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Q9UBC3

- DNM3B_HUMAN

UniProt

Q9UBC3 - DNM3B_HUMAN

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Protein
DNA (cytosine-5)-methyltransferase 3B
Gene
DNMT3B
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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 ZHX1.4 Publications

Catalytic activityi

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

Enzyme regulationi

Activated by binding to the regulatory factor DNMT3L By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei605 – 6051S-adenosyl-L-methionine By similarity
Active sitei651 – 6511 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri434 – 46431GATA-type; atypical
Add
BLAST
Zinc fingeri475 – 53157PHD-type; atypical
Add
BLAST

GO - Molecular functioni

  1. DNA (cytosine-5-)-methyltransferase activity Source: UniProtKB
  2. DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates Source: Ensembl
  3. DNA-methyltransferase activity Source: UniProtKB
  4. metal ion binding Source: UniProtKB-KW
  5. protein binding Source: UniProtKB
  6. transcription corepressor activity Source: UniProtKB
  7. unmethylated CpG binding Source: Ensembl

GO - Biological processi

  1. DNA methylation Source: UniProtKB
  2. DNA methylation on cytosine within a CG sequence Source: Ensembl
  3. S-adenosylhomocysteine metabolic process Source: Ensembl
  4. S-adenosylmethioninamine metabolic process Source: Ensembl
  5. cellular response to amino acid stimulus Source: Ensembl
  6. methylation-dependent chromatin silencing Source: Ensembl
  7. negative regulation of histone H3-K9 methylation Source: UniProtKB
  8. negative regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  9. positive regulation of gene expression Source: UniProtKB
  10. positive regulation of histone H3-K4 methylation Source: UniProtKB
  11. positive regulation of neuron differentiation Source: Ensembl
  12. protein complex localization Source: Ensembl
  13. regulation of gene expression by genetic imprinting Source: Ensembl
  14. response to drug Source: Ensembl
  15. response to ionizing radiation Source: Ensembl
Complete GO annotation...

Keywords - Molecular functioni

Activator, Methyltransferase, Repressor, Transferase

Keywords - Ligandi

DNA-binding, Metal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

ReactomeiREACT_200808. PRC2 methylates histones and DNA.
REACT_200856. NoRC negatively regulates rRNA expression.

Protein family/group databases

REBASEi4120. M.HsaDnmt3B.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA (cytosine-5)-methyltransferase 3B (EC:2.1.1.37)
Short name:
Dnmt3b
Alternative name(s):
DNA methyltransferase HsaIIIB
Short name:
DNA MTase HsaIIIB
Short name:
M.HsaIIIB
Gene namesi
Name:DNMT3B
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 20

Organism-specific databases

HGNCiHGNC:2979. DNMT3B.

Subcellular locationi

Nucleus 2 Publications

GO - Cellular componenti

  1. cytoplasm Source: Ensembl
  2. intracellular membrane-bounded organelle Source: HPA
  3. nuclear heterochromatin Source: Ensembl
  4. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

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.5 Publications
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti270 – 2701S → P in ICF1. 1 Publication
Corresponds to variant rs121908947 [ dbSNP | Ensembl ].
VAR_022579
Natural varianti585 – 5851A → V in ICF1. 2 Publications
VAR_011506
Natural varianti603 – 6031A → T in ICF1. 4 Publications
Corresponds to variant rs121908943 [ dbSNP | Ensembl ].
VAR_011499
Natural varianti606 – 6061V → A in ICF1. 2 Publications
Corresponds to variant rs146981624 [ dbSNP | Ensembl ].
VAR_011507
Natural varianti663 – 6631G → S in ICF1. 2 Publications
Corresponds to variant rs121908942 [ dbSNP | Ensembl ].
VAR_011500
Natural varianti664 – 6641L → P in ICF1. 1 Publication
VAR_022580
Natural varianti699 – 6991V → G in ICF1. 2 Publications
VAR_011508
Natural varianti726 – 7261V → G in ICF1. 4 Publications
Corresponds to variant rs121908941 [ dbSNP | Ensembl ].
VAR_011501
Natural varianti766 – 7661A → P in ICF1. 2 Publications
VAR_011509
Natural varianti806 – 8061E → ESTP in ICF1.
VAR_011502
Natural varianti814 – 8141H → R in ICF1. 2 Publications
VAR_011510
Natural varianti817 – 8171D → G in ICF1. 2 Publications
Corresponds to variant rs121908939 [ dbSNP | Ensembl ].
VAR_011503
Natural varianti818 – 8181V → M in ICF1. 3 Publications
Corresponds to variant rs121908940 [ dbSNP | Ensembl ].
VAR_011504
Natural varianti840 – 8401R → Q in ICF1. 1 Publication
Corresponds to variant rs121908946 [ dbSNP | Ensembl ].
VAR_022581

