MultifacetedProtDB - Bologna Biocomputing Group

EC number	EC number description
3.6.4.12	Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement; DNA helicase.

Structure

PDB	Resolution (Å)	PDB name
5IVW	10.0	Human core TFIIH bound to DNA within the PIC
5IY6	7.2	Human holo-PIC in the closed state
5IY7	8.6	Human holo-PIC in the open state
5IY8	7.9	Human holo-PIC in the initial transcribing state
5IY9	6.3	Human holo-PIC in the initial transcribing state (no IIS)
5OF4	4.4	The cryo-EM structure of human TFIIH
6NMI	3.7	Cryo-EM structure of the human TFIIH core complex
6O9L	7.2	Human holo-PIC in the closed state
6O9M	4.4	Structure of the human apo TFIIH
6RO4	3.5	Structure of the core TFIIH-XPA-DNA complex
6TUN	2.07	Helicase domain complex
7AD8	3.5	Core TFIIH-XPA-DNA complex with modelled p62 subunit
7EGB	3.3	TFIID-based holo PIC on SCP promoter
7EGC	3.9	p53-bound TFIID-based holo PIC on HDM2 promoter
7ENA	4.07	TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED)
7ENC	4.13	TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED)
7LBM	4.8	Structure of the human Mediator-bound transcription pre-initiation complex
7NVR	4.5	Human Mediator with RNA Polymerase II Pre-initiation complex
7NVW	4.3	TFIIH in a pre-translocated state (without ADP-BeF3)
7NVX	3.9	TFIIH in a post-translocated state (with ADP-BeF3)
7NVY	7.3	RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position
7NVZ	7.2	RNA polymerase II pre-initiation complex with closed promoter DNA in distal position
7NW0	6.6	RNA polymerase II pre-initiation complex with open promoter DNA
8GXQ	5.04	PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state
8GXS	4.16	PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state

GO term

GO ontology	GO term	GO description
Biological Process	GO:0009650	UV protection
Biological Process	GO:0006915	apoptotic process
Biological Process	GO:0030282	bone mineralization
Biological Process	GO:0032289	central nervous system myelin formation
Biological Process	GO:0007059	chromosome segregation
Biological Process	GO:0008340	determination of adult lifespan
Biological Process	GO:0040016	embryonic cleavage
Biological Process	GO:0043249	erythrocyte maturation
Biological Process	GO:0030198	extracellular matrix organization
Biological Process	GO:0035315	hair cell differentiation
Biological Process	GO:0048820	hair follicle maturation
Biological Process	GO:0060218	hematopoietic stem cell differentiation
Biological Process	GO:0071425	hematopoietic stem cell proliferation
Biological Process	GO:0001701	in utero embryonic development
Biological Process	GO:0048009	insulin-like growth factor receptor signaling pathway
Biological Process	GO:0072332	intrinsic apoptotic signaling pathway by p53 class mediator
Biological Process	GO:0000462	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
Biological Process	GO:0035264	multicellular organism growth
Biological Process	GO:0006289	nucleotide-excision repair
Biological Process	GO:0043388	positive regulation of DNA binding
Biological Process	GO:0045951	positive regulation of mitotic recombination
Biological Process	GO:0009791	post-embryonic development
Biological Process	GO:1901990	regulation of mitotic cell cycle phase transition
Biological Process	GO:0006979	response to oxidative stress
Biological Process	GO:0021510	spinal cord development
Biological Process	GO:0006366	transcription by RNA polymerase II
Biological Process	GO:0006362	transcription elongation by RNA polymerase I
Biological Process	GO:0006283	transcription-coupled nucleotide-excision repair
Molecular Function	GO:0051539	4 iron, 4 sulfur cluster binding
Molecular Function	GO:0043139	5'-3' DNA helicase activity
Molecular Function	GO:0005524	ATP binding
Molecular Function	GO:0016887	ATP hydrolysis activity
Molecular Function	GO:0003678	DNA helicase activity
Molecular Function	GO:0003684	damaged DNA binding
Molecular Function	GO:0046872	metal ion binding
Molecular Function	GO:0030674	protein-macromolecule adaptor activity
Cellular Component	GO:0070516	CAK-ERCC2 complex
Cellular Component	GO:0071817	MMXD complex
Cellular Component	GO:0005737	cytoplasm
Cellular Component	GO:0005829	cytosol
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus
Cellular Component	GO:0005819	spindle
Cellular Component	GO:0005669	transcription factor TFIID complex
Cellular Component	GO:0000439	transcription factor TFIIH core complex
Cellular Component	GO:0005675	transcription factor TFIIH holo complex

