23 Ref.24
VAR_011509
Natural variant8061E → ESTP in ICF1.
VAR_011502
Natural variant8141H → R in ICF1. Ref.23 Ref.24
VAR_011510
Natural variant8171D → G in ICF1. Ref.2 Ref.24
Corresponds to variant rs121908939 [ dbSNP | Ensembl ].
VAR_011503
Natural variant8181V → M in ICF1. Ref.2 Ref.23 Ref.24
Corresponds to variant rs121908940 [ dbSNP | Ensembl ].
VAR_011504
Natural variant8401R → Q in ICF1. Ref.24
Corresponds to variant rs121908946 [ dbSNP | Ensembl ].
VAR_022581

Experimental info

Sequence conflict5751I → T in BAG61690. Ref.4
Sequence conflict5831G → D in BAG61753. Ref.4
Sequence conflict6551S → P in BAG61690. Ref.4

Secondary structure

.......................... 853
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 1, 2000. Version 1.
Checksum: F20A67CF78951532

FASTA85395,751
        10         20         30         40         50         60 
MKGDTRHLNG EEDAGGREDS ILVNGACSDQ SSDSPPILEA IRTPEIRGRR SSSRLSKREV 

        70         80         90        100        110        120 
SSLLSYTQDL TGDGDGEDGD GSDTPVMPKL FRETRTRSES PAVRTRNNNS VSSRERHRPS 

       130        140        150        160        170        180 
PRSTRGRQGR NHVDESPVEF PATRSLRRRA TASAGTPWPS PPSSYLTIDL TDDTEDTHGT 

       190        200        210        220        230        240 
PQSSSTPYAR LAQDSQQGGM ESPQVEADSG DGDSSEYQDG KEFGIGDLVW GKIKGFSWWP 

       250        260        270        280        290        300 
AMVVSWKATS KRQAMSGMRW VQWFGDGKFS EVSADKLVAL GLFSQHFNLA TFNKLVSYRK 

       310        320        330        340        350        360 
AMYHALEKAR VRAGKTFPSS PGDSLEDQLK PMLEWAHGGF KPTGIEGLKP NNTQPVVNKS 

       370        380        390        400        410        420 
KVRRAGSRKL ESRKYENKTR RRTADDSATS DYCPAPKRLK TNCYNNGKDR GDEDQSREQM 

       430        440        450        460        470        480 
ASDVANNKSS LEDGCLSCGR KNPVSFHPLF EGGLCQTCRD RFLELFYMYD DDGYQSYCTV 

       490        500        510        520        530        540 
CCEGRELLLC SNTSCCRCFC VECLEVLVGT GTAAEAKLQE PWSCYMCLPQ RCHGVLRRRK 

       550        560        570        580        590        600 
DWNVRLQAFF TSDTGLEYEA PKLYPAIPAA RRRPIRVLSL FDGIATGYLV LKELGIKVGK 

       610        620        630        640        650        660 
YVASEVCEES IAVGTVKHEG NIKYVNDVRN ITKKNIEEWG PFDLVIGGSP CNDLSNVNPA 

       670        680        690        700        710        720 
RKGLYEGTGR LFFEFYHLLN YSRPKEGDDR PFFWMFENVV AMKVGDKRDI SRFLECNPVM 

       730        740        750        760        770        780 
IDAIKVSAAH RARYFWGNLP GMNRPVIASK NDKLELQDCL EYNRIAKLKK VQTITTKSNS 

       790        800        810        820        830        840 
IKQGKNQLFP VVMNGKEDVL WCTELERIFG FPVHYTDVSN MGRGARQKLL GRSWSVPVIR 

       850 
HLFAPLKDYF ACE 

« Hide

Isoform 2 [UniParc].

Checksum: DAD71DB275947261
Show »

FASTA83393,407
Isoform 3 [UniParc].

Checksum: E7777E3879B1D93B
Show »

FASTA77086,177
Isoform 4 [UniParc].

Checksum: 21173ED0988996FC
Show »

FASTA72480,845
Isoform 5 [UniParc].

