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Q9Y6K1

- DNM3A_HUMAN

UniProt

Q9Y6K1 - DNM3A_HUMAN

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Protein

DNA (cytosine-5)-methyltransferase 3A

Gene

DNMT3A

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. It modifies DNA in a non-processive manner and also methylates non-CpG sites. May preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. Plays a role in paternal and maternal imprinting. Required for methylation of most imprinted loci in germ cells. Acts as a transcriptional corepressor for ZBTB18. Recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. Can actively repress transcription through the recruitment of HDAC activity.1 Publication

Catalytic activityi

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

Enzyme regulationi

Activated by binding to the regulatory factor DNMT3L.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei664 – 6641S-adenosyl-L-methionineCurated
Active sitei710 – 7101PROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri493 – 52331GATA-type; atypicalPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri534 – 59057PHD-type; atypicalPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

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

GO - Biological processi

  1. C-5 methylation of cytosine Source: GOC
  2. cellular response to amino acid stimulus Source: Ensembl
  3. DNA methylation Source: UniProtKB
  4. DNA methylation involved in embryo development Source: Ensembl
  5. DNA methylation involved in gamete generation Source: Ensembl
  6. DNA methylation on cytosine within a CG sequence Source: Ensembl
  7. hypermethylation of CpG island Source: Ensembl
  8. methylation-dependent chromatin silencing Source: Ensembl
  9. negative regulation of transcription from RNA polymerase II promoter Source: Ensembl
  10. regulation of gene expression by genetic imprinting Source: UniProtKB
  11. S-adenosylhomocysteine metabolic process Source: Ensembl
  12. S-adenosylmethioninamine metabolic process Source: Ensembl
  13. spermatogenesis Source: Ensembl
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Methyltransferase, Repressor, Transferase

Keywords - Ligandi

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

Enzyme and pathway databases

BRENDAi2.1.1.37. 2681.
ReactomeiREACT_200808. PRC2 methylates histones and DNA.
REACT_228108. RMTs methylate histone arginines.
REACT_267652. DNA methylation.

Protein family/group databases

REBASEi4119. M.HsaDnmt3A.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA (cytosine-5)-methyltransferase 3A (EC:2.1.1.37)
Short name:
Dnmt3a
Alternative name(s):
DNA methyltransferase HsaIIIA
Short name:
DNA MTase HsaIIIA
Short name:
M.HsaIIIA
Gene namesi
Name:DNMT3A
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 2

Organism-specific databases

HGNCiHGNC:2978. DNMT3A.

Subcellular locationi

Nucleus 1 Publication. Cytoplasm 1 Publication
Note: Accumulates in the major satellite repeats at pericentric heterochromatin.By similarity

GO - Cellular componenti

  1. chromosome, centromeric region Source: Ensembl
  2. cytoplasm Source: UniProtKB
  3. euchromatin Source: UniProtKB
  4. nuclear heterochromatin Source: Ensembl
  5. nuclear matrix Source: UniProtKB
  6. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Involvement in diseasei

Tatton-Brown-Rahman syndrome (TBRS) [MIM:615879]: An overgrowth syndrome characterized by a distinctive facial appearance, tall stature and intellectual disability. Facial gestalt is characterized by a round face, heavy horizontal eyebrows and narrow palpebral fissures. Less common features include atrial septal defects, seizures, umbilical hernia, and scoliosis.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti310 – 3101I → N in TBRS; somatic mutation. 1 Publication
VAR_071463
Natural varianti532 – 5321G → S in TBRS; somatic mutation. 1 Publication
VAR_071464
Natural varianti548 – 5481M → K in TBRS; somatic mutation. 1 Publication
VAR_071465
Natural varianti549 – 5491C → R in TBRS; somatic mutation. 1 Publication
VAR_071466
Natural varianti648 – 6481L → P in TBRS; somatic mutation. 1 Publication
VAR_071467
Natural varianti700 – 7001P → L in TBRS; somatic mutation. 1 Publication
VAR_071468
Natural varianti749 – 7491R → C in TBRS; somatic mutation. 1 Publication
VAR_071469
Natural varianti838 – 8381N → D in TBRS; somatic mutation. 1 Publication
VAR_071470
Natural varianti902 – 9021F → S in TBRS; somatic mutation. 1 Publication
VAR_071471
Natural varianti904 – 9041P → L in TBRS; somatic mutation. 1 Publication
VAR_071472

