MultifacetedProtDB - Bologna Biocomputing Group

EC number	EC number description
2.1.1.-	Transferases; Transferring one-carbon groups; Methyltransferases;
2.1.1.37	Transferases; Transferring one-carbon groups; Methyltransferases; DNA (cytosine-5-)-methyltransferase

Structure

PDB	Resolution (Å)	PDB name
2QRV	2.89	Structure of Dnmt3a-Dnmt3L C-terminal domain complex
3A1A	2.3	Crystal Structure of the DNMT3A ADD domain
3A1B	2.292	Crystal structure of the DNMT3A ADD domain in complex with histone H3
3LLR	2.3	Crystal structure of the PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 alpha
3SVM	2.31	Human MPP8 - human DNMT3AK47me2 peptide
4QBQ	2.406	Crystal structure of DNMT3a ADD domain bound to H3 peptide
4QBR	1.902	Crystal structure of DNMT3a ADD domain G550D mutant bound to H3 peptide
4QBS	1.8	Crystal structure of DNMT3a ADD domain E545R mutant bound to H3T3ph peptide
4U7P	3.821	Crystal structure of DNMT3A-DNMT3L complex
4U7T	2.9	Crystal structure of DNMT3A-DNMT3L in complex with histone H3
5YX2	2.653	Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two CpG sites
6BRR	2.97	Crystal structure of DNMT3A (R836A)-DNMT3L in complex with DNA containing two CpG sites
6F57	3.098	Crystal structure of DNMT3A-DNMT3L in complex with single CpG-containing DNA
6PA7	2.94	The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome.
6W89	2.499	Structure of DNMT3A (R882H) in complex with CGA DNA
6W8B	2.4	Structure of DNMT3A in complex with CGA DNA
6W8D	2.598	Structure of DNMT3A (R882H) in complex with CGT DNA
6W8J	2.445	Structure of DNMT3A (R882H) in complex with CAG DNA
8BA5	1.45	Crystal structure of the DNMT3A ADD domain

GO term

GO ontology	GO term	GO description
Biological Process	GO:0090116	C-5 methylation of cytosine
Biological Process	GO:0006306	DNA methylation
Biological Process	GO:0043045	DNA methylation involved in embryo development
Biological Process	GO:0043046	DNA methylation involved in gamete generation
Biological Process	GO:0032776	DNA methylation on cytosine
Biological Process	GO:0006346	DNA methylation-dependent heterochromatin formation
Biological Process	GO:0007568	aging
Biological Process	GO:0071230	cellular response to amino acid stimulus
Biological Process	GO:1903926	cellular response to bisphenol A
Biological Process	GO:0071361	cellular response to ethanol
Biological Process	GO:0071456	cellular response to hypoxia
Biological Process	GO:0097284	hepatocyte apoptotic process
Biological Process	GO:0000278	mitotic cell cycle
Biological Process	GO:0045892	negative regulation of DNA-templated transcription
Biological Process	GO:0000122	negative regulation of transcription by RNA polymerase II
Biological Process	GO:0030182	neuron differentiation
Biological Process	GO:0010942	positive regulation of cell death
Biological Process	GO:0006349	regulation of gene expression by genomic imprinting
Biological Process	GO:0042220	response to cocaine
Biological Process	GO:0032355	response to estradiol
Biological Process	GO:0010212	response to ionizing radiation
Biological Process	GO:0010288	response to lead ion
Biological Process	GO:0009636	response to toxic substance
Biological Process	GO:0033189	response to vitamin A
Biological Process	GO:0009410	response to xenobiotic stimulus
Biological Process	GO:0007283	spermatogenesis
Molecular Function	GO:0003886	DNA (cytosine-5-)-methyltransferase activity
Molecular Function	GO:0003677	DNA binding
Molecular Function	GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding
Molecular Function	GO:0061629	RNA polymerase II-specific DNA-binding transcription factor binding
Molecular Function	GO:0003682	chromatin binding
Molecular Function	GO:0042802	identical protein binding
Molecular Function	GO:0046872	metal ion binding
Molecular Function	GO:0106363	protein-cysteine methyltransferase activity
Molecular Function	GO:0003714	transcription corepressor activity
Cellular Component	GO:0001741	XY body
Cellular Component	GO:1902494	catalytic complex
Cellular Component	GO:0000775	chromosome, centromeric region
Cellular Component	GO:0005737	cytoplasm
Cellular Component	GO:0000791	euchromatin
Cellular Component	GO:0000792	heterochromatin
Cellular Component	GO:0016363	nuclear matrix
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus

