{"entryType":"UniProtKB reviewed (Swiss-Prot)","primaryAccession":"Q9UBC3","secondaryAccessions":["A2A2E2","B4DSM8","B4DSU1","E1P5M6","E1P5M7","E7EN63","E9PBF2","Q9UBD4","Q9UJQ5","Q9UKA6","Q9UNE5","Q9Y5R9","Q9Y5S0"],"uniProtkbId":"DNM3B_HUMAN","entryAudit":{"firstPublicDate":"2001-09-26","lastAnnotationUpdateDate":"2026-11-04","lastSequenceUpdateDate":"2000-05-01","entryVersion":232,"sequenceVersion":1},"annotationScore":5.0,"organism":{"scientificName":"Homo sapiens","commonName":"Human","taxonId":9606,"lineage":["Eukaryota","Metazoa","Chordata","Craniata","Vertebrata","Euteleostomi","Mammalia","Eutheria","Euarchontoglires","Primates","Haplorrhini","Catarrhini","Hominidae","Homo"]},"proteinExistence":"1: Evidence at protein level","proteinDescription":{"recommendedName":{"fullName":{"value":"DNA (cytosine-5)-methyltransferase 3B"},"shortNames":[{"value":"Dnmt3b"}],"ecNumbers":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10647011"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"20838592"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"32083663"}],"value":"2.1.1.37"}]},"alternativeNames":[{"fullName":{"value":"DNA methyltransferase HsaIIIB"},"shortNames":[{"value":"DNA MTase HsaIIIB"},{"value":"M.HsaIIIB"}]}]},"genes":[{"geneName":{"evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"10433969"},{"evidenceCode":"ECO:0000312","source":"HGNC","id":"HGNC:2979"}],"value":"DNMT3B"}}],"comments":[{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"O88509"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10647011"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"17303076"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"18413740"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"18567530"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"20838592"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27153398"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"32083663"}],"value":"DNA (cytosine-5)-methyltransferase that mediates genome-wide de novo methylation and which is essential for the establishment of DNA methylation patterns during development (PubMed:10647011, PubMed:20838592, PubMed:32083663). Modifies DNA at CpG sites with selectivity for residues flanking the target CpG site at positions -1 and +1, and strong preference for a guanine (G) immediately following the CpG sites (PubMed:20838592, PubMed:32083663). Methylates DNA in a non-cooperative processive manner, allowing the enzyme to diffuse along DNA and methylate multiple sites before dissociation (PubMed:32083663). DNA methylation is coordinated with methylation of histones (By similarity). Plays a role in genomic imprinting (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 (PubMed:18413740). Acts as a transcriptional corepressor by associating with CBX4 and independently of DNA methylation (PubMed:18567530). Functions as a transcriptional corepressor by associating with ZHX1 (PubMed:17303076). Required for DUX4 silencing in somatic cells (PubMed:27153398)"}],"commentType":"FUNCTION"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"20838592"}],"value":"Shows DNA (cytosine-5)-methyltransferase activity"}],"commentType":"FUNCTION","molecule":"Isoform DNMT3B1"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"20838592"}],"value":"Shows DNA (cytosine-5)-methyltransferase activity"}],"commentType":"FUNCTION","molecule":"Isoform DNMT3B2"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"O88509"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27121154"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"32968275"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"41742418"}],"value":"Inactive isoform that lacks (cytosine-5)-methyltransferase activity and acts as an accessory factor for de novo DNA methylation (PubMed:27121154, PubMed:32968275). Forms a heterotetramer complex with catalytic isoforms from DNMT3A or DNMT3B, and acts as a scaffold to bridge the heterotetramer complex to nucleosomes and orient the catalytic subunit toward the accessible linker DNA (PubMed:32968275). The heterotetramer complex specifically methylates long DNA linker regions between two nucleosomes (PubMed:41742418). In contrast, short DNA linker regions, which are enriched at promoter regions, promote di-nucleosome bridging, blocking access to linker DNA, preventing methylation (PubMed:41742418). Stimulates