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi732 – 7321F → A: Loss of activity du to the incapacity to bind the regulatory subunit DNMT3L. 1 Publication

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

MIMi615879. phenotype.
Orphaneti404443. Tall stature-intellectual disability-facial dysmorphism syndrome.
PharmGKBiPA27445.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 912912DNA (cytosine-5)-methyltransferase 3APRO_0000088043Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei105 – 1051Phosphoserine3 Publications
Modified residuei243 – 2431Phosphoserine2 Publications
Modified residuei255 – 2551Phosphoserine1 Publication
Modified residuei261 – 2611Phosphothreonine1 Publication
Modified residuei267 – 2671Phosphoserine1 Publication

Post-translational modificationi

Sumoylated; sumoylation disrupts the ability to interact with histone deacetylases (HDAC1 and HDAC2) and repress transcription.By similarity

Keywords - PTMi

Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiQ9Y6K1.
PaxDbiQ9Y6K1.
PRIDEiQ9Y6K1.

PTM databases

PhosphoSiteiQ9Y6K1.

Expressioni

Tissue specificityi

Highly expressed in fetal tissues, skeletal muscle, heart, peripheral blood mononuclear cells, kidney, and at lower levels in placenta, brain, liver, colon, spleen, small intestine and lung.1 Publication

Gene expression databases

BgeeiQ9Y6K1.
CleanExiHS_DNMT3A.
ExpressionAtlasiQ9Y6K1. baseline and differential.
GenevestigatoriQ9Y6K1.

Organism-specific databases

HPAiCAB009469.
HPA026588.

Interactioni

Subunit structurei

Heterotetramer composed of 1 DNMT3A homodimer and 2 DNMT3L subunits (DNMT3L-DNMT3A-DNMT3A-DNMT3L). Interacts with UBC9, PIAS1 and PIAS2 (By similarity). Binds the ZBTB18 transcriptional repressor. Interacts with SETDB1. Associates with HDAC1 through its ADD domain. Interacts with UHRF1 (By similarity). Interacts with DNMT1 and DNMT3B. Interacts with the PRC2/EED-EZH2 complex. Interacts with MPHOSPH8. Interacts with histone H3 that is not methylated at 'Lys-4' (H3K4).By similarity7 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself4EBI-923653,EBI-923653
EEDO755302EBI-923653,EBI-923794
EZH2Q159106EBI-923653,EBI-530054
H3F3BP842437EBI-923653,EBI-120658
SETDB1Q150477EBI-923653,EBI-79691
UHRF1Q96T887EBI-923653,EBI-1548946

Protein-protein interaction databases

BioGridi108125. 53 interactions.
DIPiDIP-38004N.
IntActiQ9Y6K1. 20 interactions.
STRINGi9606.ENSP00000264709.

