MultifacetedProtDB - Bologna Biocomputing Group

EC number	EC number description
2.1.1.-	Transferases; Transferring one-carbon groups; Methyltransferases;
2.1.1.367	Transferases; Transferring one-carbon groups; Methyltransferases; [histone H3]-lysine9 N-methyltransferase

Structure

PDB	Resolution (Å)	PDB name
2IGQ	2.0	Human euchromatic histone methyltransferase 1
2RFI	1.59	Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide
3B7B	2.99	EuHMT1 (Glp) Ankyrin Repeat Domain (Structure 1)
3B95	2.99	EuHMT1 (Glp) Ankyrin Repeat Domain (Structure 2)
3FPD	2.4	G9a-like protein lysine methyltransferase inhibition by BIX-01294
3HNA	1.5	Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and mono-Methylated H3K9 Peptide
3MO0	2.78	Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E11
3MO2	2.49	human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67
3MO5	2.14	Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72
3SW9	3.05	GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me0 peptide
3SWC	2.332	GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide
4I51	1.9	Methyltransferase domain of HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, mutant Y1211A
5TTG	1.66	Crystal structure of catalytic domain of GLP with MS012
5TUZ	1.95	Structure of human GLP SET-domain (EHMT1) in complex with inhibitor MS0124
5V9J	1.74	Crystal structure of catalytic domain of GLP with MS0105
5VSD	1.85	Structure of human GLP SET-domain (EHMT1) in complex with inhibitor 13
5VSF	1.7	Structure of human GLP SET-domain (EHMT1) in complex with inhibitor 17
6BY9	2.3	Crystal structure of EHMT1
6MBO	1.591	GLP Methyltransferase with Inhibitor EML741-P212121 Crystal Form
6MBP	1.947	GLP Methyltransferase with Inhibitor EML741- P3121 Crystal Form
7T7M	2.85	Structure of human GLP SET-domain (EHMT1) in complex with covalent inhibitor (Compound 1)

GO term

GO ontology	GO term	GO description
Biological Process	GO:0006306	DNA methylation
Biological Process	GO:0006325	chromatin organization
Biological Process	GO:0140718	facultative heterochromatin formation
Biological Process	GO:0034968	histone lysine methylation
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:0018027	peptidyl-lysine dimethylation
Biological Process	GO:0018026	peptidyl-lysine monomethylation
Biological Process	GO:0120162	positive regulation of cold-induced thermogenesis
Biological Process	GO:0045995	regulation of embryonic development
Molecular Function	GO:0070742	C2H2 zinc finger domain binding
Molecular Function	GO:0046976	histone H3K27 methyltransferase activity
Molecular Function	GO:0046974	histone H3K9 methyltransferase activity
Molecular Function	GO:0140947	histone H3K9me2 methyltransferase activity
Molecular Function	GO:0008168	methyltransferase activity
Molecular Function	GO:0002039	p53 binding
Molecular Function	GO:0016279	protein-lysine N-methyltransferase activity
Molecular Function	GO:0001222	transcription corepressor binding
Molecular Function	GO:0008270	zinc ion binding
Cellular Component	GO:0000785	chromatin
Cellular Component	GO:0016604	nuclear body
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus

InterPro / Pfam

InterPro	InterPro name
IPR001214	SET domain
IPR002110	Ankyrin repeat
IPR007728	Pre-SET domain
IPR036770	Ankyrin repeat-containing domain superfamily
IPR038035	Histone-lysine N-methyltransferase EHMT1, SET domain
IPR043550	Histone-lysine N-methyltransferase EHMT1/EHMT2
IPR046341	SET domain superfamily

Pfam	Pfam name
PF00856	SET domain
PF05033	Pre-SET motif
PF12796	Ankyrin repeats (3 copies)
PF13637	Ankyrin repeats (many copies)