the activity of DNMT3A (isoforms DNMT3A1 or DNMT3A2) and DNMT3B (isoforms DNMT3B1 or DNMT3B2), with a preference for DNMT3B-mediated DNA methylation (By similarity)"}],"commentType":"FUNCTION","molecule":"Isoform DNMT3B3"},{"commentType":"CATALYTIC ACTIVITY","reaction":{"name":"a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-methyl-2'-deoxycytidine in DNA + S-adenosyl-L-homocysteine + H(+)","reactionCrossReferences":[{"database":"Rhea","id":"RHEA:13681"},{"database":"Rhea","id":"RHEA-COMP:11369"},{"database":"Rhea","id":"RHEA-COMP:11370"},{"database":"ChEBI","id":"CHEBI:15378"},{"database":"ChEBI","id":"CHEBI:57856"},{"database":"ChEBI","id":"CHEBI:59789"},{"database":"ChEBI","id":"CHEBI:85452"},{"database":"ChEBI","id":"CHEBI:85454"}],"ecNumber":"2.1.1.37","evidences":[{"evidenceCode":"ECO:0000255","source":"PROSITE-ProRule","id":"PRU10018"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10647011"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"20838592"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"32083663"}]},"physiologicalReactions":[{"directionType":"left-to-right","reactionCrossReference":{"database":"Rhea","id":"RHEA:13682"},"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10647011"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"20838592"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"32083663"}]}]},{"commentType":"CATALYTIC ACTIVITY","molecule":"Isoform DNMT3B1","reaction":{"name":"a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-methyl-2'-deoxycytidine in DNA + S-adenosyl-L-homocysteine + H(+)","reactionCrossReferences":[{"database":"Rhea","id":"RHEA:13681"},{"database":"Rhea","id":"RHEA-COMP:11369"},{"database":"Rhea","id":"RHEA-COMP:11370"},{"database":"ChEBI","id":"CHEBI:15378"},{"database":"ChEBI","id":"CHEBI:57856"},{"database":"ChEBI","id":"CHEBI:59789"},{"database":"ChEBI","id":"CHEBI:85452"},{"database":"ChEBI","id":"CHEBI:85454"}],"ecNumber":"2.1.1.37","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"20838592"}]},"physiologicalReactions":[{"directionType":"left-to-right","reactionCrossReference":{"database":"Rhea","id":"RHEA:13682"},"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"20838592"}]}]},{"commentType":"CATALYTIC ACTIVITY","molecule":"Isoform DNMT3B2","reaction":{"name":"a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-methyl-2'-deoxycytidine in DNA + S-adenosyl-L-homocysteine + H(+)","reactionCrossReferences":[{"database":"Rhea","id":"RHEA:13681"},{"database":"Rhea","id":"RHEA-COMP:11369"},{"database":"Rhea","id":"RHEA-COMP:11370"},{"database":"ChEBI","id":"CHEBI:15378"},{"database":"ChEBI","id":"CHEBI:57856"},{"database":"ChEBI","id":"CHEBI:59789"},{"database":"ChEBI","id":"CHEBI:85452"},{"database":"ChEBI","id":"CHEBI:85454"}],"ecNumber":"2.1.1.37","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"20838592"}]},"physiologicalReactions":[{"directionType":"left-to-right","reactionCrossReference":{"database":"Rhea","id":"RHEA:13682"},"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"20838592"}]}]},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"20838592"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"32083663"}],"value":"Activated by binding to the regulatory factor DNMT3L"}],"commentType":"ACTIVITY REGULATION"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"O88509"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"11735126"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"12145218"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"16357870"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"16682412"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"17303076"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"20838592"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"32083663"}],"value":"Heterotetramer composed of two catalytic DNMT3B subunits and regulatory subunit homodimer (either DNMT3L or isoform DNMT3B3 of DNMT3B) (PubMed:20838592, PubMed:32083663). Interacts with BAZ2A/TIP5, UHRF1, SUV39H1 and CBX4 (By similarity). Interacts with DNMT1 and DNMT3A, SETDB1, UBL1, UBE2I9 and ZHX1 (PubMed:11735126, PubMed:12145218, PubMed:16682412, PubMed:17303076). Interacts with the PRC2/EED-EZH2 complex (PubMed:16357870)"}],"commentType":"SUBUNIT"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"32968275"}],"value":"Heterotetramer composed