Structurei

Secondary structure

1
912
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi295 – 2984Combined sources
Beta strandi306 – 3116Combined sources
Helixi313 – 3153Combined sources
Beta strandi325 – 3306Combined sources
Turni331 – 3333Combined sources
Beta strandi336 – 3405Combined sources
Helixi341 – 3433Combined sources
Beta strandi344 – 3463Combined sources
Helixi347 – 3493Combined sources
Helixi350 – 3534Combined sources
Helixi356 – 3616Combined sources
Helixi363 – 38018Combined sources
Helixi399 – 41113Combined sources
Turni415 – 4173Combined sources
Helixi419 – 4224Combined sources
Helixi476 – 4849Combined sources
Helixi490 – 4923Combined sources
Turni495 – 4973Combined sources
Beta strandi507 – 5137Combined sources
Helixi515 – 52410Combined sources
Beta strandi532 – 5365Combined sources
Turni538 – 5403Combined sources
Beta strandi544 – 5485Combined sources
Turni552 – 5543Combined sources
Beta strandi557 – 5593Combined sources
Helixi560 – 5667Combined sources
Helixi571 – 5766Combined sources
Beta strandi578 – 5803Combined sources
Turni584 – 5863Combined sources
Beta strandi595 – 5973Combined sources
Helixi601 – 6099Combined sources
Beta strandi634 – 6396Combined sources
Turni642 – 6443Combined sources
Helixi645 – 6528Combined sources
Beta strandi657 – 6637Combined sources
Helixi667 – 67610Combined sources
Turni677 – 6793Combined sources
Beta strandi681 – 6844Combined sources
Helixi687 – 6893Combined sources
Helixi692 – 6976Combined sources
Beta strandi702 – 7065Combined sources
Helixi711 – 7133Combined sources
Turni722 – 7243Combined sources
Turni726 – 7294Combined sources
Helixi730 – 74112Combined sources
Beta strandi752 – 76110Combined sources
Helixi763 – 77311Combined sources
Helixi782 – 7843Combined sources
Beta strandi786 – 7883Combined sources
Beta strandi791 – 7966Combined sources
Beta strandi801 – 8033Combined sources
Helixi815 – 8173Combined sources
Beta strandi824 – 8307Combined sources
Beta strandi850 – 8523Combined sources
Beta strandi855 – 8573Combined sources
Helixi861 – 8688Combined sources
Turni872 – 8754Combined sources
Helixi882 – 8909Combined sources
Helixi895 – 9028Combined sources
Helixi903 – 9086Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2QRVX-ray2.89A/D/E/H627-912[»]
3A1AX-ray2.30A476-614[»]
3A1BX-ray2.29A476-614[»]
3LLRX-ray2.30A/B/C/D/E275-427[»]
3SVMX-ray2.31P40-53[»]
ProteinModelPortaliQ9Y6K1.
SMRiQ9Y6K1. Positions 283-425, 475-912.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9Y6K1.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini292 – 35059PWWPPROSITE-ProRule annotationAdd
BLAST
Domaini482 – 614133ADDPROSITE-ProRule annotationAdd
BLAST
Domaini634 – 912279SAM-dependent MTase C5-typePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni199 – 403205Interaction with DNMT1 and DNMT3BAdd
BLAST
Regioni494 – 58693Interaction with the PRC2/EED-EZH2 complexBy similarityAdd
BLAST
Regioni641 – 6455S-adenosyl-L-methionine bindingCurated
Regioni686 – 6883S-adenosyl-L-methionine bindingCurated
Regioni891 – 8933S-adenosyl-L-methionine bindingCurated

Domaini

The PWWP domain is essential for targeting to pericentric heterochromatin. It specifically recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3) (By similarity).By similarity

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.PROSITE-ProRule annotation
Contains 1 ADD domain.PROSITE-ProRule annotation
Contains 1 GATA-type zinc finger.PROSITE-ProRule annotation
Contains 1 PHD-type zinc finger.PROSITE-ProRule annotation
Contains 1 PWWP domain.PROSITE-ProRule annotation
Contains 1 SAM-dependent MTase C5-type domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri493 – 52331GATA-type; atypicalPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri534 – 59057PHD-type; atypicalPROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG70699.
GeneTreeiENSGT00390000008341.
HOGENOMiHOG000230875.
HOVERGENiHBG051381.
InParanoidiQ9Y6K1.
KOiK17398.
OMAiFVGGMCQ.
OrthoDBiEOG7MWGW6.
PhylomeDBiQ9Y6K1.
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.
[Graphical view]
PfamiPF00145. DNA_methylase. 1 hit.
PF00855. PWWP. 1 hit.
[Graphical view]
SMARTiSM00293. PWWP. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 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 (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative promoter usage and alternative splicing. Align

