MultifacetedProtDB - Bologna Biocomputing Group

EC number	EC number description
1.14.11.4	Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor; procollagen-lysine 5-dioxygenase
2.4.1.50	Transferases; Glycosyltransferases; Hexosyltransferases; procollagen galactosyltransferase
2.4.1.66	Transferases; Glycosyltransferases; Hexosyltransferases; procollagen glucosyltransferase

Structure

PDB	Resolution (Å)	PDB name
6FXK	2.7	Crystal Structure of full-length Human Lysyl Hydroxylase LH3
6FXM	2.1	Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Mn2+
6FXR	2.1	Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Gal
6FXT	2.5	Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Glc
6FXX	3.0	Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Gal, Hg2+ Soak
6FXY	2.138	Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Gal - Structure from long-wavelength S-SAD
6TE3	2.3	Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP
6TEC	2.4	Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Xylose
6TES	2.2	Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Glucuronic Acid
6TEU	3.0	Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Val80Lys mutant - Cocrystal with Fe2+, Mn2+
6TEX	2.3	Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Val80Lys mutant - Cocrystal with Fe2+, Mn2+, UDP-Glucose
6TEZ	2.7	Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Val80Lys mutant - Cocrystal with Fe2+, Mn2+, UDP-Glucuronic Acid
6WFV	1.7	The crystal structure of a collagen galactosylhydroxylysyl glucosyltransferase from human

GO term

GO ontology	GO term	GO description
Biological Process	GO:0070831	basement membrane assembly
Biological Process	GO:0030199	collagen fibril organization
Biological Process	GO:0032963	collagen metabolic process
Biological Process	GO:0001886	endothelial cell morphogenesis
Biological Process	GO:0048730	epidermis morphogenesis
Biological Process	GO:0046947	hydroxylysine biosynthetic process
Biological Process	GO:0001701	in utero embryonic development
Biological Process	GO:0060425	lung morphogenesis
Biological Process	GO:0021915	neural tube development
Biological Process	GO:0017185	peptidyl-lysine hydroxylation
Biological Process	GO:0006493	protein O-linked glycosylation
Biological Process	GO:0008104	protein localization
Biological Process	GO:0042311	vasodilation
Molecular Function	GO:0031418	L-ascorbic acid binding
Molecular Function	GO:0005506	iron ion binding
Molecular Function	GO:0046872	metal ion binding
Molecular Function	GO:0050211	procollagen galactosyltransferase activity
Molecular Function	GO:0033823	procollagen glucosyltransferase activity
Molecular Function	GO:0008475	procollagen-lysine 5-dioxygenase activity
Molecular Function	GO:0036094	small molecule binding
Cellular Component	GO:0005794	Golgi apparatus
Cellular Component	GO:0062023	collagen-containing extracellular matrix
Cellular Component	GO:0005783	endoplasmic reticulum
Cellular Component	GO:0005788	endoplasmic reticulum lumen
Cellular Component	GO:0005789	endoplasmic reticulum membrane
Cellular Component	GO:0070062	extracellular exosome
Cellular Component	GO:0005615	extracellular space
Cellular Component	GO:0005791	rough endoplasmic reticulum
Cellular Component	GO:0005802	trans-Golgi network

InterPro / Pfam

InterPro	InterPro name
IPR001006	Procollagen-lysine 5-dioxygenase, conserved site
IPR005123	Oxoglutarate/iron-dependent dioxygenase
IPR006620	Prolyl 4-hydroxylase, alpha subunit
IPR029044	Nucleotide-diphospho-sugar transferases
IPR044861	Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain

Pfam	Pfam name
PF03171	2OG-Fe(II) oxygenase superfamily

Reactome

Reactome	Reactome Name	Node type	Reactome Root	Reactome Root Name
R-HSA-1650814	Collagen biosynthesis and modifying enzymes	Internal node	R-HSA-1474244	Extracellular matrix organization

Subcellular location

Location	ECO term	Pubmed
Endoplasmic reticulum lumen	ECO:0000269	PubMed:20470363
Endoplasmic reticulum membrane	ECO:0000250
Rough endoplasmic reticulum	ECO:0000269	PubMed:10934207
Secreted	ECO:0000269	PubMed:21465473
Secreted, extracellular space	ECO:0000250