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-2559582	Senescence-Associated Secretory Phenotype (SASP)	Leaf	R-HSA-8953897	Cellular responses to stimuli
R-HSA-3214841	PKMTs methylate histone lysines	Leaf	R-HSA-4839726	Chromatin organization
R-HSA-6804760	Regulation of TP53 Activity through Methylation	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-8853884	Transcriptional Regulation by VENTX	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-8953750	Transcriptional Regulation by E2F6	Leaf	R-HSA-74160	Gene expression (Transcription)

Subcellular location

Interactor | Variant | Drug

Phenotype

HPO ID	HPO name
HP:0000006	Autosomal dominant inheritance
HP:0000023	Inguinal hernia
HP:0000028	Cryptorchidism
HP:0000035	Abnormal testis morphology
HP:0000047	Hypospadias
HP:0000054	Micropenis
HP:0000076	Vesicoureteral reflux
HP:0000077	Abnormality of the kidney
HP:0000078	Abnormality of the genital system
HP:0000083	Renal insufficiency
HP:0000158	Macroglossia
HP:0000164	Abnormality of the dentition
HP:0000179	Thick lower lip vermilion
HP:0000232	Everted lower lip vermilion
HP:0000248	Brachycephaly
HP:0000252	Microcephaly
HP:0000272	Malar flattening
HP:0000280	Coarse facial features
HP:0000303	Mandibular prognathia
HP:0000316	Hypertelorism
HP:0000365	Hearing impairment
HP:0000377	Abnormal pinna morphology
HP:0000463	Anteverted nares
HP:0000519	Developmental cataract
HP:0000540	Hypermetropia
HP:0000582	Upslanted palpebral fissure
HP:0000664	Synophrys
HP:0000695	Natal tooth
HP:0000708	Atypical behavior
HP:0000716	Depression
HP:0000717	Autism
HP:0000718	Aggressive behavior
HP:0000722	Compulsive behaviors
HP:0000729	Autistic behavior
HP:0000733	Abnormal repetitive mannerisms
HP:0000737	Irritability
HP:0000739	Anxiety
HP:0000741	Apathy
HP:0000750	Delayed speech and language development
HP:0000826	Precocious puberty
HP:0000954	Single transverse palmar crease
HP:0000974	Hyperextensible skin
HP:0001156	Brachydactyly
HP:0001182	Tapered finger
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001252	Hypotonia
HP:0001263	Global developmental delay
HP:0001270	Motor delay
HP:0001274	Agenesis of corpus callosum
HP:0001290	Generalized hypotonia
HP:0001321	Cerebellar hypoplasia
HP:0001328	Specific learning disability
HP:0001331	Absent septum pellucidum
HP:0001357	Plagiocephaly
HP:0001508	Failure to thrive
HP:0001510	Growth delay
HP:0001513	Obesity
HP:0001520	Large for gestational age
HP:0001537	Umbilical hernia
HP:0001548	Overgrowth
HP:0001627	Abnormal heart morphology
HP:0001636	Tetralogy of Fallot
HP:0001650	Aortic valve stenosis
HP:0001659	Aortic regurgitation
HP:0001671	Abnormal cardiac septum morphology
HP:0001680	Coarctation of aorta
HP:0001710	Conotruncal defect
HP:0001762	Talipes equinovarus
HP:0001999	Abnormal facial shape
HP:0002020	Gastroesophageal reflux
HP:0002023	Anal atresia
HP:0002079	Hypoplasia of the corpus callosum
HP:0002119	Ventriculomegaly
HP:0002120	Cerebral cortical atrophy
HP:0002121	Generalized non-motor (absence) seizure
HP:0002133	Status epilepticus
HP:0002171	Gliosis
HP:0002194	Delayed gross motor development
HP:0002205	Recurrent respiratory infections
HP:0002300	Mutism
HP:0002360	Sleep disturbance
HP:0002381	Aphasia
HP:0002463	Language impairment
HP:0002500	Abnormal cerebral white matter morphology
HP:0002553	Highly arched eyebrow
HP:0002714	Downturned corners of mouth
HP:0002719	Recurrent infections
HP:0002779	Tracheomalacia
HP:0002786	Tracheobronchomalacia
HP:0003196	Short nose
HP:0003745	Sporadic
HP:0004322	Short stature
HP:0005469	Flat occiput
HP:0006335	Persistence of primary teeth
HP:0006863	Severe expressive language delay
HP:0008736	Hypoplasia of penis
HP:0009909	Uplifted earlobe
HP:0010529	Echolalia
HP:0010806	U-Shaped upper lip vermilion
HP:0010808	Protruding tongue
HP:0010864	Intellectual disability, severe
HP:0011097	Epileptic spasm
HP:0011351	Moderate receptive language delay
HP:0011800	Midface retrusion
HP:0011968	Feeding difficulties
HP:0012157	Subcortical cerebral atrophy
HP:0012210	Abnormal renal morphology
HP:0012368	Flat face
HP:0100308	Cerebral cortical hemiatrophy
HP:0100541	Femoral hernia
HP:0100716	Self-injurious behavior
HP:0200005	Abnormal shape of the palpebral fissure
HP:0410263	Brain imaging abnormality