Isoform 1 (identifier: Q9Y6K1-1) [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

        10         20         30         40         50
MPAMPSSGPG DTSSSAAERE EDRKDGEEQE EPRGKEERQE PSTTARKVGR
60 70 80 90 100
PGRKRKHPPV ESGDTPKDPA VISKSPSMAQ DSGASELLPN GDLEKRSEPQ
110 120 130 140 150
PEEGSPAGGQ KGGAPAEGEG AAETLPEASR AVENGCCTPK EGRGAPAEAG
160 170 180 190 200
KEQKETNIES MKMEGSRGRL RGGLGWESSL RQRPMPRLTF QAGDPYYISK
210 220 230 240 250
RKRDEWLARW KREAEKKAKV IAGMNAVEEN QGPGESQKVE EASPPAVQQP
260 270 280 290 300
TDPASPTVAT TPEPVGSDAG DKNATKAGDD EPEYEDGRGF GIGELVWGKL
310 320 330 340 350
RGFSWWPGRI VSWWMTGRSR AAEGTRWVMW FGDGKFSVVC VEKLMPLSSF
360 370 380 390 400
CSAFHQATYN KQPMYRKAIY EVLQVASSRA GKLFPVCHDS DESDTAKAVE
410 420 430 440 450
VQNKPMIEWA LGGFQPSGPK GLEPPEEEKN PYKEVYTDMW VEPEAAAYAP
460 470 480 490 500
PPPAKKPRKS TAEKPKVKEI IDERTRERLV YEVRQKCRNI EDICISCGSL
510 520 530 540 550
NVTLEHPLFV GGMCQNCKNC FLECAYQYDD DGYQSYCTIC CGGREVLMCG
560 570 580 590 600
NNNCCRCFCV ECVDLLVGPG AAQAAIKEDP WNCYMCGHKG TYGLLRRRED
610 620 630 640 650
WPSRLQMFFA NNHDQEFDPP KVYPPVPAEK RKPIRVLSLF DGIATGLLVL
660 670 680 690 700
KDLGIQVDRY IASEVCEDSI TVGMVRHQGK IMYVGDVRSV TQKHIQEWGP
710 720 730 740 750
FDLVIGGSPC NDLSIVNPAR KGLYEGTGRL FFEFYRLLHD ARPKEGDDRP
760 770 780 790 800
FFWLFENVVA MGVSDKRDIS RFLESNPVMI DAKEVSAAHR ARYFWGNLPG
810 820 830 840 850
MNRPLASTVN DKLELQECLE HGRIAKFSKV RTITTRSNSI KQGKDQHFPV
860 870 880 890 900
FMNEKEDILW CTEMERVFGF PVHYTDVSNM SRLARQRLLG RSWSVPVIRH
910
LFAPLKEYFA CV
Length:912
Mass (Da):101,858
Last modified:January 15, 2008 - v4
Checksum:iBD1FF7C5B4F54A33
GO
Isoform 2 (identifier: Q9Y6K1-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-213: MPAMPSSGPG...DEWLARWKRE → MGILERVVRRNGRVDRSLKDECDT

Note: It is uncertain whether Met-1 or Met-35 is the initiator.

Show »
Length:723
Mass (Da):81,613
Checksum:i19341BDAE1B71C8B
GO
Isoform 3 (identifier: Q9Y6K1-3) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     151-166: KEQKETNIESMKMEGS → ESSAPGAASSGPTSIP
     167-912: Missing.

Note: Produced by alternative splicing.

