Annotations: 8ZGC

Human lysine O-link glycosylation complex, LH3/ColGalT1 with bound UDP-galactose

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Glyco_tranf_2_4, GT_PLOD	e8zgcA1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Glyco_tranf_2_4, GT_PLOD	ECOD (v295.2)
A	Ank, Ank_2, Ank_3, Ank_4, Ank_5	e8zgcA3	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Ank, Ank_2, Ank_3, Ank_4, Ank_5	ECOD (v295.2)
C [auth U]	Autophagy_act_C	e8zgcU1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Autophagy_act_C	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E [auth C], F [auth D]	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 reactio ...	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
A, B, E [auth C], F [auth D]	PF25238	OGFOD2-like domain (OGFOD2-like)	OGFOD2-like domain	This domain is found in human 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 2 (OGFOD2), Procollagen -lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1) and similar eukaryotic proteins. It is often found immediately N-terminal to Pf ...	This domain is found in human 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 2 (OGFOD2), Procollagen -lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1) and similar eukaryotic proteins. It is often found immediately N-terminal to Pfam:PF03171 and is predicted to show a predominantly alpha configuration.	Domain
A, B, E [auth C], F [auth D]	PF25342	PLOD GT domain (GT_PLOD)	PLOD GT domain	This entry represents the N-terminal GT domain found in the family of collagen lysyl hydroxylases (LH or PLOD). Enzymes belonging this family catalyse the lysine hydroxylation of collagens using Fe2+, 2-oxoglutarate, ascorbate and molecular oxygen [1 ...	This entry represents the N-terminal GT domain found in the family of collagen lysyl hydroxylases (LH or PLOD). Enzymes belonging this family catalyse the lysine hydroxylation of collagens using Fe2+, 2-oxoglutarate, ascorbate and molecular oxygen [1,2]. In humans, PLOD genes encode for three LH enzyme isoforms sharing significant sequence similarity. Mutations in PLOD genes that reduce or abolish their activity are associated with severe connective tissue diseases including Ehlers-Danlos and Bruck syndromes [3,4]. PLOD3 is considered the evolutionary ancestor of the family as this isoform is the only one capable of further processing of hydroxylysines through glycosylation, whereas other isoforms might have lost such capability during evolution. These enzymes consist of three domains encompassing multiple active sites. The two N-terminal domains have a topology typical for glycosyltransferases whereas the C-terminal has a DSBH fold. The domain represented by this entry is the only catalytically active domain and is the solely responsible for the glycosyltransferase activity.	Domain
C [auth U], D [auth V], G [auth W], H [auth X]	PF01755	Glycosyltransferase family 25 (LPS biosynthesis protein) (Glyco_transf_25)	Glycosyltransferase family 25 (LPS biosynthesis protein)	-	Family
C [auth U], D [auth V], G [auth W], H [auth X]	PF13704	Glycosyltransferase family 25, N-terminal domain (Glyco_tranf_2_4)	Glycosyltransferase family 25, N-terminal domain	This entry represents the N-terminal domain of enzymes that are members of glycosyltransferase family 25. Glycosyltransferase family 25 (GT25) comprises enzymes with primary function in bacterial lipopolysaccharide biosynthesis. These enzymes catalys ...	This entry represents the N-terminal domain of enzymes that are members of glycosyltransferase family 25. Glycosyltransferase family 25 (GT25) comprises enzymes with primary function in bacterial lipopolysaccharide biosynthesis. These enzymes catalyse the transfer of various sugars onto the growing lipopolysaccharide chain during its biosynthesis [1]. Some members such as UDP-Glc:hydroxylysine O-glucosyltransferase and occidiofungin beta-xylosyltransferase participate in other glycan modifications.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, E [auth C], F [auth D]	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3	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 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 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 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 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	carbohydrate derivative biosynthetic process protein O-linked glycosylation via galactose glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process macromolecule biosynthetic process biosynthetic process protein O-linked glycosylation metabolic process cellular process protein metabolic process macromolecule metabolic process collagen biosynthetic process carbohydrate derivative biosynthetic process protein O-linked glycosylation via galactose glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process macromolecule biosynthetic process biosynthetic process protein O-linked glycosylation metabolic process cellular process protein metabolic process macromolecule metabolic process collagen biosynthetic process collagen metabolic process cellular component organization collagen fibril organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle extracellular matrix external encapsulating structure rough endoplasmic reticulum intracellular organelle intracellular anatomical structure extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle extracellular matrix external encapsulating structure 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
C [auth U], D [auth V], G [auth W], H [auth X]	Procollagen galactosyltransferase 1	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	carbohydrate derivative biosynthetic process protein O-linked glycosylation via galactose glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process macromolecule biosynthetic process biosynthetic process protein O-linked glycosylation metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of biological process carbohydrate derivative biosynthetic process protein O-linked glycosylation via galactose glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process macromolecule biosynthetic process biosynthetic process protein O-linked glycosylation metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of biological process regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of collagen fibril organization biological regulation positive regulation of biological process positive regulation of extracellular matrix organization collagen fibril organization extracellular matrix organization cellular component organization cellular component organization or biogenesis regulation of extracellular matrix organization regulation of collagen fibril organization positive regulation of cellular process extracellular structure organization external encapsulating structure organization	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, E [auth C], F [auth D]	IPR050757	Collagen-modifying Glycosyltransferase 25	Family
A, B, E [auth C], F [auth D]	IPR006620	Prolyl 4-hydroxylase, alpha subunit	Domain
A, B, E [auth C], F [auth D]	IPR057589	PLOD1-3-like, GT domain	Domain
A, B, E [auth C], F [auth D]	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain
A, B, E [auth C], F [auth D]	IPR044861	Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain	Domain
A, B, E [auth C], F [auth D]	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
A, B, E [auth C], F [auth D]	IPR001006	Procollagen-lysine 5-dioxygenase, conserved site	Conserved Site
C [auth U], D [auth V], G [auth W], H [auth X]	IPR050757	Collagen-modifying Glycosyltransferase 25	Family
C [auth U], D [auth V], G [auth W], H [auth X]	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
C [auth U], D [auth V], G [auth W], H [auth X]	IPR002654	Glycosyl transferase, family 25	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, E [auth C], F [auth D]	: 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
C [auth U], D [auth V], G [auth W], H [auth X]	: Q8NBJ5	amyotrophic lateral sclerosis glioblastoma osteosarcoma tuberculosis breast cancer IgA glomerulonephritis ovarian cancer diabetes mellitus lung carcinoma pancreatic intraductal papillary-mucinous neoplasm

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.