InterPro / Pfam

InterPro	InterPro name
IPR001945	RAD3/XPD family
IPR002464	DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site
IPR006554	Helicase-like, DEXD box c2 type
IPR006555	ATP-dependent helicase, C-terminal
IPR010614	RAD3-like helicase, DEAD
IPR010643	Helical and beta-bridge domain
IPR013020	ATP-dependent helicase Rad3/Chl1-like
IPR014013	Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type
IPR027417	P-loop containing nucleoside triphosphate hydrolase
IPR045028	Helicase superfamily 1/2, DinG/Rad3-like

Pfam	Pfam name
PF06733	DEAD_2
PF06777	Helical and beta-bridge domain
PF13307	Helicase C-terminal domain

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-112382	Formation of RNA Pol II elongation complex	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-113418	Formation of the Early Elongation Complex	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-167152	Formation of HIV elongation complex in the absence of HIV Tat	Leaf	R-HSA-1643685	Disease
R-HSA-167158	Formation of the HIV-1 Early Elongation Complex	Leaf	R-HSA-1643685	Disease
R-HSA-167160	RNA Pol II CTD phosphorylation and interaction with CE during HIV infection	Leaf	R-HSA-1643685	Disease
R-HSA-167161	HIV Transcription Initiation	Leaf	R-HSA-1643685	Disease
R-HSA-167162	RNA Polymerase II HIV Promoter Escape	Leaf	R-HSA-1643685	Disease
R-HSA-167172	Transcription of the HIV genome	Internal node	R-HSA-1643685	Disease
R-HSA-167200	Formation of HIV-1 elongation complex containing HIV-1 Tat	Leaf	R-HSA-1643685	Disease
R-HSA-167246	Tat-mediated elongation of the HIV-1 transcript	Internal node	R-HSA-1643685	Disease
R-HSA-2564830	Cytosolic iron-sulfur cluster assembly	Leaf	R-HSA-1430728	Metabolism
R-HSA-427413	NoRC negatively regulates rRNA expression	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-5696395	Formation of Incision Complex in GG-NER	Leaf	R-HSA-73894	DNA Repair
R-HSA-5696400	Dual Incision in GG-NER	Leaf	R-HSA-73894	DNA Repair
R-HSA-674695	RNA Polymerase II Pre-transcription Events	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-6781823	Formation of TC-NER Pre-Incision Complex	Leaf	R-HSA-73894	DNA Repair
R-HSA-6781827	Transcription-Coupled Nucleotide Excision Repair (TC-NER)	Internal node	R-HSA-73894	DNA Repair
R-HSA-6782135	Dual incision in TC-NER	Leaf	R-HSA-73894	DNA Repair
R-HSA-6782210	Gap-filling DNA repair synthesis and ligation in TC-NER	Leaf	R-HSA-73894	DNA Repair
R-HSA-6796648	TP53 Regulates Transcription of DNA Repair Genes	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-72086	mRNA Capping	Leaf	R-HSA-8953854	Metabolism of RNA
R-HSA-73762	RNA Polymerase I Transcription Initiation	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-73772	RNA Polymerase I Promoter Escape	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-73776	RNA Polymerase II Promoter Escape	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-73779	RNA Polymerase II Transcription Pre-Initiation And Promoter Opening	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-73863	RNA Polymerase I Transcription Termination	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-75953	RNA Polymerase II Transcription Initiation	Leaf	R-HSA-74160	Gene expression (Transcription)
R-HSA-75955	RNA Polymerase II Transcription Elongation	Internal node	R-HSA-74160	Gene expression (Transcription)
R-HSA-76042	RNA Polymerase II Transcription Initiation And Promoter Clearance	Internal node	R-HSA-74160	Gene expression (Transcription)
R-HSA-77075	RNA Pol II CTD phosphorylation and interaction with CE	Leaf	R-HSA-74160	Gene expression (Transcription)