of two regulatory DNMT3B3 subunits and a catalytic homodimer (either isoforms DNMT3A1 or DNMT3A2 of DNMT3A or isoforms DNMT3B1 or DNMT3B2 of DNMT3B)"}],"commentType":"SUBUNIT","molecule":"Isoform DNMT3B3"},{"commentType":"INTERACTION","interactions":[{"interactantOne":{"uniProtKBAccession":"Q9UBC3","intActId":"EBI-80125"},"interactantTwo":{"uniProtKBAccession":"Q9Y6K1","geneName":"DNMT3A","intActId":"EBI-923653"},"numberOfExperiments":4,"organismDiffer":false},{"interactantOne":{"uniProtKBAccession":"Q9UBC3","intActId":"EBI-80125"},"interactantTwo":{"uniProtKBAccession":"O75530","geneName":"EED","intActId":"EBI-923794"},"numberOfExperiments":4,"organismDiffer":false},{"interactantOne":{"uniProtKBAccession":"Q9UBC3","intActId":"EBI-80125"},"interactantTwo":{"uniProtKBAccession":"Q96KQ7","geneName":"EHMT2","intActId":"EBI-744366"},"numberOfExperiments":2,"organismDiffer":false},{"interactantOne":{"uniProtKBAccession":"Q9UBC3","intActId":"EBI-80125"},"interactantTwo":{"uniProtKBAccession":"Q15910","geneName":"EZH2","intActId":"EBI-530054"},"numberOfExperiments":14,"organismDiffer":false},{"interactantOne":{"uniProtKBAccession":"Q9UBC3","intActId":"EBI-80125"},"interactantTwo":{"uniProtKBAccession":"P63165","geneName":"SUMO1","intActId":"EBI-80140"},"numberOfExperiments":4,"organismDiffer":false},{"interactantOne":{"uniProtKBAccession":"Q9UBC3","intActId":"EBI-80125"},"interactantTwo":{"uniProtKBAccession":"P63279","geneName":"UBE2I","intActId":"EBI-80168"},"numberOfExperiments":3,"organismDiffer":false},{"interactantOne":{"uniProtKBAccession":"Q9UBC3","intActId":"EBI-80125"},"interactantTwo":{"uniProtKBAccession":"Q96T88","geneName":"UHRF1","intActId":"EBI-1548946"},"numberOfExperiments":7,"organismDiffer":false},{"interactantOne":{"uniProtKBAccession":"Q9UBC3","intActId":"EBI-80125"},"interactantTwo":{"uniProtKBAccession":"Q9QR71","geneName":"LANA1","intActId":"EBI-15602554"},"numberOfExperiments":2,"organismDiffer":true},{"interactantOne":{"uniProtKBAccession":"Q9UBC3-1","intActId":"EBI-6083193"},"interactantTwo":{"uniProtKBAccession":"Q9UKY1","geneName":"ZHX1","intActId":"EBI-347767"},"numberOfExperiments":6,"organismDiffer":false}]},{"commentType":"SUBCELLULAR LOCATION","note":{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"O88509"}],"value":"Accumulates in the major satellite repeats at pericentric heterochromatin"}]},"subcellularLocations":[{"location":{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"11735126"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"12145218"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"17303076"}],"value":"Nucleus","id":"SL-0191"}},{"location":{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"O88509"}],"value":"Chromosome","id":"SL-0468"}}]},{"commentType":"SUBCELLULAR LOCATION","molecule":"Isoform DNMT3B3","note":{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"32968275"}],"value":"Localizes to chromatin"}]},"subcellularLocations":[{"location":{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"32968275"}],"value":"Nucleus","id":"SL-0191"}},{"location":{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"32968275"}],"value":"Chromosome","id":"SL-0468"}}]},{"commentType":"ALTERNATIVE PRODUCTS","events":["Alternative splicing"],"isoforms":[{"name":{"value":"DNMT3B1"},"isoformIds":["Q9UBC3-1"],"isoformSequenceStatus":"Displayed"},{"name":{"value":"DNMT3B2"},"isoformIds":["Q9UBC3-2"],"sequenceIds":["VSP_005637"],"isoformSequenceStatus":"Described"},{"name":{"value":"DNMT3B3"},"isoformIds":["Q9UBC3-3"],"sequenceIds":["VSP_005637","VSP_005638"],"isoformSequenceStatus":"Described"},{"name":{"value":"4"},"isoformIds":["Q9UBC3-4"],"sequenceIds":["VSP_005637","VSP_005639","VSP_005640"],"isoformSequenceStatus":"Described"},{"name":{"value":"5"},"isoformIds":["Q9UBC3-5"],"sequenceIds":["VSP_005637","VSP_005641"],"isoformSequenceStatus":"Described"},{"name":{"value":"6"},"isoformIds":["Q9UBC3-6"],"sequenceIds":["VSP_005636","VSP_005637"],"isoformSequenceStatus":"Described"},{"name":{"value":"7"},"isoformIds":["Q9UBC3-7"],"sequenceIds":["VSP_045874","VSP_005637","VSP_045876"],"isoformSequenceStatus":"Described"},{"name":{"value":"8"},"isoformIds":["Q9UBC3-8"],"sequenceIds":["VSP_045875","VSP_005637","VSP_045876"],"isoformSequenceStatus":"Described"}]},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10433969"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10647011"}],"value":"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"}],"commentType":"TISSUE