Keywords - Diseasei

Disease mutation

Organism-specific databases

MIMi242860. phenotype.
Orphaneti2268. ICF syndrome.
PharmGKBiPA27446.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 853853DNA (cytosine-5)-methyltransferase 3B
PRO_0000088045Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei82 – 821Phosphoserine1 Publication
Modified residuei96 – 961Phosphothreonine1 Publication
Modified residuei100 – 1001Phosphoserine1 Publication
Modified residuei110 – 1101Phosphoserine1 Publication
Modified residuei136 – 1361Phosphoserine2 Publications
Modified residuei195 – 1951Phosphoserine1 Publication
Modified residuei202 – 2021Phosphoserine1 Publication
Modified residuei209 – 2091Phosphoserine1 Publication
Modified residuei410 – 4101Citrulline By similarity

Post-translational modificationi

Sumoylated.1 Publication
Citrullinated by PADI4 By similarity.

Keywords - PTMi

Citrullination, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiQ9UBC3.
PaxDbiQ9UBC3.
PRIDEiQ9UBC3.

PTM databases

PhosphoSiteiQ9UBC3.

Expressioni

Tissue specificityi

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.

Gene expression databases

ArrayExpressiQ9UBC3.
BgeeiQ9UBC3.
CleanExiHS_DNMT3B.
GenevestigatoriQ9UBC3.

Organism-specific databases

HPAiHPA001595.

Interactioni

Subunit structurei

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.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
EEDO755304EBI-80125,EBI-923794
EZH2Q159108EBI-80125,EBI-530054
SUMO1P631654EBI-80125,EBI-80140
UBE2IP632793EBI-80125,EBI-80168
UHRF1Q96T887EBI-80125,EBI-1548946
ZHX1Q9UKY14EBI-6083193,EBI-347767

Protein-protein interaction databases

BioGridi108126. 61 interactions.
DIPiDIP-30000N.
IntActiQ9UBC3. 23 interactions.
MINTiMINT-2820816.
STRINGi9606.ENSP00000328547.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi228 – 2314
Beta strandi239 – 2446
Helixi246 – 2494
Beta strandi258 – 2636
Turni264 – 2663
Beta strandi269 – 2735
Turni274 – 2763
Beta strandi277 – 2793
Helixi283 – 2864
Helixi289 – 2946
Helixi296 – 31318
Helixi325 – 33713
Turni341 – 3433
Helixi345 – 3484

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3FLGX-ray1.80A206-355[»]
3QKJX-ray2.04A/B/C/D206-355[»]
ProteinModelPortaliQ9UBC3.
SMRiQ9UBC3. Positions 216-350, 415-852.

Miscellaneous databases

EvolutionaryTraceiQ9UBC3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini225 – 28359PWWP
Add
BLAST
Domaini423 – 555133ADD
Add
BLAST
Domaini575 – 853279SAM-dependent MTase C5-type
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 298298Interaction with DNMT1 and DNMT3A
Add
BLAST
Regioni435 – 52793Interaction with the PRC2/EED-EZH2 complex By similarity
Add
BLAST
Regioni582 – 5865S-adenosyl-L-methionine binding By similarity
Regioni627 – 6293S-adenosyl-L-methionine binding By similarity
Regioni832 – 8343S-adenosyl-L-methionine binding By similarity

Domaini

The PWWP domain is essential for targeting to pericentric heterochromatin.

Sequence similaritiesi

Contains 1 ADD domain.
Contains 1 PWWP domain.

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG70699.
HOVERGENiHBG051381.
InParanoidiQ9UBC3.
KOiK17399.
OMAiLEWAHGG.
OrthoDBiEOG7MWGW6.
PhylomeDBiQ9UBC3.
TreeFamiTF329039.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR025766. ADD.
IPR018117. C5_DNA_meth_AS.
IPR001525. C5_MeTfrase.
IPR025811. C5_MeTrfase_3.
IPR000313. PWWP_dom.
IPR029063. SAM-dependent_MTases-like.
IPR011011. Znf_FYVE_PHD.
[Graphical view]
PfamiPF00145. DNA_methylase. 1 hit.
PF00855. PWWP. 1 hit.
[Graphical view]
SMARTiSM00293. PWWP. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
SSF57903. SSF57903. 1 hit.
PROSITEiPS51533. ADD. 1 hit.
PS00094. C5_MTASE_1. 1 hit.
PS50812. PWWP. 1 hit.
PS51679. SAM_MT_C5. 1 hit.
[Graphical view]

Sequences (8)i

Sequence statusi: Complete.

