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Showing Protein DNA (cytosine-5)-methyltransferase 3B (HMDBP02251)

IdentificationBiological propertiesGene propertiesProtein propertiesExternal linksReferencesXMLShow 3 metabolites
Identification
HMDB Protein ID HMDBP02251
Secondary Accession Numbers
  • 7736
Name DNA (cytosine-5)-methyltransferase 3B
Synonyms
  1. DNA MTase HsaIIIB
  2. DNA methyltransferase HsaIIIB
  3. Dnmt3b
  4. M.HsaIIIB
Gene Name DNMT3B
Protein Type Unknown
Biological Properties
General Function Involved in DNA binding
Specific 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.
Pathways
  • Cysteine and methionine metabolism
Reactions
S-Adenosylmethionine + DNA → S-Adenosylhomocysteine + DNA containing 5-methylcytosine details
S-Adenosylmethionine + DNA cytosine → S-Adenosylhomocysteine + DNA 5-methylcytosine details
GO Classification
Biological Process
DNA methylation involved in embryo development
DNA methylation on cytosine within a CG sequence
methylation-dependent chromatin silencing
S-adenosylhomocysteine metabolic process
S-adenosylmethioninamine metabolic process
negative regulation of histone H3-K9 methylation
positive regulation of histone H3-K4 methylation
positive regulation of neuron differentiation
response to ionizing radiation
protein complex localization
cellular response to amino acid stimulus
response to drug
negative regulation of transcription from RNA polymerase II promoter
regulation of gene expression by genetic imprinting
positive regulation of gene expression
Cellular Component
cytoplasm
nucleus
chromosome, centromeric region
nuclear heterochromatin
Function
ion binding
cation binding
metal ion binding
binding
transition metal ion binding
zinc ion binding
nucleic acid binding
dna binding
Molecular Function
metal ion binding
DNA (cytosine-5-)-methyltransferase activity
DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates
unmethylated CpG binding
transcription corepressor activity
Process
metabolic process
macromolecule metabolic process
cellular macromolecule metabolic process
dna metabolic process
dna modification
dna alkylation
dna methylation
Cellular Location
  1. Nucleus
Gene Properties
Chromosome Location 20
Locus 20q11.2
SNPs DNMT3B
Gene Sequence 
>2562 bp
ATGAAGGGAGACACCAGGCATCTCAATGGAGAGGAGGACGCCGGCGGGAGGGAAGACTCG
ATCCTCGTCAACGGGGCCTGCAGCGACCAGTCCTCCGACTCGCCCCCAATCCTGGAGGCT
ATCCGCACCCCGGAGATCAGAGGCCGAAGATCAAGCTCGCGACTCTCCAAGAGGGAGGTG
TCCAGTCTGCTAAGCTACACACAGGACTTGACAGGCGATGGCGACGGGGAAGATGGGGAT
GGCTCTGACACCCCAGTCATGCCAAAGCTCTTCCGGGAAACCAGGACTCGTTCAGAAAGC
CCAGCTGTCCGAACTCGAAATAACAACAGTGTCTCCAGCCGGGAGAGGCACAGGCCTTCC
CCACGTTCCACCCGAGGCCGGCAGGGCCGCAACCATGTGGACGAGTCCCCCGTGGAGTTC
CCGGCTACCAGGTCCCTGAGACGGCGGGCAACAGCATCGGCAGGAACGCCATGGCCGTCC
CCTCCCAGCTCTTACCTTACCATCGACCTCACAGACGACACAGAGGACACACATGGGACG
