MultifacetedProtDB - Bologna Biocomputing Group

Structure

PDB	Resolution (Å)	PDB name
1QK9		The solution structure of the domain from MeCP2 that binds to methylated DNA
3C2I	2.5	The Crystal Structure of Methyl-CpG Binding Domain of Human MeCP2 in Complex with a Methylated DNA Sequence from BDNF
5BT2	2.2	MeCP2 MBD domain (A140V) in complex with methylated DNA
6C1Y	2.3	mbd of human mecp2 in complex with methylated DNA
6OGJ	1.8	MeCP2 MBD in complex with DNA
6OGK	1.65	MeCP2 MBD in complex with DNA
6YWW	2.102	MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion

GO term

GO ontology	GO term	GO description
Biological Process	GO:0007219	Notch signaling pathway
Biological Process	GO:0008344	adult locomotory behavior
Biological Process	GO:0001662	behavioral fear response
Biological Process	GO:0006576	biogenic amine metabolic process
Biological Process	GO:0032048	cardiolipin metabolic process
Biological Process	GO:0050432	catecholamine secretion
Biological Process	GO:0021549	cerebellum development
Biological Process	GO:0016358	dendrite development
Biological Process	GO:0060079	excitatory postsynaptic potential
Biological Process	GO:0014009	glial cell proliferation
Biological Process	GO:0008211	glucocorticoid metabolic process
Biological Process	GO:0006541	glutamine metabolic process
Biological Process	GO:0031507	heterochromatin formation
Biological Process	GO:0016573	histone acetylation
Biological Process	GO:0016571	histone methylation
Biological Process	GO:0006020	inositol metabolic process
Biological Process	GO:0007616	long-term memory
Biological Process	GO:0060291	long-term synaptic potentiation
Biological Process	GO:0007052	mitotic spindle organization
Biological Process	GO:0045892	negative regulation of DNA-templated transcription
Biological Process	GO:0016525	negative regulation of angiogenesis
Biological Process	GO:0043537	negative regulation of blood vessel endothelial cell migration
Biological Process	GO:0010629	negative regulation of gene expression
Biological Process	GO:0043524	negative regulation of neuron apoptotic process
Biological Process	GO:0051151	negative regulation of smooth muscle cell differentiation
Biological Process	GO:0000122	negative regulation of transcription by RNA polymerase II
Biological Process	GO:2000820	negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation
Biological Process	GO:0001976	nervous system process involved in regulation of systemic arterial blood pressure
Biological Process	GO:0042551	neuron maturation
Biological Process	GO:0046470	phosphatidylcholine metabolic process
Biological Process	GO:1905643	positive regulation of DNA methylation
Biological Process	GO:0010971	positive regulation of G2/M transition of mitotic cell cycle
Biological Process	GO:0008284	positive regulation of cell population proliferation
Biological Process	GO:0060252	positive regulation of glial cell proliferation
Biological Process	GO:1900114	positive regulation of histone H3-K9 trimethylation
Biological Process	GO:0090063	positive regulation of microtubule nucleation
Biological Process	GO:0045944	positive regulation of transcription by RNA polymerase II
Biological Process	GO:0009791	post-embryonic development
Biological Process	GO:0019230	proprioception
Biological Process	GO:0008104	protein localization
Biological Process	GO:0006349	regulation of gene expression by genomic imprinting
Biological Process	GO:0002087	regulation of respiratory gaseous exchange by nervous system process
Biological Process	GO:0007585	respiratory gaseous exchange by respiratory system
Biological Process	GO:0001666	response to hypoxia
Biological Process	GO:0051707	response to other organism
Biological Process	GO:0019233	sensory perception of pain
Biological Process	GO:0035176	social behavior
Biological Process	GO:0001964	startle response
Biological Process	GO:0007416	synapse assembly
Biological Process	GO:0099191	trans-synaptic signaling by BDNF
Biological Process	GO:0021591	ventricular system development
Biological Process	GO:0008542	visual learning
Molecular Function	GO:0003677	DNA binding
Molecular Function	GO:0003700	DNA-binding transcription factor activity
Molecular Function	GO:0003723	RNA binding
Molecular Function	GO:0003682	chromatin binding
Molecular Function	GO:0010385	double-stranded methylated DNA binding
Molecular Function	GO:0003729	mRNA binding
Molecular Function	GO:0008327	methyl-CpG binding
Molecular Function	GO:0060090	molecular adaptor activity
Molecular Function	GO:0140693	molecular condensate scaffold activity
Molecular Function	GO:0003676	nucleic acid binding
Molecular Function	GO:1990841	promoter-specific chromatin binding
Molecular Function	GO:0035197	siRNA binding
Molecular Function	GO:0003714	transcription corepressor activity
Cellular Component	GO:0005813	centrosome
Cellular Component	GO:0005829	cytosol
Cellular Component	GO:0005615	extracellular space
Cellular Component	GO:0000792	heterochromatin
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus
Cellular Component	GO:0098794	postsynapse

