MultifacetedProtDB - Bologna Biocomputing Group

EC number	EC number description
5.4.99.-	Isomerases; Intramolecular transferases; Transferring other groups;
5.4.99.12	Isomerases; Intramolecular transferases; Transferring other groups; tRNA pseudouridine38-40 synthase

Structure

PDB	Resolution (Å)	PDB name
4IQM	1.8	Crystal structure of the catalytic domain of human Pus1
4ITS	1.85	Crystal structure of the catalytic domain of human Pus1 with MES in the active site
4J37	1.75	Crystal structure of the catalytic domain of human Pus1
4NZ6	2.0	Steroid receptor RNA Activator (SRA) modification by the human Pseudouridine Synthase 1 (hPus1p): RNA binding, activity, and atomic model
4NZ7	2.7	Steroid receptor RNA Activator (SRA) modification by the human Pseudouridine Synthase 1 (hPus1p): RNA binding, activity, and atomic model

GO term

GO ontology	GO term	GO description
Biological Process	GO:0008380	RNA splicing
Biological Process	GO:0006397	mRNA processing
Biological Process	GO:1990481	mRNA pseudouridine synthesis
Biological Process	GO:0070902	mitochondrial tRNA pseudouridine synthesis
Biological Process	GO:0031119	tRNA pseudouridine synthesis
Molecular Function	GO:0003723	RNA binding
Molecular Function	GO:0009982	pseudouridine synthase activity
Molecular Function	GO:0002153	steroid receptor RNA activator RNA binding
Molecular Function	GO:0000049	tRNA binding
Molecular Function	GO:0106029	tRNA pseudouridine synthase activity
Cellular Component	GO:0005737	cytoplasm
Cellular Component	GO:0005759	mitochondrial matrix
Cellular Component	GO:0005739	mitochondrion
Cellular Component	GO:0005654	nucleoplasm
Cellular Component	GO:0005634	nucleus

InterPro	InterPro name
IPR001406	Pseudouridine synthase I, TruA
IPR020094	Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal
IPR020095	Pseudouridine synthase I, TruA, C-terminal
IPR020097	Pseudouridine synthase I, TruA, alpha/beta domain
IPR020103	Pseudouridine synthase, catalytic domain superfamily
IPR041708	Pseudouridine synthase PUS1/ PUS2-like

Pfam	Pfam name
PF01416	tRNA pseudouridine synthase

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-6782315	tRNA modification in the nucleus and cytosol	Internal node	R-HSA-8953854	Metabolism of RNA
R-HSA-6787450	tRNA modification in the mitochondrion	Leaf	R-HSA-8953854	Metabolism of RNA

Location	ECO term	Pubmed
Cytoplasm	ECO:0000305	PubMed:15772074
Mitochondrion	ECO:0000305	PubMed:15772074
Mitochondrion	ECO:0000305	PubMed:17056637
Nucleus	ECO:0000305	PubMed:15772074
Nucleus	ECO:0000305	PubMed:17056637

