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.
3.6.4.13	Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement; RNA helicase

Structure

PDB	Resolution (Å)	PDB name
2GJK	2.6	Structural and functional insights into the human Upf1 helicase core
2GK6	2.4	Structural and Functional insights into the human Upf1 helicase core
2GK7	2.8	Structural and Functional insights into the human Upf1 helicase core
2IYK	2.95	Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor UPF1
2WJV	2.85	Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2
2WJY	2.5	Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2 Orthorhombic form
2XZO	2.395	Upf1 helicase - RNA complex
2XZP	2.72	Upf1 helicase
6EJ5	3.34	A conserved structural element in the RNA helicase UPF1 regulates its catalytic activity in an isoform-specific manner
6Z3R	2.97	Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ

GO term

GO ontology	GO term	GO description
Biological Process	GO:0061158	3'-UTR-mediated mRNA destabilization
Biological Process	GO:0032508	DNA duplex unwinding
Biological Process	GO:0006281	DNA repair
Biological Process	GO:0006260	DNA replication
Biological Process	GO:0044770	cell cycle phase transition
Biological Process	GO:0071347	cellular response to interleukin-1
Biological Process	GO:0071222	cellular response to lipopolysaccharide
Biological Process	GO:0071044	histone mRNA catabolic process
Biological Process	GO:0006406	mRNA export from nucleus
Biological Process	GO:0000956	nuclear-transcribed mRNA catabolic process
Biological Process	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
Biological Process	GO:0061014	positive regulation of mRNA catabolic process
Biological Process	GO:0032204	regulation of telomere maintenance
Biological Process	GO:0006449	regulation of translational termination
Biological Process	GO:0032201	telomere maintenance via semi-conservative replication
Molecular Function	GO:0005524	ATP binding
Molecular Function	GO:0016887	ATP hydrolysis activity
Molecular Function	GO:0003723	RNA binding
Molecular Function	GO:0003724	RNA helicase activity
Molecular Function	GO:0003682	chromatin binding
Molecular Function	GO:0036121	double-stranded DNA helicase activity
Molecular Function	GO:0004386	helicase activity
Molecular Function	GO:0044877	protein-containing complex binding
Molecular Function	GO:0042162	telomeric DNA binding
Molecular Function	GO:0008270	zinc ion binding
Cellular Component	GO:0000932	P-body
Cellular Component	GO:0000785	chromatin
Cellular Component	GO:0000781	chromosome, telomeric region
Cellular Component	GO:0005737	cytoplasm
Cellular Component	GO:0005829	cytosol
Cellular Component	GO:0035145	exon-exon junction complex
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus
Cellular Component	GO:0048471	perinuclear region of cytoplasm
Cellular Component	GO:0044530	supraspliceosomal complex

InterPro / Pfam

InterPro	InterPro name
IPR006935	Helicase/UvrB, N-terminal
IPR018999	RNA helicase UPF1, Cys/His rich zinc-binding domain
IPR027417	P-loop containing nucleoside triphosphate hydrolase
IPR040812	RNA helicase UPF1, 1B domain
IPR041677	DNA2/NAM7 helicase, helicase domain
IPR041679	DNA2/NAM7 helicase-like, C-terminal
IPR045055	DNA2/NAM7-like helicase
IPR047187	Upf1-like, C-terminal helicase domain

Pfam	Pfam name
PF04851	Type III restriction enzyme, res subunit
PF09416	RNA helicase (UPF2 interacting domain)
PF13086	AAA domain
PF13087	AAA domain
PF18141	RNA helicase UPF1, 1B domain

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	Leaf	R-HSA-8953854	Metabolism of RNA
R-HSA-975957	Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	Leaf	R-HSA-8953854	Metabolism of RNA

Subcellular location

Location	ECO term	Pubmed
Cytoplasm	ECO:0000269	PubMed:11163187
Cytoplasm, P-body
Cytoplasm, perinuclear region	ECO:0000250
Nucleus	ECO:0000269	PubMed:11163187
Nucleus	ECO:0000269	PubMed:18362360