InterPro / Pfam

InterPro	InterPro name
IPR001739	Methyl-CpG DNA binding
IPR016177	DNA-binding domain superfamily
IPR017353	Methyl-CpG binding protein MeCP2
IPR045138	Methyl-CpG binding protein MeCP2/MBD4

Pfam	Pfam name
PF01429	Methyl-CpG binding domain

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-8986944	Transcriptional Regulation by MECP2	Internal node	R-HSA-74160	Gene expression (Transcription)
R-HSA-9022534	Loss of MECP2 binding ability to 5hmC-DNA	Leaf	R-HSA-1643685	Disease
R-HSA-9022535	Loss of phosphorylation of MECP2 at T308	Leaf	R-HSA-1643685	Disease
R-HSA-9022537	Loss of MECP2 binding ability to the NCoR/SMRT complex	Leaf	R-HSA-1643685	Disease
R-HSA-9022538	Loss of MECP2 binding ability to 5mC-DNA	Leaf	R-HSA-1643685	Disease
R-HSA-9022692	Regulation of MECP2 expression and activity	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9022699	MECP2 regulates neuronal receptors and channels	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9022702	MECP2 regulates transcription of neuronal ligands	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9022707	MECP2 regulates transcription factors	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9022927	MECP2 regulates transcription of genes involved in GABA signaling	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-9725371	Nuclear events stimulated by ALK signaling in cancer	Leaf	R-HSA-1643685	Disease