Subcellular location

Location	ECO term	Pubmed
Cytoplasm, cytoskeleton, spindle	ECO:0000269	PubMed:20797633
Nucleus	ECO:0000269	PubMed:20797633
Nucleus	ECO:0000269	PubMed:23585563

Interactor | Variant | Drug

Phenotype

HPO ID	HPO name
HP:0001508	Failure to thrive
HP:0000519	Developmental cataract
HP:0002353	EEG abnormality
HP:0000207	Triangular mouth
HP:0001263	Global developmental delay
HP:0000400	Macrotia
HP:0001838	Rocker bottom foot
HP:0001792	Small nail
HP:0001511	Intrauterine growth retardation
HP:0003355	Aminoaciduria
HP:0001518	Small for gestational age
HP:0045055	Tiger tail banding
HP:0007587	Numerous pigmented freckles
HP:0002514	Cerebral calcification
HP:0000483	Astigmatism
HP:0007633	Bilateral microphthalmos
HP:0002750	Delayed skeletal maturation
HP:0000509	Conjunctivitis
HP:0002751	Kyphoscoliosis
HP:0000988	Skin rash
HP:0001025	Urticaria
HP:0008070	Sparse hair
HP:0000656	Ectropion
HP:0009755	Ankyloblepharon
HP:0003139	Panhypogammaglobulinemia
HP:0003593	Infantile onset
HP:0002664	Neoplasm
HP:0001257	Spasticity
HP:0100275	Diffuse cerebellar atrophy
HP:0001808	Fragile nails
HP:0000546	Retinal degeneration
HP:0002071	Abnormality of extrapyramidal motor function
HP:0008619	Bilateral sensorineural hearing impairment
HP:0000411	Protruding ear
HP:0005487	Prominent metopic ridge
HP:0000568	Microphthalmia
HP:0001260	Dysarthria
HP:0000482	Microcornea
HP:0002376	Developmental regression
HP:0001338	Partial agenesis of the corpus callosum
HP:0008064	Ichthyosis
HP:0000444	Convex nasal ridge
HP:0000238	Hydrocephalus
HP:0002299	Brittle hair
HP:0006970	Periventricular leukomalacia
HP:0001276	Hypertonia
HP:0000280	Coarse facial features
HP:0007759	Opacification of the corneal stroma
HP:0000601	Hypotelorism
HP:0000365	Hearing impairment
HP:0002024	Malabsorption
HP:0000621	Entropion
HP:0011344	Severe global developmental delay
HP:0000488	Retinopathy
HP:0009886	Trichorrhexis nodosa
HP:0002861	Melanoma
HP:0000164	Abnormality of the dentition
HP:0002213	Fine hair
HP:0000028	Cryptorchidism
HP:0011001	Increased bone mineral density
HP:0002562	Low-set nipples
HP:0004315	Decreased circulating IgG level
HP:0012740	Papilloma
HP:0007034	Generalized hyperreflexia
HP:0001903	Anemia
HP:0000316	Hypertelorism
HP:0000938	Osteopenia
HP:0012760	Reduced social reciprocity
HP:0005214	Intestinal obstruction
HP:0000505	Visual impairment
HP:0000470	Short neck
HP:0001019	Erythroderma
HP:0001363	Craniosynostosis
HP:0025428	Bronchospasm
HP:0000608	Macular degeneration
HP:0001029	Poikiloderma
HP:0100585	Telangiectasia of the skin
HP:0034354	Trichoschisis
HP:0001596	Alopecia
HP:0001315	Reduced tendon reflexes
HP:0001034	Hypermelanotic macule
HP:0000135	Hypogonadism
HP:0004493	Craniofacial hyperostosis
HP:0004337	Abnormality of amino acid metabolism
HP:0001249	Intellectual disability
HP:0002209	Sparse scalp hair
HP:0000286	Epicanthus
HP:0002860	Squamous cell carcinoma
HP:0000648	Optic atrophy
HP:0000491	Keratitis
HP:0001290	Generalized hypotonia
HP:0002719	Recurrent infections
HP:0001009	Telangiectasia
HP:0002119	Ventriculomegaly
HP:0001480	Freckling
HP:0000232	Everted lower lip vermilion
HP:0000639	Nystagmus
HP:0100490	Camptodactyly of finger
HP:0002120	Cerebral cortical atrophy
HP:0003777	Pili torti
HP:0001268	Mental deterioration
HP:0001251	Ataxia