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adrenal gland	glandular cells	Low	Approved
appendix	glandular cells	Low	Approved
bone marrow	hematopoietic cells	Low	Approved
breast	glandular cells	Low	Approved
bronchus	respiratory epithelial cells	Medium	Approved
caudate	glial cells	Low	Approved
caudate	neuronal cells	Low	Approved
cerebral cortex	glial cells	Low	Approved
cerebral cortex	neuronal cells	Low	Approved
cervix	squamous epithelial cells	Low	Approved
colon	glandular cells	Medium	Approved
duodenum	glandular cells	Low	Approved
endometrium 1	cells in endometrial stroma	Low	Approved
endometrium 2	cells in endometrial stroma	Low	Approved
endometrium 2	glandular cells	Medium	Approved
epididymis	glandular cells	Low	Approved
esophagus	squamous epithelial cells	Medium	Approved
fallopian tube	glandular cells	Medium	Approved
gallbladder	glandular cells	Medium	Approved
kidney	cells in glomeruli	Low	Approved
kidney	cells in tubules	Medium	Approved
lung	alveolar cells type I	Medium	Approved
lung	alveolar cells type II	Medium	Approved
lung	macrophages	Low	Approved
nasopharynx	respiratory epithelial cells	Medium	Approved
pancreas	exocrine glandular cells	Low	Approved
parathyroid gland	glandular cells	Low	Approved
placenta	trophoblastic cells	Medium	Approved
prostate	glandular cells	Medium	Approved
rectum	glandular cells	Medium	Approved
salivary gland	glandular cells	Low	Approved
seminal vesicle	glandular cells	Low	Approved
skin 1	keratinocytes	Low	Approved
skin 2	epidermal cells	Low	Approved
smooth muscle	smooth muscle cells	Low	Approved
stomach 1	glandular cells	Medium	Approved
stomach 2	glandular cells	Medium	Approved
testis	cells in seminiferous ducts	Medium	Approved
thyroid gland	glandular cells	Medium	Approved
tonsil	squamous epithelial cells	Low	Approved
urinary bladder	urothelial cells	Medium	Approved
vagina	squamous epithelial cells	Medium	Approved

Disease

Disease name	MONDO ID	ICD10	ICD10 chapter	OMIM	Orphanet
kleefstra syndrome due to a point mutation	MONDO:0016865	Q87	chapter17, Congenital malformations, deformations and chromosomal abnormalities		Orphanet:261652
kleefstra syndrome 1	MONDO:0027407	Q87	chapter17, Congenital malformations, deformations and chromosomal abnormalities	OMIM:610253

Location	ECO term	Pubmed
Chromosome
Nucleus

Summary of Q9H9B1

Gene: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D
Protein: Histone-lysine N-methyltransferase EHMT1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of Q9H9B1

Gene: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D Protein: Histone-lysine N-methyltransferase EHMT1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D
Protein: Histone-lysine N-methyltransferase EHMT1