Show »
Length:166
Mass (Da):16,866
Checksum:i78756A71196D61B5
GO

Sequence cautioni

The sequence AAL57039.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAN40037.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti310 – 3101I → N in TBRS; somatic mutation. 1 Publication
VAR_071463
Natural varianti532 – 5321G → S in TBRS; somatic mutation. 1 Publication
VAR_071464
Natural varianti548 – 5481M → K in TBRS; somatic mutation. 1 Publication
VAR_071465
Natural varianti549 – 5491C → R in TBRS; somatic mutation. 1 Publication
VAR_071466
Natural varianti648 – 6481L → P in TBRS; somatic mutation. 1 Publication
VAR_071467
Natural varianti699 – 6991G → D in a patient with chronic myelomonocytic leukemia. 1 Publication
VAR_067234
Natural varianti700 – 7001P → L in TBRS; somatic mutation. 1 Publication
VAR_071468
Natural varianti731 – 7311Missing in a patient with chronic myelomonocytic leukemia. 1 Publication
VAR_067235
Natural varianti749 – 7491R → C in TBRS; somatic mutation. 1 Publication
VAR_071469
Natural varianti838 – 8381N → D in TBRS; somatic mutation. 1 Publication
VAR_071470
Natural varianti882 – 8821R → C in a patient with chronic myelomonocytic leukemia; somatic mutation. 1 Publication
VAR_067236
Natural varianti882 – 8821R → H in a patient with chronic myelomonocytic leukemia; somatic mutation. 1 Publication
VAR_067237
Natural varianti882 – 8821R → P in a patient with chronic myelomonocytic leukemia; somatic mutation. 1 Publication
VAR_067238
Natural varianti902 – 9021F → S in TBRS; somatic mutation. 1 Publication
VAR_071471
Natural varianti904 – 9041P → L in TBRS; somatic mutation. 1 Publication
VAR_071472

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 213213MPAMP…RWKRE → MGILERVVRRNGRVDRSLKD ECDT in isoform 2. 1 PublicationVSP_046254Add
BLAST
Alternative sequencei151 – 16616KEQKE…KMEGS → ESSAPGAASSGPTSIP in isoform 3. 1 PublicationVSP_040998Add
BLAST
Alternative sequencei167 – 912746Missing in isoform 3. 1 PublicationVSP_040999Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF067972 mRNA. Translation: AAD33084.2.
AF480163 mRNA. Translation: AAN40037.1. Different initiation.
AF331856 mRNA. Translation: AAL57039.1. Different initiation.
AC012074 Genomic DNA. Translation: AAY14761.1.
CH471053 Genomic DNA. Translation: EAX00727.1.
BC032392 mRNA. Translation: AAH32392.1.
BC043617 mRNA. Translation: AAH43617.1.
BC051864 mRNA. Translation: AAH51864.1.
CCDSiCCDS1718.2. [Q9Y6K1-2]
CCDS33157.1. [Q9Y6K1-1]
CCDS46232.1. [Q9Y6K1-3]
RefSeqiNP_072046.2. NM_022552.4. [Q9Y6K1-1]
NP_715640.2. NM_153759.3. [Q9Y6K1-2]
NP_783328.1. NM_175629.2. [Q9Y6K1-1]
NP_783329.1. NM_175630.1. [Q9Y6K1-3]
XP_005264232.1. XM_005264175.2. [Q9Y6K1-1]
XP_005264233.1. XM_005264176.1. [Q9Y6K1-1]
XP_005264234.1. XM_005264177.2.
UniGeneiHs.515840.

Genome annotation databases

EnsembliENST00000264709; ENSP00000264709; ENSG00000119772. [Q9Y6K1-1]
ENST00000321117; ENSP00000324375; ENSG00000119772. [Q9Y6K1-1]
ENST00000380746; ENSP00000370122; ENSG00000119772. [Q9Y6K1-2]
ENST00000402667; ENSP00000384237; ENSG00000119772.
ENST00000406659; ENSP00000384852; ENSG00000119772. [Q9Y6K1-3]
GeneIDi1788.
KEGGihsa:1788.
UCSCiuc002rgc.4. human. [Q9Y6K1-1]
uc002rgf.3. human. [Q9Y6K1-3]

Polymorphism databases

DMDMi166215081.