This entry describes 8 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q9UBC3-1) [UniParc]FASTAAdd to Basket

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.

« Hide

MKGDTRHLNG EEDAGGREDS ILVNGACSDQ SSDSPPILEA IRTPEIRGRR    50
SSSRLSKREV SSLLSYTQDL TGDGDGEDGD GSDTPVMPKL FRETRTRSES 100
PAVRTRNNNS VSSRERHRPS PRSTRGRQGR NHVDESPVEF PATRSLRRRA 150
TASAGTPWPS PPSSYLTIDL TDDTEDTHGT PQSSSTPYAR LAQDSQQGGM 200
ESPQVEADSG DGDSSEYQDG KEFGIGDLVW GKIKGFSWWP AMVVSWKATS 250
KRQAMSGMRW VQWFGDGKFS EVSADKLVAL GLFSQHFNLA TFNKLVSYRK 300
AMYHALEKAR VRAGKTFPSS PGDSLEDQLK PMLEWAHGGF KPTGIEGLKP 350
NNTQPVVNKS KVRRAGSRKL ESRKYENKTR RRTADDSATS DYCPAPKRLK 400
TNCYNNGKDR GDEDQSREQM ASDVANNKSS LEDGCLSCGR KNPVSFHPLF 450
EGGLCQTCRD RFLELFYMYD DDGYQSYCTV CCEGRELLLC SNTSCCRCFC 500
VECLEVLVGT GTAAEAKLQE PWSCYMCLPQ RCHGVLRRRK DWNVRLQAFF 550
TSDTGLEYEA PKLYPAIPAA RRRPIRVLSL FDGIATGYLV LKELGIKVGK 600
YVASEVCEES IAVGTVKHEG NIKYVNDVRN ITKKNIEEWG PFDLVIGGSP 650
CNDLSNVNPA RKGLYEGTGR LFFEFYHLLN YSRPKEGDDR PFFWMFENVV 700
AMKVGDKRDI SRFLECNPVM IDAIKVSAAH RARYFWGNLP GMNRPVIASK 750
NDKLELQDCL EYNRIAKLKK VQTITTKSNS IKQGKNQLFP VVMNGKEDVL 800
WCTELERIFG FPVHYTDVSN MGRGARQKLL GRSWSVPVIR HLFAPLKDYF 850
ACE 853
Length:853
Mass (Da):95,751
Last modified:May 1, 2000 - v1
Checksum:iF20A67CF78951532
GO
Isoform 2 (identifier: Q9UBC3-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     356-375: Missing.

Show »
Length:833
Mass (Da):93,407
Checksum:iDAD71DB275947261
GO
Isoform 3 (identifier: Q9UBC3-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     356-375: Missing.
     745-807: Missing.

Show »
Length:770
Mass (Da):86,177
Checksum:iE7777E3879B1D93B
GO
Isoform 4 (identifier: Q9UBC3-4) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     356-375: Missing.
     744-744: R → S
     745-853: Missing.

Show »
Length:724
Mass (Da):80,845
Checksum:i21173ED0988996FC
GO
Isoform 5 (identifier: Q9UBC3-5) [UniParc]FASTAAdd to Basket

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

Show »
Length:792
Mass (Da):88,572
Checksum:iC6721C7241B9283A
GO
Isoform 6 (identifier: Q9UBC3-6) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MEPSPEPPSLESM
     356-375: Missing.

Show »
Length:845
Mass (Da):94,689
Checksum:iCFA82BB96B59EFBF
GO
Isoform 7 (identifier: Q9UBC3-7) [UniParc]FASTAAdd to Basket

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.

Show »
Length:694
Mass (Da):77,719
Checksum:i6C59147487ABA6DC
GO
Isoform 8 (identifier: Q9UBC3-8) [UniParc]FASTAAdd to Basket

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.