InterPro / Pfam

InterPro	InterPro name
IPR000313	PWWP domain
IPR001525	C-5 cytosine methyltransferase
IPR018117	DNA methylase, C-5 cytosine-specific, active site
IPR025766	ADD domain
IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
IPR040552	DNMT3, cysteine rich ADD domain
IPR044108	DNA (cytosine-5)-methyltransferase 3A, ADD domain

Pfam	Pfam name
PF00145	C-5 cytosine-specific DNA methylase
PF00855	PWWP domain
PF17980	Cysteine rich ADD domain in DNMT3

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-212300	PRC2 methylates histones and DNA	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-3214858	RMTs methylate histone arginines	Leaf	R-HSA-4839726	Chromatin organization
R-HSA-4655427	SUMOylation of DNA methylation proteins	Leaf	R-HSA-392499	Metabolism of proteins
R-HSA-5334118	DNA methylation	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9710421	Defective pyroptosis	Leaf	R-HSA-1643685	Disease

Subcellular location

Location	ECO term	Pubmed
Chromosome	ECO:0000269	PubMed:12138111
Cytoplasm	ECO:0000269	PubMed:12145218
Nucleus	ECO:0000269	PubMed:12138111
Nucleus	ECO:0000269	PubMed:12145218

Interactor | Variant | Drug

Phenotype

HPO ID	HPO name
HP:0000006	Autosomal dominant inheritance
HP:0000028	Cryptorchidism
HP:0000076	Vesicoureteral reflux
HP:0000093	Proteinuria
HP:0000096	Glomerular sclerosis
HP:0000098	Tall stature
HP:0000233	Thin vermilion border
HP:0000252	Microcephaly
HP:0000256	Macrocephaly
HP:0000280	Coarse facial features
HP:0000286	Epicanthus
HP:0000303	Mandibular prognathia
HP:0000311	Round face
HP:0000316	Hypertelorism
HP:0000337	Broad forehead
HP:0000405	Conductive hearing impairment
HP:0000463	Anteverted nares
HP:0000486	Strabismus
HP:0000574	Thick eyebrow
HP:0000581	Blepharophimosis
HP:0000609	Optic nerve hypoplasia
HP:0000708	Atypical behavior
HP:0000718	Aggressive behavior
HP:0000739	Anxiety
HP:0000740	Episodic paroxysmal anxiety
HP:0000750	Delayed speech and language development
HP:0000790	Hematuria
HP:0000878	11 pairs of ribs
HP:0000980	Pallor
HP:0001069	Episodic hyperhidrosis
HP:0001095	Hypertensive retinopathy
HP:0001230	Broad metacarpals
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001252	Hypotonia
HP:0001256	Intellectual disability, mild
HP:0001263	Global developmental delay
HP:0001293	Cranial nerve compression
HP:0001337	Tremor
HP:0001342	Cerebral hemorrhage
HP:0001382	Joint hypermobility
HP:0001428	Somatic mutation
HP:0001511	Intrauterine growth retardation