Interactor | Variant | Drug

Phenotype

HPO ID	HPO name
HP:0000007	Autosomal recessive inheritance
HP:0000164	Abnormality of the dentition
HP:0000272	Malar flattening
HP:0000307	Pointed chin
HP:0000369	Low-set ears
HP:0000407	Sensorineural hearing impairment
HP:0000463	Anteverted nares
HP:0000518	Cataract
HP:0000545	Myopia
HP:0000586	Shallow orbits
HP:0000926	Platyspondyly
HP:0000938	Osteopenia
HP:0000978	Bruising susceptibility
HP:0001263	Global developmental delay
HP:0001511	Intrauterine growth retardation
HP:0001776	Bilateral talipes equinovarus
HP:0001873	Thrombocytopenia
HP:0002119	Ventriculomegaly
HP:0002132	Porencephalic cyst
HP:0002164	Nail dysplasia
HP:0002208	Coarse hair
HP:0002650	Scoliosis
HP:0002680	J-shaped sella turcica
HP:0002714	Downturned corners of mouth
HP:0002756	Pathologic fracture
HP:0002987	Elbow flexion contracture
HP:0003090	Hypoplasia of the capital femoral epiphysis
HP:0003196	Short nose
HP:0003393	Thenar muscle atrophy
HP:0003645	Prolonged partial thromboplastin time
HP:0004944	Dilatation of the cerebral artery
HP:0006184	Decreased palmar creases
HP:0008897	Postnatal growth retardation
HP:0009110	Diaphragmatic eventration
HP:0009471	Contracture of the proximal interphalangeal joint of the 3rd finger
HP:0009540	Contracture of the proximal interphalangeal joint of the 2nd finger
HP:0010557	Overlapping fingers
HP:0011461	Fetal onset
HP:0012368	Flat face
HP:0025019	Arterial rupture
HP:0032199	Abnormal prothrombin time

Tissue and cell type

Tissue	Cell type	Expression level	Reliability
adipose tissue	adipocytes	Medium	Approved
adrenal gland	glandular cells	Medium	Approved
appendix	glandular cells	Medium	Approved
appendix	lymphoid tissue	Low	Approved
bone marrow	hematopoietic cells	Low	Approved
breast	glandular cells	Medium	Approved
bronchus	respiratory epithelial cells	Medium	Approved
caudate	glial cells	Low	Approved
caudate	neuronal cells	Medium	Approved
cerebellum	cells in granular layer	Medium	Approved
cerebellum	cells in molecular layer	Medium	Approved
cerebral cortex	endothelial cells	High	Approved
cerebral cortex	glial cells	High	Approved
cerebral cortex	neuronal cells	Medium	Approved
cerebral cortex	neuropil	Medium	Approved
cervix	squamous epithelial cells	Low	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	Low	Approved
endometrium 2	glandular cells	Medium	Approved
epididymis	glandular cells	Medium	Approved
fallopian tube	glandular cells	Medium	Approved
gallbladder	glandular cells	Medium	Approved
heart muscle	cardiomyocytes	High	Approved
hippocampus	glial cells	Medium	Approved
hippocampus	neuronal cells	Low	Approved
kidney	cells in glomeruli	High	Approved
kidney	cells in tubules	Medium	Approved
lung	alveolar cells	Medium	Approved
lung	macrophages	High	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	Medium	Approved
ovary	follicle cells	Low	Approved
pancreas	exocrine glandular cells	Low	Approved
pancreas	pancreatic endocrine cells	Medium	Approved
parathyroid gland	glandular cells	Low	Approved
placenta	decidual cells	High	Approved
placenta	trophoblastic cells	Medium	Approved
prostate	glandular cells	Low	Approved
rectum	glandular cells	Medium	Approved
seminal vesicle	glandular cells	Medium	Approved
skeletal muscle	myocytes	Low	Approved
skin 1	fibroblasts	Low	Approved
skin 1	keratinocytes	Low	Approved
skin 1	melanocytes	High	Approved
skin 2	epidermal cells	High	Approved
small intestine	glandular cells	Medium	Approved
soft tissue 1	peripheral nerve	High	Approved
soft tissue 2	fibroblasts	Medium	Approved
soft tissue 2	peripheral nerve	High	Approved
stomach 1	glandular cells	Medium	Approved
stomach 2	glandular cells	Medium	Approved
testis	Leydig cells	Low	Approved
testis	cells in seminiferous ducts	Medium	Approved
thyroid gland	glandular cells	Medium	Approved
tonsil	non-germinal center cells	Low	Approved
urinary bladder	urothelial cells	Low	Approved

Summary of O60568

Gene: PLOD3
Protein: Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Summary of O60568

Gene: PLOD3 Protein: Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3

Structure

GO term

InterPro / Pfam

Reactome

Subcellular location

Interactor | Variant | Drug

Phenotype

Tissue and cell type

Disease

Gene: PLOD3
Protein: Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3