Subcellular location

Location	ECO term	Pubmed
Nucleus	ECO:0000250

Interactor | Variant | Drug

Phenotype

HPO ID	HPO name
HP:0000470	Short neck
HP:0011800	Midface retrusion
HP:0200055	Small hand
HP:0031793	Increased serum leptin
HP:0008947	Infantile muscular hypotonia
HP:0002882	Sudden episodic apnea
HP:0001298	Encephalopathy
HP:0000758	Abnormal nonverbal communicative behavior
HP:0000716	Depression
HP:0000426	Prominent nasal bridge
HP:0002063	Rigidity
HP:0003808	Abnormal muscle tone
HP:0000713	Agitation
HP:0002019	Constipation
HP:0000218	High palate
HP:0001300	Parkinsonism
HP:0002650	Scoliosis
HP:0030215	Inappropriate crying
HP:0000463	Anteverted nares
HP:0002353	EEG abnormality
HP:0006919	Abnormal aggressive, impulsive or violent behavior
HP:0002371	Loss of speech
HP:0002061	Lower limb spasticity
HP:0002039	Anorexia
HP:0011188	Focal EEG discharges with secondary generalization
HP:0100703	Tongue thrusting
HP:0000739	Anxiety
HP:0000748	Inappropriate laughter
HP:0032169	Severe infection
HP:0002194	Delayed gross motor development
HP:0001635	Congestive heart failure
HP:0012450	Chronic constipation
HP:0003676	Progressive
HP:0000400	Macrotia
HP:0003781	Excessive salivation
HP:0001319	Neonatal hypotonia
HP:0000232	Everted lower lip vermilion
HP:0003677	Slowly progressive
HP:0003577	Congenital onset
HP:0025403	Stooped posture
HP:0010845	EEG with generalized slow activity
HP:0003487	Babinski sign
HP:0001510	Growth delay
HP:0001118	Juvenile cataract
HP:0004322	Short stature
HP:0002078	Truncal ataxia
HP:0025387	Pill-rolling tremor
HP:0007021	Pain insensitivity
HP:0000709	Psychosis
HP:0001256	Intellectual disability, mild
HP:0025430	High-pitched cry
HP:0002395	Lower limb hyperreflexia
HP:0002333	Motor deterioration
HP:0000771	Gynecomastia
HP:0032588	Hand apraxia
HP:0001258	Spastic paraplegia
HP:0005484	Secondary microcephaly
HP:0002916	Abnormality of chromosome segregation
HP:0000712	Emotional lability
HP:0000721	Lack of spontaneous play
HP:0000431	Wide nasal bridge
HP:0001082	Cholecystitis
HP:0001417	X-linked inheritance
HP:0001773	Short foot
HP:0002104	Apnea
HP:0012171	Stereotypical hand wringing
HP:0000272	Malar flattening
HP:0002322	Resting tremor
HP:0002876	Episodic tachypnea
HP:0100022	Abnormality of movement
HP:0003593	Infantile onset
HP:0011463	Childhood onset
HP:0002120	Cerebral cortical atrophy
HP:0001336	Myoclonus
HP:0002362	Shuffling gait
HP:0004299	Hernia of the abdominal wall
HP:0000717	Autism
HP:0001251	Ataxia
HP:0001337	Tremor
HP:0000582	Upslanted palpebral fissure
HP:0002205	Recurrent respiratory infections
HP:0001508	Failure to thrive
HP:0002191	Progressive spasticity
HP:0002093	Respiratory insufficiency
HP:0032792	Tonic seizure
HP:0008762	Repetitive compulsive behavior
HP:0002121	Generalized non-motor (absence) seizure
HP:0002342	Intellectual disability, moderate
HP:0007302	Bipolar affective disorder
HP:0004305	Involuntary movements
HP:0000252	Microcephaly
HP:0001347	Hyperreflexia
HP:0012719	Functional abnormality of the gastrointestinal tract
HP:0000248	Brachycephaly
HP:0008872	Feeding difficulties in infancy
HP:0001387	Joint stiffness
HP:0001371	Flexion contracture
HP:0006801	Hyperactive deep tendon reflexes
HP:0005135	Abnormal T-wave
HP:0001266	Choreoathetosis
HP:0002187	Intellectual disability, profound
HP:0000767	Pectus excavatum
HP:0000297	Facial hypotonia
HP:0012332	Abnormal autonomic nervous system physiology
HP:0002151	Increased serum lactate
HP:0010804	Tented upper lip vermilion
HP:0000750	Delayed speech and language development
HP:0001288	Gait disturbance
HP:0002133	Status epilepticus
HP:0100852	Abnormal fear/anxiety-related behavior
HP:0007110	Central hypoventilation
HP:0004209	Clinodactyly of the 5th finger
HP:0010521	Gait apraxia
HP:0012469	Infantile spasms
HP:0003763	Bruxism
HP:0001761	Pes cavus
HP:0000817	Reduced eye contact
HP:0001239	Wrist flexion contracture
HP:0002020	Gastroesophageal reflux
HP:0011451	Primary microcephaly
HP:0001344	Absent speech
HP:0000508	Ptosis
HP:0002751	Kyphoscoliosis
HP:0002066	Gait ataxia
HP:0001297	Stroke
HP:0002136	Broad-based gait
HP:0000253	Progressive microcephaly
HP:0004326	Cachexia
HP:0002167	Abnormality of speech or vocalization
HP:0030217	Limb apraxia
HP:0002015	Dysphagia
HP:0000347	Micrognathia
HP:0000053	Macroorchidism
HP:0045084	Limb myoclonus
HP:0003202	Skeletal muscle atrophy
HP:0003144	Increased serum serotonin
HP:0002072	Chorea
HP:0007281	Developmental stagnation
HP:0011344	Severe global developmental delay
HP:0007824	Total ophthalmoplegia
HP:0011968	Feeding difficulties
HP:0000581	Blepharophimosis
HP:0000735	Impaired social interactions
HP:0002510	Spastic tetraplegia
HP:0001513	Obesity
HP:0001252	Hypotonia
HP:0001257	Spasticity
HP:0032989	Delayed ability to roll over
HP:0004325	Decreased body weight
HP:0001419	X-linked recessive inheritance
HP:0002126	Polymicrogyria
HP:0025336	Delayed ability to sit
HP:0002186	Apraxia
HP:0001423	X-linked dominant inheritance
HP:0000164	Abnormality of the dentition
HP:0000718	Aggressive behavior
HP:0008936	Axial hypotonia
HP:0005324	Disturbance of facial expression
HP:0007328	Impaired pain sensation
HP:0003542	Increased serum pyruvate
HP:0001263	Global developmental delay
HP:0002750	Delayed skeletal maturation
HP:0001332	Dystonia
HP:0006887	Intellectual disability, progressive
HP:0005709	2-3 toe cutaneous syndactyly
HP:0005184	Prolonged QTc interval
HP:0000026	Male hypogonadism
HP:0001987	Hyperammonemia
HP:0032988	Persistent head lag
HP:0031936	Delayed ability to walk
HP:0010864	Intellectual disability, severe
HP:0002307	Drooling
HP:0002332	Lack of peer relationships
HP:0002490	Increased CSF lactate
HP:0002376	Developmental regression
HP:0001250	Seizure
HP:0002067	Bradykinesia
HP:0000723	Restrictive behavior
HP:0000687	Widely spaced teeth
HP:0000286	Epicanthus
HP:0031473	Hostility
HP:0002355	Difficulty walking
HP:0000733	Abnormal repetitive mannerisms
HP:0000711	Restlessness
HP:0000160	Narrow mouth
HP:0002808	Kyphosis
HP:0002719	Recurrent infections
HP:0025269	Panic attack
HP:0001249	Intellectual disability
HP:0005280	Depressed nasal bridge
HP:0002064	Spastic gait
HP:0000256	Macrocephaly
HP:0000729	Autistic behavior
HP:0004302	Functional motor deficit
HP:0002793	Abnormal pattern of respiration
HP:0000369	Low-set ears
HP:0002360	Sleep disturbance
HP:0000047	Hypospadias
HP:0002505	Loss of ambulation
HP:0000752	Hyperactivity
HP:0000028	Cryptorchidism
HP:0002540	Inability to walk
HP:0000737	Irritability
HP:0004879	Intermittent hyperventilation
HP:0002123	Generalized myoclonic seizure
HP:0002300	Mutism