HP:0001513	Obesity
HP:0001528	Hemihypertrophy
HP:0001537	Umbilical hernia
HP:0001548	Overgrowth
HP:0001566	Widely-spaced maxillary central incisors
HP:0001605	Vocal cord paralysis
HP:0001618	Dysphonia
HP:0001629	Ventricular septal defect
HP:0001631	Atrial septal defect
HP:0001635	Congestive heart failure
HP:0001643	Patent ductus arteriosus
HP:0001653	Mitral regurgitation
HP:0001824	Weight loss
HP:0001831	Short toe
HP:0001962	Palpitations
HP:0002000	Short columella
HP:0002002	Deep philtrum
HP:0002018	Nausea
HP:0002119	Ventriculomegaly
HP:0002263	Exaggerated cupid's bow
HP:0002308	Chiari malformation
HP:0002331	Recurrent paroxysmal headache
HP:0002342	Intellectual disability, moderate
HP:0002373	Febrile seizure (within the age range of 3 months to 6 years)
HP:0002376	Developmental regression
HP:0002574	Episodic abdominal pain
HP:0002616	Aortic root aneurysm
HP:0002640	Hypertension associated with pheochromocytoma
HP:0002650	Scoliosis
HP:0002668	Paraganglioma
HP:0002751	Kyphoscoliosis
HP:0002864	Paraganglioma of head and neck
HP:0003072	Hypercalcemia
HP:0003345	Elevated urinary norepinephrine
HP:0003508	Proportionate short stature
HP:0003510	Severe short stature
HP:0003574	Positive regitine blocking test
HP:0003577	Congenital onset
HP:0003639	Elevated urinary epinephrine
HP:0004325	Decreased body weight
HP:0004442	Sagittal craniosynostosis
HP:0004684	Talipes valgus
HP:0004808	Acute myeloid leukemia
HP:0005180	Tricuspid regurgitation
HP:0006009	Broad phalanx
HP:0006737	Extraadrenal pheochromocytoma
HP:0006748	Adrenal pheochromocytoma
HP:0007099	Chiari type I malformation
HP:0007302	Bipolar affective disorder
HP:0008070	Sparse hair
HP:0008094	Widely spaced toes
HP:0008629	Pulsatile tinnitus
HP:0008947	Infantile muscular hypotonia
HP:0009803	Short phalanx of finger
HP:0010049	Short metacarpal
HP:0010499	Patellar subluxation
HP:0010532	Paroxysmal vertigo
HP:0010803	Everted upper lip vermilion
HP:0010864	Intellectual disability, severe
HP:0011228	Horizontal eyebrow
HP:0011407	Proportionate tall stature
HP:0011688	Supraventricular tachycardia with an accessory connection mediated pathway
HP:0011703	Sinus tachycardia
HP:0011979	Elevated urinary dopamine
HP:0012324	Myeloid leukemia
HP:0012378	Fatigue
HP:0025116	Fetal distress
HP:0025269	Panic attack
HP:0031284	Flushing
HP:0040197	Encephalomalacia
HP:0045025	Narrow palpebral fissure
HP:0100634	Neuroendocrine neoplasm
HP:0100749	Chest pain
HP:0100753	Schizophrenia