Checksum: C6721C7241B9283A
Show »

FASTA79288,572
Isoform 6 [UniParc].

Checksum: CFA82BB96B59EFBF
Show »

FASTA84594,689
Isoform 7 [UniParc].

Checksum: 6C59147487ABA6DC
Show »

FASTA69477,719
Isoform 8 [UniParc].

Checksum: E4465A68EC2334A0
Show »

FASTA72881,311

References

« Hide 'large scale' references
[1]"Cloning, expression and chromosome locations of the human DNMT3 gene family."
Xie S., Wang Z., Okano M., Nogami M., Li Y., He W.-W., Okumura K., Li E.
Gene 236:87-95(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2 AND 3).
Tissue: Fetal testis and Small intestine.
[2]"Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene."
Xu G.-L., Bestor T.H., Bourc'his D., Hsieh C.-L., Tommerup N., Bugge M., Hulten M., Qu X., Russo J.J., Viegas-Pequignot E.
Nature 402:187-191(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 6), VARIANTS ICF1 SER-663; GLY-726; GLY-817 AND MET-818.
Tissue: Testis.
[3]"Cloning, expression and characterization of human DNMT3 genes."
Ni J., Pradhan S., Roberts R.J.
Submitted (DEC-2000) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[4]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 7 AND 8).
Tissue: Brain.
[5]"The DNA sequence and comparative analysis of human chromosome 20."
Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E. expand/collapse author list , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.
Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]"The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors."
Robertson K.D., Uzvolgyi E., Liang G., Talmadge C., Sumegi J., Gonzales F.A., Jones P.A.
Nucleic Acids Res. 27:2291-2298(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 636-853 (ISOFORMS 1; 4 AND 5).
Tissue: Testis.
[8]"Dnmt3b, de novo DNA methyltransferase, interacts with SUMO-1 and Ubc9 through its N-terminal region and is subject to modification by SUMO-1."
Kang E.S., Park C.W., Chung J.H.
Biochem. Biophys. Res. Commun. 289:862-868(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH UBL1 AND UBE2I9, SUMOYLATION, SUBCELLULAR LOCATION.
[9]"Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases."
Kim G.-D., Ni J., Kelesoglu N., Roberts R.J., Pradhan S.
EMBO J. 21:4183-4195(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH DNMT1 AND DNMT3A, SUBCELLULAR LOCATION.
[10]"The histone methyltransferase SETDB1 and the DNA methyltransferase DNMT3A interact directly and localize to promoters silenced in cancer cells."
Li H., Rauch T., Chen Z.-X., Szabo P.E., Riggs A.D., Pfeifer G.P.
J. Biol. Chem. 281:19489-19500(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH SETDB1.
[11]"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] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH THE PRC2/EED-EZH2 COMPLEX.
[12]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)
[13]"Zinc-fingers and homeoboxes 1 (ZHX1) binds DNA methyltransferase (DNMT) 3B to enhance DNMT3B-mediated transcriptional repression."
Kim S.H., Park J., Choi M.C., Kim H.P., Park J.H., Jung Y., Lee J.H., Oh D.Y., Im S.A., Bang Y.J., Kim T.Y.
Biochem. Biophys. Res. Commun. 355:318-323(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH ZHX1.
[14]"Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer."
Schlesinger Y., Straussman R., Keshet I., Farkash S., Hecht M., Zimmerman J., Eden E., Yakhini Z., Ben-Shushan E., Reubinoff B.E., Bergman Y., Simon I., Cedar H.
Nat. Genet. 39:232-236(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: DE NOVO DNA METHYLATION OF TARGET GENES.
[15]"DNA methyltransferase 1 and 3B activate BAG-1 expression via recruitment of CTCFL/BORIS and modulation of promoter histone methylation."
Sun L., Huang L., Nguyen P., Bisht K.S., Bar-Sela G., Ho A.S., Bradbury C.M., Yu W., Cui H., Lee S., Trepel J.B., Feinberg A.P., Gius D.
Cancer Res. 68:2726-2735(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[16]"DNA methyltransferase 3B acts as a co-repressor of the human polycomb protein hPc2 to repress fibroblast growth factor receptor 3 transcription."
Kim S.-H., Park J., Choi M.-C., Park J.-H., Kim H.-P., Lee J.-H., Oh D.-Y., Im S.-A., Bang Y.-J., Kim T.-Y.
Int. J. Biochem. Cell Biol. 40:2462-2471(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[17]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-136, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[18]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-82; THR-96; SER-100; SER-110; SER-136; SER-195; SER-202 AND SER-209, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[19]"Crystal structure of the PWWP domain of human DNA (cytosine-5-)-methyltransferase 3 beta."
Structural genomics consortium (SGC)
Submitted (MAR-2009) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 206-355.
[20]"Structural and histone binding ability characterizations of human PWWP domains."
Wu H., Zeng H., Lam R., Tempel W., Amaya M.F., Xu C., Dombrovski L., Qiu W., Wang Y., Min J.
PLoS ONE 6:E18919-E18919(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.04 ANGSTROMS) OF 380-509.
[21]"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] [Europe PMC] [Abstract]
Cited for: VARIANTS ICF1 THR-603 AND SER-THR-PRO-806 INS.
[22]"The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome."
Hansen R.S., Wijmenga C., Luo P., Stanek A.M., Canfield T.K., Weemaes C.M.R., Gartler S.M.
Proc. Natl. Acad. Sci. U.S.A. 96:14412-14417(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS ICF1 THR-603; GLY-726 AND SER-THR-PRO-806 INS.
[23]"Genetic variation in ICF syndrome: evidence for genetic heterogeneity."
Wijmenga C., Hansen R.S., Gimelli G., Bjoerck E.J., Davies E.G., Valentine D., Belohradsky B.H., van Dongen J.J., Smeets D.F.C.M., van den Heuvel L.P.W.J., Luyten J.A.F.M., Strengman E., Weemaes C.M.R., Pearson P.L.
Hum. Mutat. 16:509-517(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS ICF1 VAL-585; THR-603; ALA-606; GLY-699; GLY-726; PRO-766; ARG-814 AND MET-818.
[24]"DNMT3B mutations and DNA methylation defect define two types of ICF syndrome."
Jiang Y.L., Rigolet M., Bourc'his D., Nigon F., Bokesoy I., Fryns J.-P., Hulten M., Jonveaux P., Maraschio P., Megarbane A., Moncla A., Viegas-Pequignot E.
Hum. Mutat. 25:56-63(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS ICF1 PRO-270; VAL-585; THR-603; ALA-606; SER-663; PRO-664; GLY-699; GLY-726; PRO-766; ARG-814; GLY-817; MET-818 AND GLN-840.
+Additional computationally mapped references.