Keywords - Coding sequence diversityi

Alternative promoter usage, Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF067972 mRNA. Translation: AAD33084.2 .
AF480163 mRNA. Translation: AAN40037.1 . Different initiation.
AF331856 mRNA. Translation: AAL57039.1 . Different initiation.
AC012074 Genomic DNA. Translation: AAY14761.1 .
CH471053 Genomic DNA. Translation: EAX00727.1 .
BC032392 mRNA. Translation: AAH32392.1 .
BC043617 mRNA. Translation: AAH43617.1 .
BC051864 mRNA. Translation: AAH51864.1 .
CCDSi CCDS1718.2. [Q9Y6K1-2 ]
CCDS33157.1. [Q9Y6K1-1 ]
CCDS46232.1. [Q9Y6K1-3 ]
RefSeqi NP_072046.2. NM_022552.4. [Q9Y6K1-1 ]
NP_715640.2. NM_153759.3. [Q9Y6K1-2 ]
NP_783328.1. NM_175629.2. [Q9Y6K1-1 ]
NP_783329.1. NM_175630.1. [Q9Y6K1-3 ]
XP_005264232.1. XM_005264175.2. [Q9Y6K1-1 ]
XP_005264233.1. XM_005264176.1. [Q9Y6K1-1 ]
XP_005264234.1. XM_005264177.2.
UniGenei Hs.515840.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2QRV X-ray 2.89 A/D/E/H 627-912 [» ]
3A1A X-ray 2.30 A 476-614 [» ]
3A1B X-ray 2.29 A 476-614 [» ]
3LLR X-ray 2.30 A/B/C/D/E 275-427 [» ]
3SVM X-ray 2.31 P 40-53 [» ]
ProteinModelPortali Q9Y6K1.
SMRi Q9Y6K1. Positions 283-425, 475-912.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 108125. 53 interactions.
DIPi DIP-38004N.
IntActi Q9Y6K1. 20 interactions.
STRINGi 9606.ENSP00000264709.

Chemistry

BindingDBi Q9Y6K1.
ChEMBLi CHEMBL3137291.

Protein family/group databases

REBASEi 4119. M.HsaDnmt3A.

PTM databases

PhosphoSitei Q9Y6K1.

Polymorphism databases

DMDMi 166215081.

Proteomic databases

MaxQBi Q9Y6K1.
PaxDbi Q9Y6K1.
PRIDEi Q9Y6K1.

Protocols and materials databases

DNASUi 1788.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000264709 ; ENSP00000264709 ; ENSG00000119772 . [Q9Y6K1-1 ]
ENST00000321117 ; ENSP00000324375 ; ENSG00000119772 . [Q9Y6K1-1 ]
ENST00000380746 ; ENSP00000370122 ; ENSG00000119772 . [Q9Y6K1-2 ]
ENST00000402667 ; ENSP00000384237 ; ENSG00000119772 .
ENST00000406659 ; ENSP00000384852 ; ENSG00000119772 . [Q9Y6K1-3 ]
GeneIDi 1788.
KEGGi hsa:1788.
UCSCi uc002rgc.4. human. [Q9Y6K1-1 ]
uc002rgf.3. human. [Q9Y6K1-3 ]

Organism-specific databases

CTDi 1788.
GeneCardsi GC02M025455.
HGNCi HGNC:2978. DNMT3A.
HPAi CAB009469.
HPA026588.
MIMi 602769. gene.
615879. phenotype.
neXtProti NX_Q9Y6K1.
Orphaneti 404443. Tall stature-intellectual disability-facial dysmorphism syndrome.
PharmGKBi PA27445.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG70699.
GeneTreei ENSGT00390000008341.
HOGENOMi HOG000230875.
HOVERGENi HBG051381.
InParanoidi Q9Y6K1.
KOi K17398.
OMAi FVGGMCQ.
OrthoDBi EOG7MWGW6.
PhylomeDBi Q9Y6K1.
TreeFami TF329039.