Phenotype

HPO ID	HPO name
HP:0000007	Autosomal recessive inheritance
HP:0000218	High palate
HP:0000252	Microcephaly
HP:0000316	Hypertelorism
HP:0000343	Long philtrum
HP:0000347	Micrognathia
HP:0000457	Depressed nasal ridge
HP:0000501	Glaucoma
HP:0000580	Pigmentary retinopathy
HP:0000823	Delayed puberty
HP:0000980	Pallor
HP:0001249	Intellectual disability
HP:0001252	Hypotonia
HP:0001290	Generalized hypotonia
HP:0001324	Muscle weakness
HP:0001388	Joint laxity
HP:0001508	Failure to thrive
HP:0001510	Growth delay
HP:0001903	Anemia
HP:0001924	Sideroblastic anemia
HP:0001931	Hypochromic anemia
HP:0001935	Microcytic anemia
HP:0001939	Abnormality of metabolism/homeostasis
HP:0002091	Restrictive ventilatory defect
HP:0002151	Increased serum lactate
HP:0002650	Scoliosis
HP:0002808	Kyphosis
HP:0003128	Lactic acidosis
HP:0003196	Short nose
HP:0003198	Myopathy
HP:0003200	Ragged-red muscle fibers
HP:0003281	Increased circulating ferritin concentration
HP:0003307	Hyperlordosis
HP:0003323	Progressive muscle weakness
HP:0003391	Gowers sign
HP:0003457	EMG abnormality
HP:0003546	Exercise intolerance
HP:0003593	Infantile onset
HP:0003688	Cytochrome C oxidase-negative muscle fibers
HP:0003691	Scapular winging
HP:0003737	Mitochondrial myopathy
HP:0008347	Decreased activity of mitochondrial complex IV
HP:0009055	Generalized limb muscle atrophy
HP:0009743	Distichiasis
HP:0011463	Childhood onset
HP:0011923	Decreased activity of mitochondrial complex I
HP:0012132	Erythroid hyperplasia
HP:0020081	Pappenheimer bodies
HP:0040075	Hypopituitarism

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adrenal gland	glandular cells	High	Approved
appendix	glandular cells	High	Approved
appendix	lymphoid tissue	Medium	Approved
bone marrow	hematopoietic cells	High	Approved
breast	glandular cells	High	Approved
breast	myoepithelial cells	Medium	Approved
bronchus	respiratory epithelial cells	High	Approved
caudate	glial cells	Low	Approved
caudate	neuronal cells	Low	Approved
cerebellum	Purkinje cells	High	Approved
cerebellum	cells in granular layer	Medium	Approved
cerebral cortex	endothelial cells	Low	Approved
cerebral cortex	glial cells	Medium	Approved
cerebral cortex	neuronal cells	Medium	Approved
cerebral cortex	neuropil	Medium	Approved
cervix	glandular cells	Medium	Approved
cervix	squamous epithelial cells	Medium	Approved
colon	endothelial cells	Medium	Approved
colon	glandular cells	High	Approved
colon	peripheral nerve/ganglion	High	Approved
duodenum	glandular cells	High	Approved
endometrium 1	cells in endometrial stroma	Medium	Approved
endometrium 1	glandular cells	Medium	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	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	Low	Approved
lymph node	non-germinal center cells	Low	Approved
nasopharynx	respiratory epithelial cells	Medium	Approved
oral mucosa	squamous epithelial cells	High	Approved
pancreas	exocrine glandular cells	Medium	Approved
pancreas	pancreatic endocrine cells	Medium	Approved
parathyroid gland	glandular cells	Low	Approved
prostate	glandular cells	Medium	Approved
rectum	glandular cells	High	Approved
seminal vesicle	glandular cells	High	Approved
skeletal muscle	myocytes	High	Approved
skin 1	Langerhans	Medium	Approved
skin 1	fibroblasts	Medium	Approved
skin 1	keratinocytes	Medium	Approved
skin 1	melanocytes	Medium	Approved
skin 2	epidermal cells	High	Approved
small intestine	glandular cells	High	Approved
smooth muscle	smooth muscle cells	Medium	Approved
soft tissue 1	chondrocytes	Medium	Approved
soft tissue 1	fibroblasts	Medium	Approved
soft tissue 1	peripheral nerve	High	Approved
soft tissue 2	chondrocytes	Medium	Approved
soft tissue 2	fibroblasts	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	Medium	Approved
tonsil	non-germinal center cells	Medium	Approved
tonsil	squamous epithelial cells	High	Approved
urinary bladder	urothelial cells	High	Approved
vagina	squamous epithelial cells	Medium	Approved

Summary of Q9Y606

Gene: PUS1, PP8985
Protein: Pseudouridylate synthase 1 homolog

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of Q9Y606

Gene: PUS1, PP8985 Protein: Pseudouridylate synthase 1 homolog

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: PUS1, PP8985
Protein: Pseudouridylate synthase 1 homolog