Web resources

DNMT3Bbase

DNMT3B mutation db

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF156487 mRNA. Translation: AAD53062.1.
AF156488 mRNA. Translation: AAD53063.1.
AF176228 mRNA. Translation: AAF04015.1.
AF331857 mRNA. Translation: AAL57040.1.
AK299821 mRNA. Translation: BAG61690.1.
AK299915 mRNA. Translation: BAG61753.1.
AL035071 Genomic DNA. Translation: CAB53069.1.
AL035071 Genomic DNA. Translation: CAB53070.1.
AL035071 Genomic DNA. Translation: CAB53071.1.
AL035071 Genomic DNA. Translation: CAM27373.1.
CH471077 Genomic DNA. Translation: EAW76351.1.
CH471077 Genomic DNA. Translation: EAW76352.1.
CH471077 Genomic DNA. Translation: EAW76353.1.
CH471077 Genomic DNA. Translation: EAW76354.1.
CH471077 Genomic DNA. Translation: EAW76356.1.
AF129267 mRNA. Translation: AAD31432.1.
AF129268 mRNA. Translation: AAD31433.1.
AF129269 mRNA. Translation: AAD31434.1.
RefSeqNP_001193984.1. NM_001207055.1.
NP_001193985.1. NM_001207056.1.
NP_008823.1. NM_006892.3.
NP_787044.1. NM_175848.1.
NP_787045.1. NM_175849.1.
NP_787046.1. NM_175850.2.
UniGeneHs.643024.
Hs.713611.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3FLGX-ray1.80A206-355[»]
3QKJX-ray2.04A/B/C/D380-509[»]
ProteinModelPortalQ9UBC3.
SMRQ9UBC3. Positions 216-350, 415-852.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid108126. 61 interactions.
DIPDIP-30000N.
IntActQ9UBC3. 23 interactions.
MINTMINT-2820816.
STRING9606.ENSP00000328547.