HP:0000347	Micrognathia
HP:0008734	Decreased testicular size
HP:0005105	Abnormal nasal morphology
HP:0001618	Dysphonia
HP:0000992	Cutaneous photosensitivity
HP:0010551	Paraplegia/paraparesis
HP:0003196	Short nose
HP:0002293	Alopecia of scalp
HP:0001598	Concave nail
HP:0001371	Flexion contracture
HP:0002671	Basal cell carcinoma
HP:0001807	Ridged nail
HP:0000963	Thin skin
HP:0002829	Arthralgia
HP:0004322	Short stature
HP:0012378	Fatigue
HP:0001059	Pterygium
HP:0001252	Hypotonia
HP:0012733	Macule
HP:0007703	Abnormality of retinal pigmentation
HP:0002066	Gait ataxia
HP:0000320	Bird-like facies
HP:0008391	Dystrophic fingernails
HP:0004326	Cachexia
HP:0001537	Umbilical hernia
HP:0000046	Small scrotum
HP:0001097	Keratoconjunctivitis sicca
HP:0000252	Microcephaly
HP:0001265	Hyporeflexia
HP:0001875	Neutropenia
HP:0000448	Prominent nose
HP:0001053	Hypopigmented skin patches
HP:0000524	Conjunctival telangiectasia
HP:0001072	Thickened skin
HP:0000278	Retrognathia
HP:0000995	Melanocytic nevus
HP:0001522	Death in infancy
HP:0000431	Wide nasal bridge
HP:0007360	Aplasia/Hypoplasia of the cerebellum
HP:0000545	Myopia
HP:0006297	Enamel hypoplasia
HP:0000613	Photophobia
HP:0006538	Recurrent bronchopulmonary infections
HP:0002080	Intention tremor
HP:0001373	Joint dislocation
HP:0002099	Asthma
HP:0001638	Cardiomyopathy
HP:0001510	Growth delay
HP:0007495	Prematurely aged appearance
HP:0010649	Flat nasal alae
HP:0003577	Congenital onset
HP:0000964	Eczema
HP:0001250	Seizure
HP:0000490	Deeply set eye
HP:0007381	Congenital exfoliative erythroderma
HP:0100012	Neoplasm of the eye
HP:0008872	Feeding difficulties in infancy
HP:0002634	Arteriosclerosis
HP:0007485	Absence of subcutaneous fat
HP:0000498	Blepharitis
HP:0000407	Sensorineural hearing impairment
HP:0011496	Corneal neovascularization
HP:0002028	Chronic diarrhea
HP:0001809	Split nail
HP:0006739	Squamous cell carcinoma of the skin
HP:0002197	Generalized-onset seizure
HP:0410219	Hypoplasia of mandible relative to maxilla
HP:0008404	Nail dystrophy
HP:0000133	Gonadal dysgenesis
HP:0001266	Choreoathetosis
HP:0001883	Talipes
HP:0001387	Joint stiffness
HP:0008386	Aplasia/Hypoplasia of the nails
HP:0002804	Arthrogryposis multiplex congenita
HP:0001945	Fever
HP:0007108	Demyelinating peripheral neuropathy
HP:0001629	Ventricular septal defect
HP:0001197	Abnormality of prenatal development or birth
HP:0000007	Autosomal recessive inheritance
HP:0000565	Esotropia
HP:0000962	Hyperkeratosis
HP:0000958	Dry skin
HP:0002705	High, narrow palate
HP:0025548	Increased mean corpuscular hemoglobin concentration
HP:0010978	Abnormality of immune system physiology
HP:0003819	Death in childhood
HP:0009830	Peripheral neuropathy
HP:0007256	Abnormal pyramidal sign
HP:0000054	Micropenis
HP:0010783	Erythema
HP:0003079	Defective DNA repair after ultraviolet radiation damage
HP:0002942	Thoracic kyphosis
HP:0100543	Cognitive impairment
HP:0007266	Cerebral dysmyelination
HP:0004334	Dermal atrophy
HP:0000518	Cataract
HP:0001217	Clubbing
HP:0002828	Multiple joint contractures
HP:0001289	Confusion
HP:0000651	Diplopia
HP:0006887	Intellectual disability, progressive
HP:0000670	Carious teeth
HP:0007479	Congenital nonbullous ichthyosiform erythroderma
HP:0000486	Strabismus
HP:0000750	Delayed speech and language development