Tissue and cell type

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

Disease name	MONDO ID	ICD10	ICD10 chapter	OMIM	Orphanet
angelman syndrome	MONDO:0007113	Q93	chapter17, Congenital malformations, deformations and chromosomal abnormalities	OMIM:105830	Orphanet:72
x-linked intellectual disability-psychosis-macroorchidism syndrome	MONDO:0010235	F71	chapter5, Mental and behavioural disorders	OMIM:300055	Orphanet:3077
syndromic x-linked intellectual disability lubs type	MONDO:0010283	Q87	chapter17, Congenital malformations, deformations and chromosomal abnormalities	OMIM:300260	Orphanet:1762
syndromic x-linked intellectual disability lubs type	MONDO:0010283	Q99	chapter17, Congenital malformations, deformations and chromosomal abnormalities	OMIM:300260	Orphanet:1762
autism- susceptibility to- x-linked 3	MONDO:0010342	F84	chapter5, Mental and behavioural disorders	OMIM:300496
severe neonatal-onset encephalopathy with microcephaly	MONDO:0010397	Q02	chapter17, Congenital malformations, deformations and chromosomal abnormalities	OMIM:300673	Orphanet:209370
rett syndrome	MONDO:0010726	F84	chapter5, Mental and behavioural disorders	OMIM:312750	Orphanet:778
atypical rett syndrome	MONDO:0017746	F84	chapter5, Mental and behavioural disorders		Orphanet:3095
non-syndromic x-linked intellectual disability	MONDO:0019181	F70	chapter5, Mental and behavioural disorders	OMIMPS:309530	Orphanet:777

Summary of P51608

Gene: MECP2
Protein: Methyl-CpG-binding protein 2

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of P51608

Gene: MECP2 Protein: Methyl-CpG-binding protein 2

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: MECP2
Protein: Methyl-CpG-binding protein 2