6TEC

Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP-Xylose

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03171	2OG-Fe(II) oxygenase superfamily (2OG-FeII_Oxy)	2OG-Fe(II) oxygenase superfamily	This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1]. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reacti ...	This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1]. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site [3]. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3	UDP-glycosyltransferase activity catalytic activity, acting on a protein glycosyltransferase activity transferase activity galactosyltransferase activity hexosyltransferase activity procollagen galactosyltransferase activity catalytic activity UDP-galactosyltransferase activity peptidyl-lysine 5-dioxygenase activity oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen procollagen-lysine 5-dioxygenase activity 2-oxoglutarate-dependent dioxygenase activity UDP-glycosyltransferase activity catalytic activity, acting on a protein glycosyltransferase activity transferase activity galactosyltransferase activity hexosyltransferase activity procollagen galactosyltransferase activity catalytic activity UDP-galactosyltransferase activity peptidyl-lysine 5-dioxygenase activity oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen procollagen-lysine 5-dioxygenase activity 2-oxoglutarate-dependent dioxygenase activity dioxygenase activity organic acid binding binding carbohydrate binding vitamin binding ion binding organic cyclic compound binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding small molecule binding cation binding transition metal ion binding iron ion binding metal ion binding procollagen glucosyltransferase activity glucosyltransferase activity	developmental process epithelium development endothelial cell differentiation cellular developmental process endothelium development cell development tissue development epithelial cell differentiation cell morphogenesis endothelial cell development anatomical structure morphogenesis epithelial cell development endothelial cell morphogenesis epithelial cell morphogenesis cell differentiation developmental process epithelium development endothelial cell differentiation cellular developmental process endothelium development cell development tissue development epithelial cell differentiation cell morphogenesis endothelial cell development anatomical structure morphogenesis epithelial cell development endothelial cell morphogenesis epithelial cell morphogenesis cell differentiation anatomical structure development cellular process tissue morphogenesis epidermis morphogenesis epidermis development morphogenesis of an epithelium protein localization localization cellular localization cellular macromolecule localization macromolecule localization multicellular organismal process tube development animal organ development respiratory tube development multicellular organism development lung morphogenesis lung development respiratory system development animal organ morphogenesis system development cellular component organization collagen fibril organization extracellular matrix organization cellular component organization or biogenesis supramolecular fiber organization extracellular structure organization external encapsulating structure organization embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development regulation of tube diameter system process regulation of tube size biological regulation circulatory system process vascular process in circulatory system blood vessel diameter maintenance regulation of biological quality vasodilation blood circulation regulation of anatomical structure size cellular component biogenesis cellular component assembly basement membrane assembly extracellular matrix assembly basement membrane organization collagen metabolic process metabolic process neural tube development nervous system development organonitrogen compound metabolic process peptidyl-lysine modification primary metabolic process peptidyl-lysine hydroxylation organic substance metabolic process macromolecule modification peptidyl-amino acid modification protein hydroxylation protein metabolic process macromolecule metabolic process protein modification process oxoacid metabolic process cellular biosynthetic process aspartate family amino acid biosynthetic process organonitrogen compound biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process non-proteinogenic amino acid metabolic process organic substance biosynthetic process small molecule metabolic process non-proteinogenic amino acid biosynthetic process hydroxylysine metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process L-amino acid biosynthetic process L-amino acid metabolic process cellular modified amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process cellular modified amino acid biosynthetic process hydroxylysine biosynthetic process proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process carbohydrate derivative metabolic process carbohydrate derivative biosynthetic process glycoprotein biosynthetic process glycoprotein metabolic process protein glycosylation macromolecule biosynthetic process glycosylation macromolecule glycosylation protein O-linked glycosylation	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix rough endoplasmic reticulum intracellular organelle intracellular anatomical structure endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system organelle subcompartment membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane Golgi apparatus subcompartment Golgi apparatus trans-Golgi network membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006620	Prolyl 4-hydroxylase, alpha subunit	Domain
A	IPR005123	Oxoglutarate/iron-dependent dioxygenase	Domain
A	IPR044861	Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain	Domain
A	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
A	IPR001006	Procollagen-lysine 5-dioxygenase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O60568	connective tissue disorder due to lysyl hydroxylase-3 deficiency attention deficit hyperactivity disorder, inattentive type Ehlers-Danlos syndrome intellectual disability pilocytic astrocytoma tuberculosis Barrett esophagus esophageal adenocarcinoma malignant glioma psoriasis glioblastoma ovarian cancer thoracic aortic aneurysm

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.