CCCCAGAGCAGCAGTACCCCCTACGCCCGCCTAGCCCAGGACAGCCAGCAGGGGGGCATG
GAGTCCCCGCAGGTGGAGGCAGACAGTGGAGATGGAGACAGTTCAGAGTATCAGGATGGG
AAGGAGTTTGGAATAGGGGACCTCGTGTGGGGAAAGATCAAGGGCTTCTCCTGGTGGCCC
GCCATGGTGGTGTCTTGGAAGGCCACCTCCAAGCGACAGGCTATGTCTGGCATGCGGTGG
GTCCAGTGGTTTGGCGATGGCAAGTTCTCCGAGGTCTCTGCAGACAAACTGGTGGCACTG
GGGCTGTTCAGCCAGCACTTTAATTTGGCCACCTTCAATAAGCTCGTCTCCTATCGAAAA
GCCATGTACCATGCTCTGGAGAAAGCTAGGGTGCGAGCTGGCAAGACCTTCCCCAGCAGC
CCTGGAGACTCATTGGAGGACCAGCTGAAGCCCATGTTGGAGTGGGCCCACGGGGGCTTC
AAGCCCACTGGGATCGAGGGCCTCAAACCCAACAACACGCAACCAGTGGTTAATAAGTCG
AAGGTGCGTCGTGCAGGCAGTAGGAAATTAGAATCAAGGAAATACGAGAACAAGACTCGA
AGACGCACAGCTGACGACTCAGCCACCTCTGACTACTGCCCCGCACCCAAGCGCCTCAAG
ACAAATTGCTATAACAACGGCAAAGACCGAGGGGATGAAGATCAGAGCCGAGAACAAATG
GCTTCAGATGTTGCCAACAACAAGAGCAGCCTGGAAGATGGCTGTTTGTCTTGTGGCAGG
AAAAACCCCGTGTCCTTCCACCCTCTCTTTGAGGGGGGGCTCTGTCAGACATGCCGGGAT
CGCTTCCTTGAGCTGTTTTACATGTATGATGACGATGGCTATCAGTCTTACTGCACTGTG
TGCTGCGAGGGCCGAGAGCTGCTGCTTTGCAGCAACACGAGCTGCTGCCGGTGTTTCTGT
GTGGAGTGCCTGGAGGTGCTGGTGGGCACAGGCACAGCGGCCGAGGCCAAGCTTCAGGAG
CCCTGGAGCTGTTACATGTGTCTCCCGCAGCGCTGTCATGGCGTCCTGCGGCGCCGGAAG
GACTGGAACGTGCGCCTGCAGGCCTTCTTCACCAGTGACACGGGGCTTGAATATGAAGCC
CCCAAGCTGTACCCTGCCATTCCCGCAGCCCGAAGGCGGCCCATTCGAGTCCTGTCATTG
TTTGATGGCATCGCGACAGGCTACCTAGTCCTCAAAGAGTTGGGCATAAAGGTAGGAAAG
TACGTCGCTTCTGAAGTGTGTGAGGAGTCCATTGCTGTTGGAACCGTGAAGCACGAGGGG
AATATCAAATACGTGAACGACGTGAGGAACATCACAAAGAAAAATATTGAAGAATGGGGC
CCATTTGACTTGGTGATTGGCGGAAGCCCATGCAACGATCTCTCAAATGTGAATCCAGCC
AGGAAAGGCCTGTATGAGGGTACAGGCCGGCTCTTCTTCGAATTTTACCACCTGCTGAAT
TACTCACGCCCCAAGGAGGGTGATGACCGGCCGTTCTTCTGGATGTTTGAGAATGTTGTA
GCCATGAAGGTTGGCGACAAGAGGGACATCTCACGGTTCCTGGAGTGTAATCCAGTGATG
ATTGATGCCATCAAAGTTTCTGCTGCTCACAGGGCCCGATACTTCTGGGGCAACCTACCC
GGGATGAACAGGCCCGTGATAGCATCAAAGAATGATAAACTCGAGCTGCAGGACTGCTTG
GAATACAATAGGATAGCCAAGTTAAAGAAAGTACAGACAATAACCACCAAGTCGAACTCG
ATCAAACAGGGGAAAAACCAACTTTTCCCTGTTGTCATGAATGGCAAAGAAGATGTTTTG
TGGTGCACTGAGCTCGAAAGGATCTTTGGCTTTCCTGTGCACTACACAGACGTGTCCAAC
ATGGGCCGTGGTGCCCGCCAGAAGCTGCTGGGAAGGTCCTGGAGCGTGCCTGTCATCCGA
CACCTCTTCGCCCCTCTGAAGGACTACTTTGCATGTGAATAG
Protein Properties
Number of Residues 853
Molecular Weight 81309.795
Theoretical pI 7.035
Pfam Domain Function
Signals Not Available
Transmembrane Regions Not Available
Protein Sequence 
>DNA (cytosine-5)-methyltransferase 3B
MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREV
SSLLSYTQDLTGDGDGEDGDGSDTPVMPKLFRETRTRSESPAVRTRNNNSVSSRERHRPS
PRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTIDLTDDTEDTHGT
PQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWP
AMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRK
AMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPVVNKS
KVRRAGSRKLESRKYENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQM
ASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTV
CCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRK
DWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGK
YVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPA
RKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVM
IDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLKKVQTITTKSNS
IKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIR
HLFAPLKDYFACE
GenBank ID Protein 5901940
UniProtKB/Swiss-Prot ID Q9UBC3
UniProtKB/Swiss-Prot Entry Name DNM3B_HUMAN
PDB IDs
GenBank Gene ID NM_006892.3
GeneCard ID DNMT3B
GenAtlas ID DNMT3B
HGNC ID HGNC:2979
References
General References
  1. Deloukas P, Matthews LH, Ashurst J, Burton J, Gilbert JG, Jones M, Stavrides G, Almeida JP, Babbage AK, Bagguley CL, Bailey J, Barlow KF, Bates KN, Beard LM, Beare DM, Beasley OP, Bird CP, Blakey SE, Bridgeman AM, Brown AJ, Buck D, Burrill W, Butler AP, Carder C, Carter NP, Chapman JC, Clamp M, Clark G, Clark LN, Clark SY, Clee CM, Clegg S, Cobley VE, Collier RE, Connor R, Corby NR, Coulson A, Coville GJ, Deadman R, Dhami P, Dunn M, Ellington AG, Frankland JA, Fraser A, French L, Garner P, Grafham DV, Griffiths C, Griffiths MN, Gwilliam R, Hall RE, Hammond S, Harley JL, Heath PD, Ho S, Holden JL, Howden PJ, Huckle E, Hunt AR, Hunt SE, Jekosch K, Johnson CM, Johnson D, Kay MP, Kimberley AM, King A, Knights A, Laird GK, Lawlor S, Lehvaslaiho MH, Leversha M, Lloyd C, Lloyd DM, Lovell JD, Marsh VL, Martin SL, McConnachie LJ, McLay K, McMurray AA, Milne S, Mistry D, Moore MJ, Mullikin JC, Nickerson T, Oliver K, Parker A, Patel R, Pearce TA, Peck AI, Phillimore BJ, Prathalingam SR, Plumb RW, Ramsay H, Rice CM, Ross MT, Scott CE, Sehra HK, Shownkeen R, Sims S, Skuce CD, Smith ML, Soderlund C, Steward CA, Sulston JE, Swann M, Sycamore N, Taylor R, Tee L, Thomas DW, Thorpe A, Tracey A, Tromans AC, Vaudin M, Wall M, Wallis JM, Whitehead SL, Whittaker P, Willey DL, Williams L, Williams SA, Wilming L, Wray PW, Hubbard T, Durbin RM, Bentley DR, Beck S, Rogers J: The DNA sequence and comparative analysis of human chromosome 20. Nature. 2001 Dec 20-27;414(6866):865-71. [PubMed:11780052 ]
  2. Li H, Rauch T, Chen ZX, Szabo PE, Riggs AD, Pfeifer GP: The histone methyltransferase SETDB1 and the DNA methyltransferase DNMT3A interact directly and localize to promoters silenced in cancer cells. J Biol Chem. 2006 Jul 14;281(28):19489-500. Epub 2006 May 8. [PubMed:16682412 ]
  3. Xie S, Wang Z, Okano M, Nogami M, Li Y, He WW, Okumura K, Li E: Cloning, expression and chromosome locations of the human DNMT3 gene family. Gene. 1999 Aug 5;236(1):87-95. [PubMed:10433969 ]
  4. Kim GD, Ni J, Kelesoglu N, Roberts RJ, Pradhan S: Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases. EMBO J. 2002 Aug 1;21(15):4183-95. [PubMed:12145218 ]