Enzyme and pathway databases

BRENDAi 2.1.1.37. 2681.
Reactomei REACT_200808. PRC2 methylates histones and DNA.
REACT_228108. RMTs methylate histone arginines.
REACT_267652. DNA methylation.

Miscellaneous databases

ChiTaRSi DNMT3A. human.
EvolutionaryTracei Q9Y6K1.
GenomeRNAii 1788.
NextBioi 7279.
PROi Q9Y6K1.
SOURCEi Search...

Gene expression databases

Bgeei Q9Y6K1.
CleanExi HS_DNMT3A.
ExpressionAtlasi Q9Y6K1. baseline and differential.
Genevestigatori Q9Y6K1.

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.
[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.
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] (ISOFORM 1).
    Tissue: Fetal testis.
  2. "A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation."
    Chen T., Ueda Y., Xie S., Li E.
    J. Biol. Chem. 277:38746-38754(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
  3. "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: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH DNMT1 AND DNMT3B, SUBCELLULAR LOCATION.
  4. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
    Tissue: Lung, PNS and Skin.
  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: TISSUE SPECIFICITY.
  8. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
    Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
    Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-105, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  9. "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.
  10. Cited for: FUNCTION, INTERACTION WITH THE PRC2/EED-EZH2 COMPLEX.
  11. "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.
  12. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-105, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  13. "Methyl-H3K9-binding protein MPP8 mediates E-cadherin gene silencing and promotes tumour cell motility and invasion."
    Kokura K., Sun L., Bedford M.T., Fang J.
    EMBO J. 29:3673-3687(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH MPHOSPH8.
  14. "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-243, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  15. "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-105; SER-243; SER-255; THR-261 AND SER-267, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  16. Cited for: INVOLVEMENT IN TBRS, VARIANTS TBRS ASN-310; SER-532; LYS-548; ARG-549; PRO-648; LEU-700; CYS-749; ASP-838; SER-902 AND LEU-904.
  17. "Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation."
    Jia D., Jurkowska R.Z., Zhang X., Jeltsch A., Cheng X.
    Nature 449:248-251(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.89 ANGSTROMS) OF 627-909 IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE, SUBUNIT, MUTAGENESIS OF PHE-732.
  18. "Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain."
    Otani J., Nankumo T., Arita K., Inamoto S., Ariyoshi M., Shirakawa M.
    EMBO Rep. 10:1235-1241(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.29 ANGSTROMS) OF 476-614 IN COMPLEXES WITH ZINC AND WITH HISTONE H3 PEPTIDE, SUBUNIT.
  19. "MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a."
    Chang Y., Sun L., Kokura K., Horton J.R., Fukuda M., Espejo A., Izumi V., Koomen J.M., Bedford M.T., Zhang X., Shinkai Y., Fang J., Cheng X.
    Nat. Commun. 2:533-533(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.31 ANGSTROMS) OF 40-53 IN COMPLEX WITH MPHOSPH8, INTERACTION WITH MPHOSPH8.
  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 (2.30 ANGSTROMS) OF 275-427.
  21. "Mutational spectrum analysis of chronic myelomonocytic leukemia includes genes associated with epigenetic regulation: UTX, EZH2, and DNMT3A."
    Jankowska A.M., Makishima H., Tiu R.V., Szpurka H., Huang Y., Traina F., Visconte V., Sugimoto Y., Prince C., O'Keefe C., Hsi E.D., List A., Sekeres M.A., Rao A., McDevitt M.A., Maciejewski J.P.
    Blood 118:3932-3941(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANTS ASP-699; PHE-731 DEL; CYS-882; HIS-882 AND PRO-882.

Entry informationi

Entry nameiDNM3A_HUMAN
AccessioniPrimary (citable) accession number: Q9Y6K1
Secondary accession number(s): E9PEB8
, Q86TE8, Q86XF5, Q8IZV0, Q8WXU9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: January 15, 2008
Last modified: November 26, 2014
This is version 133 of the entry and version 4 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 2
    Human chromosome 2: 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

Dasty 3