Show »
Length:728
Mass (Da):81,311
Checksum:iE4465A68EC2334A0
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti54 – 541R → P.
Corresponds to variant rs17123590 [ dbSNP | Ensembl ].
VAR_033885
Natural varianti270 – 2701S → P in ICF1. 1 Publication
Corresponds to variant rs121908947 [ dbSNP | Ensembl ].
VAR_022579
Natural varianti585 – 5851A → V in ICF1. 2 Publications
VAR_011506
Natural varianti603 – 6031A → T in ICF1. 4 Publications
Corresponds to variant rs121908943 [ dbSNP | Ensembl ].
VAR_011499
Natural varianti606 – 6061V → A in ICF1. 2 Publications
Corresponds to variant rs146981624 [ dbSNP | Ensembl ].
VAR_011507
Natural varianti663 – 6631G → S in ICF1. 2 Publications
Corresponds to variant rs121908942 [ dbSNP | Ensembl ].
VAR_011500
Natural varianti664 – 6641L → P in ICF1. 1 Publication
VAR_022580
Natural varianti699 – 6991V → G in ICF1. 2 Publications
VAR_011508
Natural varianti726 – 7261V → G in ICF1. 4 Publications
Corresponds to variant rs121908941 [ dbSNP | Ensembl ].
VAR_011501
Natural varianti766 – 7661A → P in ICF1. 2 Publications
VAR_011509
Natural varianti806 – 8061E → ESTP in ICF1.
VAR_011502
Natural varianti814 – 8141H → R in ICF1. 2 Publications
VAR_011510
Natural varianti817 – 8171D → G in ICF1. 2 Publications
Corresponds to variant rs121908939 [ dbSNP | Ensembl ].
VAR_011503
Natural varianti818 – 8181V → M in ICF1. 3 Publications
Corresponds to variant rs121908940 [ dbSNP | Ensembl ].
VAR_011504
Natural varianti840 – 8401R → Q in ICF1. 1 Publication
Corresponds to variant rs121908946 [ dbSNP | Ensembl ].
VAR_022581

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 11M → MEPSPEPPSLESM in isoform 6.
VSP_005636
Alternative sequencei69 – 14476Missing in isoform 7.
VSP_045874Add
BLAST
Alternative sequencei103 – 14442Missing in isoform 8.
VSP_045875Add
BLAST
Alternative sequencei356 – 37520Missing in isoform 2, isoform 3, isoform 4, isoform 5, isoform 6, isoform 7 and isoform 8.
VSP_005637Add
BLAST
Alternative sequencei744 – 80663Missing in isoform 7 and isoform 8.
VSP_045876Add
BLAST
Alternative sequencei744 – 7441R → S in isoform 4.
VSP_005639
Alternative sequencei745 – 853109Missing in isoform 4.
VSP_005640Add
BLAST
Alternative sequencei745 – 80763Missing in isoform 3.
VSP_005638Add
BLAST
Alternative sequencei768 – 85386LKKVQ…YFACE → DLWLSCALHRRVQHGPWCPP EAAGKVLERACHPTPLRPSE GLLCM in isoform 5.
VSP_005641Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti575 – 5751I → T in BAG61690. 1 Publication
Sequence conflicti583 – 5831G → D in BAG61753. 1 Publication
Sequence conflicti655 – 6551S → P in BAG61690. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
CCDSiCCDS13204.1. [Q9UBC3-6]
CCDS13205.1. [Q9UBC3-1]
CCDS13206.1. [Q9UBC3-2]
CCDS13207.1. [Q9UBC3-3]
CCDS56183.1. [Q9UBC3-8]
CCDS56184.1. [Q9UBC3-7]
RefSeqiNP_001193984.1. NM_001207055.1. [Q9UBC3-8]
NP_001193985.1. NM_001207056.1. [Q9UBC3-7]
NP_008823.1. NM_006892.3. [Q9UBC3-1]
NP_787044.1. NM_175848.1. [Q9UBC3-2]
NP_787045.1. NM_175849.1. [Q9UBC3-3]
NP_787046.1. NM_175850.2. [Q9UBC3-6]
UniGeneiHs.643024.
Hs.713611.

Genome annotation databases

EnsembliENST00000201963; 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]
GeneIDi1789.
KEGGihsa:1789.
UCSCiuc002wyc.3. human. [Q9UBC3-1]
uc002wyd.3. human. [Q9UBC3-2]
uc002wye.3. human. [Q9UBC3-3]
uc002wyf.3. human. [Q9UBC3-6]