  5. Robertson KD, Uzvolgyi E, Liang G, Talmadge C, Sumegi J, Gonzales FA, Jones PA: The human DNA methyltransferases (DNMTs) 1, 3a and 3b: coordinate mRNA expression in normal tissues and overexpression in tumors. Nucleic Acids Res. 1999 Jun 1;27(11):2291-8. [PubMed:10325416 ]
  6. Vire E, Brenner C, Deplus R, Blanchon L, Fraga M, Didelot C, Morey L, Van Eynde A, Bernard D, Vanderwinden JM, Bollen M, Esteller M, Di Croce L, de Launoit Y, Fuks F: The Polycomb group protein EZH2 directly controls DNA methylation. Nature. 2006 Feb 16;439(7078):871-4. Epub 2005 Dec 14. [PubMed:16357870 ]
  7. Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, Zimmerman J, Eden E, Yakhini Z, Ben-Shushan E, Reubinoff BE, Bergman Y, Simon I, Cedar H: Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet. 2007 Feb;39(2):232-6. Epub 2006 Dec 31. [PubMed:17200670 ]
  8. Xu GL, Bestor TH, Bourc'his D, Hsieh CL, Tommerup N, Bugge M, Hulten M, Qu X, Russo JJ, Viegas-Pequignot E: Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature. 1999 Nov 11;402(6758):187-91. [PubMed:10647011 ]
  9. Kang ES, Park CW, Chung JH: Dnmt3b, de novo DNA methyltransferase, interacts with SUMO-1 and Ubc9 through its N-terminal region and is subject to modification by SUMO-1. Biochem Biophys Res Commun. 2001 Dec 14;289(4):862-8. [PubMed:11735126 ]
  10. Sun L, Huang L, Nguyen P, Bisht KS, Bar-Sela G, Ho AS, Bradbury CM, Yu W, Cui H, Lee S, Trepel JB, Feinberg AP, Gius D: DNA methyltransferase 1 and 3B activate BAG-1 expression via recruitment of CTCFL/BORIS and modulation of promoter histone methylation. Cancer Res. 2008 Apr 15;68(8):2726-35. doi: 10.1158/0008-5472.CAN-07-6654. [PubMed:18413740 ]
  11. Kim SH, Park J, Choi MC, Park JH, Kim HP, Lee JH, Oh DY, Im SA, Bang YJ, Kim TY: DNA methyltransferase 3B acts as a co-repressor of the human polycomb protein hPc2 to repress fibroblast growth factor receptor 3 transcription. Int J Biochem Cell Biol. 2008;40(11):2462-71. doi: 10.1016/j.biocel.2008.04.018. Epub 2008 May 18. [PubMed:18567530 ]
  12. Okano M, Bell DW, Haber DA, Li E: DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell. 1999 Oct 29;99(3):247-57. [PubMed:10555141 ]
  13. Hansen RS, Wijmenga C, Luo P, Stanek AM, Canfield TK, Weemaes CM, Gartler SM: The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14412-7. [PubMed:10588719 ]
  14. Wijmenga C, Hansen RS, Gimelli G, Bjorck EJ, Davies EG, Valentine D, Belohradsky BH, van Dongen JJ, Smeets DF, van den Heuvel LP, Luyten JA, Strengman E, Weemaes C, Pearson PL: Genetic variation in ICF syndrome: evidence for genetic heterogeneity. Hum Mutat. 2000 Dec;16(6):509-17. [PubMed:11102980 ]
  15. Jiang YL, Rigolet M, Bourc'his D, Nigon F, Bokesoy I, Fryns JP, Hulten M, Jonveaux P, Maraschio P, Megarbane A, Moncla A, Viegas-Pequignot E: DNMT3B mutations and DNA methylation defect define two types of ICF syndrome. Hum Mutat. 2005 Jan;25(1):56-63. [PubMed:15580563 ]