InnateDB: Systems Biology of the Innate Immune Response

Homo sapiens Protein: DNMT3B

Summary

InnateDB Protein

IDBP-65405.7

Last Modified

2014-10-13 [Report errors or provide feedback]

Gene Symbol

DNMT3B

Protein Name

DNA (cytosine-5-)-methyltransferase 3 beta

Synonyms

ICF; ICF1; M.HsaIIIB;

Species

Homo sapiens

Ensembl Protein

ENSP00000313397

InnateDB Gene

IDBG-65401 (DNMT3B)

Protein Structure

UniProt Annotation

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. {ECO:0000250, ECO:0000269PubMed:16357870, ECO:0000269PubMed:17303076, ECO:0000269PubMed:18413740, ECO:0000269PubMed:18567530}.

Subcellular Localization

Nucleus {ECO:0000269PubMed:11735126, ECO:0000269PubMed:12145218}.

Disease Associations

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. {ECO:0000269PubMed:10555141, ECO:0000269PubMed:10588719, ECO:0000269PubMed:10647011, ECO:0000269PubMed:11102980, ECO:0000269PubMed:15580563}. Note=The disease is caused by mutations affecting the gene represented in this entry.

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.

Comments

Interactions

Number of Interactions

This gene and/or its encoded proteins are associated with 110 experimentally validated interaction(s) in this database.
They are also associated with 11 interaction(s) predicted by orthology.

Experimentally validated
Total	110 [view]
Protein-Protein	106 [view]
Protein-DNA	3 [view]
Protein-RNA	0
DNA-DNA	1 [view]
RNA-RNA	0
DNA-RNA	0

Predicted by orthology
Total	11 [view]

Gene Ontology

Molecular Function

Accession	GO Term
GO:0003714	transcription corepressor activity
GO:0003886	DNA (cytosine-5-)-methyltransferase activity
GO:0005515	protein binding
GO:0008168	methyltransferase activity
GO:0009008	DNA-methyltransferase activity
GO:0046872	metal ion binding

Biological Process

GO:0000122	negative regulation of transcription from RNA polymerase II promoter
GO:0006306	DNA methylation
GO:0010628	positive regulation of gene expression
GO:0051571	positive regulation of histone H3-K4 methylation
GO:0051573	negative regulation of histone H3-K9 methylation

Cellular Component

GO:0005634	nucleus
GO:0043231	intracellular membrane-bounded organelle

Protein Structure and Domains

PDB ID

InterPro

IPR000313 PWWP domain
IPR001525 C-5 cytosine methyltransferase
IPR011011 Zinc finger, FYVE/PHD-type
IPR029063 S-adenosyl-L-methionine-dependent methyltransferase-like

PFAM

PF00855
PF00145

PRINTS

PR00105

PIRSF

SMART

SM00293

TIGRFAMs

Post-translational Modifications

Modification

Cross-References

SwissProt