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adrenal gland	glandular cells	Medium	Approved
appendix	glandular cells	Medium	Approved
appendix	lymphoid tissue	Medium	Approved
bone marrow	hematopoietic cells	Low	Approved
breast	glandular cells	Medium	Approved
breast	myoepithelial cells	Medium	Approved
bronchus	respiratory epithelial cells	Medium	Approved
caudate	neuronal cells	Medium	Approved
cerebellum	Purkinje cells	Medium	Approved
cerebellum	cells in granular layer	Low	Approved
cerebellum	cells in molecular layer	Medium	Approved
cerebral cortex	endothelial cells	Low	Approved
cerebral cortex	glial cells	Medium	Approved
cerebral cortex	neuronal cells	Medium	Approved
cervix	glandular cells	Low	Approved
cervix	squamous epithelial cells	Medium	Approved
colon	endothelial cells	Medium	Approved
colon	glandular cells	Medium	Approved
colon	peripheral nerve/ganglion	High	Approved
duodenum	glandular cells	Medium	Approved
endometrium 1	glandular cells	Medium	Approved
endometrium 2	cells in endometrial stroma	Low	Approved
endometrium 2	glandular cells	Medium	Approved
epididymis	glandular cells	Medium	Approved
esophagus	squamous epithelial cells	Medium	Approved
fallopian tube	glandular cells	Medium	Approved
gallbladder	glandular cells	Medium	Approved
heart muscle	cardiomyocytes	Low	Approved
hippocampus	glial cells	Medium	Approved
hippocampus	neuronal cells	Medium	Approved
kidney	cells in tubules	Medium	Approved
liver	hepatocytes	Low	Approved
lung	alveolar cells	Low	Approved
lung	macrophages	Medium	Approved
lymph node	germinal center cells	Medium	Approved
lymph node	non-germinal center cells	Medium	Approved
nasopharynx	respiratory epithelial cells	Medium	Approved
oral mucosa	squamous epithelial cells	Medium	Approved
ovary	follicle cells	Medium	Approved
ovary	ovarian stroma cells	Low	Approved
pancreas	exocrine glandular cells	Medium	Approved
pancreas	pancreatic endocrine cells	Medium	Approved
parathyroid gland	glandular cells	Medium	Approved
placenta	decidual cells	Medium	Approved
placenta	trophoblastic cells	Medium	Approved
prostate	glandular cells	Medium	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	Low	Approved
skin 1	keratinocytes	Medium	Approved
skin 1	melanocytes	Low	Approved
skin 2	epidermal cells	Medium	Approved
small intestine	glandular cells	Medium	Approved
soft tissue 1	chondrocytes	Low	Approved
stomach 1	glandular cells	Medium	Approved
stomach 2	glandular cells	Medium	Approved
testis	Leydig cells	Low	Approved
testis	elongated or late spermatids	Low	Approved
testis	pachytene spermatocytes	High	Approved
testis	preleptotene spermatocytes	Low	Approved
testis	sertoli cells	Low	Approved
testis	spermatogonia cells	Medium	Approved
thyroid gland	glandular cells	Medium	Approved
tonsil	germinal center cells	Medium	Approved
tonsil	non-germinal center cells	Medium	Approved
tonsil	squamous epithelial cells	Medium	Approved
urinary bladder	urothelial cells	Medium	Approved
vagina	squamous epithelial cells	Medium	Approved

Summary of Q92900

Gene: UPF1, KIAA0221, RENT1
Protein: Regulator of nonsense transcripts 1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of Q92900

Gene: UPF1, KIAA0221, RENT1 Protein: Regulator of nonsense transcripts 1

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: UPF1, KIAA0221, RENT1
Protein: Regulator of nonsense transcripts 1