SPECIFICITY"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10433969"}],"value":"Expressed in all tissues except brain, skeletal muscle and PBMC"}],"commentType":"TISSUE SPECIFICITY","molecule":"Isoform DNMT3B1"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10433969"}],"value":"Ubiquitously expressed"}],"commentType":"TISSUE SPECIFICITY","molecule":"Isoform DNMT3B3"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10325416"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10433969"}],"value":"Expressed in all tissues except brain, skeletal muscle, lung and prostate"}],"commentType":"TISSUE SPECIFICITY","molecule":"Isoform 4"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10325416"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10433969"}],"value":"Detectable only in testis and at very low level in brain and prostate"}],"commentType":"TISSUE SPECIFICITY","molecule":"Isoform 5"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"O88509"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"41742418"}],"value":"The PWWP domain specifically recognizes and binds histone H3 dimethylated at 'Lys-36' (H3K36me2) (PubMed:41742418). H3K36me2 recognition is however blocked when the heterotrameric complex bridges di-nucleosomes with short linkers (PubMed:41742418). The PWWP domain is essential for targeting to pericentric heterochromatin (By similarity)"}],"commentType":"DOMAIN"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"11735126"}],"value":"Sumoylated"}],"commentType":"PTM"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"O88509"}],"value":"Citrullinated by PADI4"}],"commentType":"PTM"},{"commentType":"DISEASE","disease":{"diseaseId":"Immunodeficiency-centromeric instability-facial anomalies syndrome 1","diseaseAccession":"DI-01813","acronym":"ICF1","description":"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.","diseaseCrossReference":{"database":"MIM","id":"242860"},"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10555141"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10588719"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"10647011"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"11102980"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"15580563"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"21120685"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27734333"}]},"note":{"texts":[{"value":"The disease is caused by variants affecting the gene represented in this entry"}]}},{"commentType":"DISEASE","disease":{"diseaseId":"Facioscapulohumeral muscular dystrophy 4, digenic","diseaseAccession":"DI-06197","acronym":"FSHD4","description":"A digenic form of facioscapulohumeral muscular dystrophy, a degenerative muscle disease characterized by slowly progressive weakness of the muscles of the face, upper-arm, and shoulder girdle. With disease progression, other muscles may also become affected. There is significant clinical variability and incomplete penetrance.","diseaseCrossReference":{"database":"MIM","id":"619478"},"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27153398"}]},"note":{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27153398"}],"value":"The disease is caused by variants affecting distinct genetic loci, including the gene represented in this entry. DNMT3B mutations lead to DUX4 expression in somatic tissues, including muscle cells, when a haplotype on chromosome 4 is permissive for DUX4 expression. Ectopic expression of DUX4 in skeletal muscle activates the expression of stem cell and germline genes, and, when overexpressed in somatic cells, DUX4 can ultimately lead to cell death"}]}},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000255","source":"PROSITE-ProRule","id":"PRU01016"}],"value":"Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family"}],"commentType":"SIMILARITY"},{"commentType":"WEB RESOURCE","resourceName":"DNMT3Bbase","resourceUrl":"https://databases.lovd.nl/shared/genes/DNMT3B","ftp":false,"note":"DNMT3B mutation db"}],"features":[{"type":"Chain","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":853,"modifier":"EXACT"}},"description":"DNA (cytosine-5)-methyltransferase 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