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adrenal gland	glandular cells	Low	Approved
bone marrow	hematopoietic cells	Low	Approved
breast	adipocytes	Low	Approved
breast	glandular cells	Medium	Approved
breast	myoepithelial cells	Low	Approved
bronchus	respiratory epithelial cells	Medium	Approved
caudate	neuronal cells	Medium	Approved
cerebellum	Purkinje cells	Medium	Approved
cerebral cortex	neuronal cells	Medium	Approved
cerebral cortex	neuropil	Low	Approved
cervix	glandular cells	Medium	Approved
cervix	squamous epithelial cells	Medium	Approved
colon	glandular cells	Medium	Approved
duodenum	glandular cells	Medium	Approved
endometrium 2	glandular cells	Medium	Approved
epididymis	glandular cells	Low	Approved
esophagus	squamous epithelial cells	Medium	Approved
gallbladder	glandular cells	Medium	Approved
heart muscle	cardiomyocytes	Medium	Approved
hippocampus	neuronal cells	Medium	Approved
kidney	cells in glomeruli	Low	Approved
kidney	cells in tubules	Medium	Approved
lung	macrophages	Low	Approved
lymph node	germinal center cells	Medium	Approved
lymph node	non-germinal center cells	Low	Approved
nasopharynx	respiratory epithelial cells	Medium	Approved
oral mucosa	squamous epithelial cells	Medium	Approved
ovary	follicle cells	Medium	Approved
parathyroid gland	glandular cells	Medium	Approved
placenta	decidual cells	High	Approved
placenta	trophoblastic cells	Medium	Approved
prostate	glandular cells	Low	Approved
rectum	glandular cells	Medium	Approved
salivary gland	glandular cells	Medium	Approved
seminal vesicle	glandular cells	Medium	Approved
skeletal muscle	myocytes	Medium	Approved
skin 1	Langerhans	Medium	Approved
skin 1	fibroblasts	Medium	Approved
skin 1	keratinocytes	High	Approved
skin 1	melanocytes	Medium	Approved
skin 2	epidermal cells	Medium	Approved
small intestine	glandular cells	Medium	Approved
smooth muscle	smooth muscle cells	Medium	Approved
soft tissue 1	chondrocytes	Medium	Approved
soft tissue 1	peripheral nerve	Medium	Approved
stomach 1	glandular cells	Medium	Approved
stomach 2	glandular cells	Medium	Approved
testis	Leydig cells	High	Approved
testis	cells in seminiferous ducts	High	Approved
thyroid gland	glandular cells	Medium	Approved
tonsil	non-germinal center cells	Low	Approved
tonsil	squamous epithelial cells	Medium	Approved
urinary bladder	urothelial cells	Medium	Approved
vagina	squamous epithelial cells	Medium	Approved

Disease

Disease name	MONDO ID	ICD10	ICD10 chapter	OMIM	Orphanet
xeroderma pigmentosum group d	MONDO:0010212	Q82	chapter17, Congenital malformations, deformations and chromosomal abnormalities	OMIM:278730	Orphanet:276258
trichothiodystrophy 1, photosensitive	MONDO:0011125	L67	chapter12, Diseases of the skin and subcutaneous tissue	OMIM:601675	Orphanet:670
cerebrooculofacioskeletal syndrome 2	MONDO:0012553	Q87	chapter17, Congenital malformations, deformations and chromosomal abnormalities	OMIM:610756

Summary of P18074

Gene: ERCC2, XPD, XPDC
Protein: General transcription and DNA repair factor IIH helicase subunit XPD

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of P18074

Gene: ERCC2, XPD, XPDC Protein: General transcription and DNA repair factor IIH helicase subunit XPD

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: ERCC2, XPD, XPDC
Protein: General transcription and DNA repair factor IIH helicase subunit XPD