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adipose tissue	adipocytes	Medium	Approved
adrenal gland	glandular cells	High	Approved
appendix	glandular cells	High	Approved
appendix	lymphoid tissue	High	Approved
bone marrow	hematopoietic cells	Low	Approved
breast	adipocytes	High	Approved
breast	glandular cells	High	Approved
breast	myoepithelial cells	High	Approved
bronchus	respiratory epithelial cells	High	Approved
caudate	glial cells	Medium	Approved
caudate	neuronal cells	Medium	Approved
cerebellum	cells in granular layer	High	Approved
cerebellum	cells in molecular layer	Low	Approved
cerebral cortex	endothelial cells	Medium	Approved
cerebral cortex	glial cells	Medium	Approved
cerebral cortex	neuronal cells	Medium	Approved
cerebral cortex	neuropil	Medium	Approved
cervix	glandular cells	High	Approved
cervix	squamous epithelial cells	High	Approved
colon	endothelial cells	High	Approved
colon	glandular cells	High	Approved
colon	peripheral nerve/ganglion	High	Approved
duodenum	glandular cells	High	Approved
endometrium 1	cells in endometrial stroma	Low	Approved
endometrium 1	glandular cells	High	Approved
endometrium 2	cells in endometrial stroma	Medium	Approved
endometrium 2	glandular cells	High	Approved
epididymis	glandular cells	High	Approved
esophagus	squamous epithelial cells	High	Approved
fallopian tube	glandular cells	High	Approved
gallbladder	glandular cells	High	Approved
heart muscle	cardiomyocytes	Medium	Approved
hippocampus	glial cells	Low	Approved
hippocampus	neuronal cells	Medium	Approved
kidney	cells in glomeruli	High	Approved
kidney	cells in tubules	High	Approved
liver	cholangiocytes	Low	Approved
liver	hepatocytes	High	Approved
lung	alveolar cells	Medium	Approved
lung	macrophages	High	Approved
lymph node	germinal center cells	High	Approved
lymph node	non-germinal center cells	High	Approved
nasopharynx	respiratory epithelial cells	High	Approved
oral mucosa	squamous epithelial cells	High	Approved
ovary	follicle cells	High	Approved
ovary	ovarian stroma cells	Medium	Approved
pancreas	exocrine glandular cells	High	Approved
pancreas	pancreatic endocrine cells	High	Approved
parathyroid gland	glandular cells	High	Approved
placenta	decidual cells	High	Approved
placenta	trophoblastic cells	High	Approved
prostate	glandular cells	Medium	Approved
rectum	glandular cells	High	Approved
salivary gland	glandular cells	High	Approved
seminal vesicle	glandular cells	High	Approved
skeletal muscle	myocytes	High	Approved
skin 1	Langerhans	High	Approved
skin 1	fibroblasts	High	Approved
skin 1	keratinocytes	High	Approved
skin 1	melanocytes	High	Approved
skin 2	epidermal cells	High	Approved
small intestine	glandular cells	High	Approved
smooth muscle	smooth muscle cells	High	Approved
soft tissue 1	fibroblasts	High	Approved
soft tissue 1	peripheral nerve	Medium	Approved
soft tissue 2	fibroblasts	High	Approved
soft tissue 2	peripheral nerve	Medium	Approved
spleen	cells in red pulp	Medium	Approved
spleen	cells in white pulp	Medium	Approved
stomach 1	glandular cells	High	Approved
stomach 2	glandular cells	High	Approved
testis	Leydig cells	High	Approved
testis	cells in seminiferous ducts	High	Approved
thyroid gland	glandular cells	High	Approved
tonsil	germinal center cells	High	Approved
tonsil	non-germinal center cells	High	Approved
tonsil	squamous epithelial cells	High	Approved
urinary bladder	urothelial cells	High	Approved
vagina	squamous epithelial cells	High	Approved

Disease name	MONDO ID	ICD10	ICD10 chapter	OMIM	Orphanet
lung adenocarcinoma	MONDO:0005061	C34	chapter2, Neoplasms		Orphanet:415268
tall stature-intellectual disability-facial dysmorphism syndrome	MONDO:0014382	Q87	chapter17, Congenital malformations, deformations and chromosomal abnormalities	OMIM:615879	Orphanet:404443
sporadic pheochromocytoma/secreting paraganglioma	MONDO:0017190	C74	chapter2, Neoplasms		Orphanet:276621
sporadic pheochromocytoma/secreting paraganglioma	MONDO:0017190	D35	chapter2, Neoplasms		Orphanet:276621
glioblastoma	MONDO:0018177	C71	chapter2, Neoplasms		Orphanet:360
acute myeloid leukemia	MONDO:0018874	C92	chapter2, Neoplasms	OMIM:601626	Orphanet:519
myelodysplastic syndrome	MONDO:0018881	D46	chapter2, Neoplasms	OMIM:614286	Orphanet:52688
heyn-sproul-jackson syndrome	MONDO:0032882	-	-	OMIM:618724

Summary of Q9Y6K1

Gene: DNMT3A
Protein: DNA (cytosine-5)-methyltransferase 3A

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of Q9Y6K1

Gene: DNMT3A Protein: DNA (cytosine-5)-methyltransferase 3A

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: DNMT3A
Protein: DNA (cytosine-5)-methyltransferase 3A