Chemistry

BindingDBQ9UBC3.
ChEMBLCHEMBL6095.

Protein family/group databases

REBASE4120. M.HsaDnmt3B.

PTM databases

PhosphoSiteQ9UBC3.

Polymorphism databases

DMDM17375667.

Proteomic databases

PaxDbQ9UBC3.
PRIDEQ9UBC3.

Protocols and materials databases

DNASU1789.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000201963; ENSP00000201963; ENSG00000088305. [Q9UBC3-6]
ENST00000328111; ENSP00000328547; ENSG00000088305. [Q9UBC3-1]
ENST00000344505; ENSP00000345105; ENSG00000088305. [Q9UBC3-5]
ENST00000348286; ENSP00000337764; ENSG00000088305. [Q9UBC3-3]
ENST00000353855; ENSP00000313397; ENSG00000088305. [Q9UBC3-2]
ENST00000443239; ENSP00000403169; ENSG00000088305. [Q9UBC3-8]
ENST00000456297; ENSP00000412305; ENSG00000088305. [Q9UBC3-7]
GeneID1789.
KEGGhsa:1789.
UCSCuc002wyc.3. human. [Q9UBC3-1]
uc002wyd.3. human. [Q9UBC3-2]
uc002wye.3. human. [Q9UBC3-3]
uc002wyf.3. human. [Q9UBC3-6]

Organism-specific databases

CTD1789.
GeneCardsGC20P031350.
HGNCHGNC:2979. DNMT3B.
HPAHPA001595.
MIM242860. phenotype.
602900. gene.
neXtProtNX_Q9UBC3.
Orphanet2268. ICF syndrome.
PharmGKBPA27446.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG70699.
HOVERGENHBG051381.
InParanoidQ9UBC3.
KOK17399.
OMALEWAHGG.
OrthoDBEOG7MWGW6.
PhylomeDBQ9UBC3.
TreeFamTF329039.

Gene expression databases

ArrayExpressQ9UBC3.
BgeeQ9UBC3.
CleanExHS_DNMT3B.
GenevestigatorQ9UBC3.

Family and domain databases

InterProIPR025766. ADD.
IPR018117. C5_DNA_meth_AS.
IPR001525. C5_MeTfrase.
IPR025811. C5_MeTrfase_3.
IPR000313. PWWP_dom.
IPR011011. Znf_FYVE_PHD.
[Graphical view]
PfamPF00145. DNA_methylase. 1 hit.
PF00855. PWWP. 1 hit.
[Graphical view]
SMARTSM00293. PWWP. 1 hit.
[Graphical view]
SUPFAMSSF57903. SSF57903. 1 hit.
PROSITEPS51533. ADD. 1 hit.
PS00094. C5_MTASE_1. 1 hit.
PS50812. PWWP. 1 hit.
PS51679. SAM_MT_C5. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9UBC3.
GeneWikiDNMT3B.
GenomeRNAi1789.
NextBio7289.
PROQ9UBC3.
SOURCESearch...

Entry information

Entry nameDNM3B_HUMAN
AccessionPrimary (citable) accession number: Q9UBC3
Secondary accession number(s): A2A2E2 expand/collapse secondary AC list , B4DSM8, B4DSU1, E1P5M6, E1P5M7, E7EN63, E9PBF2, Q9UBD4, Q9UJQ5, Q9UKA6, Q9UNE5, Q9Y5R9, Q9Y5S0
Entry history
Integrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: May 1, 2000
Last modified: April 16, 2014
This is version 140 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 20

Human chromosome 20: entries, gene names and cross-references to MIM