Polymorphism databases

DMDMi17375667.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

DNMT3Bbase

DNMT3B mutation db

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
CCDSi CCDS13204.1. [Q9UBC3-6 ]
CCDS13205.1. [Q9UBC3-1 ]
CCDS13206.1. [Q9UBC3-2 ]
CCDS13207.1. [Q9UBC3-3 ]
CCDS56183.1. [Q9UBC3-8 ]
CCDS56184.1. [Q9UBC3-7 ]
RefSeqi NP_001193984.1. NM_001207055.1. [Q9UBC3-8 ]
NP_001193985.1. NM_001207056.1. [Q9UBC3-7 ]
NP_008823.1. NM_006892.3. [Q9UBC3-1 ]
NP_787044.1. NM_175848.1. [Q9UBC3-2 ]
NP_787045.1. NM_175849.1. [Q9UBC3-3 ]
NP_787046.1. NM_175850.2. [Q9UBC3-6 ]
UniGenei Hs.643024.
Hs.713611.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3FLG X-ray 1.80 A 206-355 [» ]
3QKJ X-ray 2.04 A/B/C/D 206-355 [» ]
ProteinModelPortali Q9UBC3.
SMRi Q9UBC3. Positions 216-350, 415-852.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 108126. 61 interactions.
DIPi DIP-30000N.
IntActi Q9UBC3. 23 interactions.
MINTi MINT-2820816.
STRINGi 9606.ENSP00000328547.

Chemistry

BindingDBi Q9UBC3.
ChEMBLi CHEMBL6095.

Protein family/group databases

REBASEi 4120. M.HsaDnmt3B.

PTM databases

PhosphoSitei Q9UBC3.

Polymorphism databases

DMDMi 17375667.

Proteomic databases

MaxQBi Q9UBC3.
PaxDbi Q9UBC3.
PRIDEi Q9UBC3.

Protocols and materials databases

DNASUi 1789.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000201963 ; 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 ]
GeneIDi 1789.
KEGGi hsa:1789.
UCSCi uc002wyc.3. human. [Q9UBC3-1 ]
uc002wyd.3. human. [Q9UBC3-2 ]
uc002wye.3. human. [Q9UBC3-3 ]
uc002wyf.3. human. [Q9UBC3-6 ]

Organism-specific databases

CTDi 1789.
GeneCardsi GC20P031350.
HGNCi HGNC:2979. DNMT3B.
HPAi HPA001595.
MIMi 242860. phenotype.
602900. gene.
neXtProti NX_Q9UBC3.
Orphaneti 2268. ICF syndrome.
PharmGKBi PA27446.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG70699.
HOVERGENi HBG051381.
InParanoidi Q9UBC3.
KOi K17399.
OMAi LEWAHGG.
OrthoDBi EOG7MWGW6.
PhylomeDBi Q9UBC3.
TreeFami TF329039.

Enzyme and pathway databases

Reactomei REACT_200808. PRC2 methylates histones and DNA.
REACT_200856. NoRC negatively regulates rRNA expression.

Miscellaneous databases

EvolutionaryTracei Q9UBC3.
GeneWikii DNMT3B.
GenomeRNAii 1789.
NextBioi 7289.
PROi Q9UBC3.
SOURCEi Search...

Gene expression databases

ArrayExpressi Q9UBC3.
Bgeei Q9UBC3.
CleanExi HS_DNMT3B.
Genevestigatori Q9UBC3.

Family and domain databases

Gene3Di 3.40.50.150. 1 hit.
InterProi IPR025766. ADD.
IPR018117. C5_DNA_meth_AS.
IPR001525. C5_MeTfrase.
IPR025811. C5_MeTrfase_3.
IPR000313. PWWP_dom.
IPR029063. SAM-dependent_MTases-like.
IPR011011. Znf_FYVE_PHD.
[Graphical view ]
Pfami PF00145. DNA_methylase. 1 hit.
PF00855. PWWP. 1 hit.
[Graphical view ]
SMARTi SM00293. PWWP. 1 hit.
[Graphical view ]
SUPFAMi SSF53335. SSF53335. 1 hit.
SSF57903. SSF57903. 1 hit.
PROSITEi PS51533. ADD. 1 hit.
PS00094. C5_MTASE_1. 1 hit.
PS50812. PWWP. 1 hit.
PS51679. SAM_MT_C5. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.
    , 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. 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. Cited for: FUNCTION, INTERACTION WITH THE PRC2/EED-EZH2 COMPLEX.
  12. "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.
  13. "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.
  14. "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.
  15. "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.
  16. "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.
  17. "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].
  18. "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.
  19. "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.
  20. "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.
  21. "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.
  22. Cited for: VARIANTS ICF1 VAL-585; THR-603; ALA-606; GLY-699; GLY-726; PRO-766; ARG-814 AND MET-818.
  23. 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.

Entry informationi

Entry nameiDNM3B_HUMAN
AccessioniPrimary (citable) accession number: Q9UBC3
Secondary accession number(s): A2A2E2
, B4DSM8, B4DSU1, E1P5M6, E1P5M7, E7EN63, E9PBF2, Q9UBD4, Q9UJQ5, Q9UKA6, Q9UNE5, Q9Y5R9, Q9Y5S0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: May 1, 2000
Last modified: September 3, 2014
This is version 144 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

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