2AGD | pdb_00002agd

Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-I(M340H-B4Gal-T1) in Complex with GlcNAc-beta1,4-Man-alpha1,3-Man-beta-OR

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2agda_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	beta 1,4 galactosyltransferase (b4GalT1)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2agdb_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	beta 1,4 galactosyltransferase (b4GalT1)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2agdc_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	beta 1,4 galactosyltransferase (b4GalT1)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8073551	3000077	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8073551	3000077	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8073551	3000077	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Glyco_transf_7N	e2agdA1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: Glyco_transf_7N	ECOD (1.6)
B	Glyco_transf_7N	e2agdB1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: Glyco_transf_7N	ECOD (1.6)
C	Glyco_transf_7N	e2agdC1	A: a/b three-layered sandwiches	X: Nucleotide-diphospho-sugar transferases (From Topology)	H: Nucleotide-diphospho-sugar transferases (From Topology)	T: Nucleotide-diphospho-sugar transferases	F: Glyco_transf_7N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
B	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
C	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF02709	N-terminal domain of galactosyltransferase (Glyco_transf_7C)	N-terminal domain of galactosyltransferase	-	Family
A, B, C	PF13733	N-terminal region of glycosyl transferase group 7 (Glyco_transf_7N)	N-terminal region of glycosyl transferase group 7	This is the N-terminal half of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases. EC:2.4.1.90, N-acetyllactosamine syn ...	This is the N-terminal half of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases. EC:2.4.1.90, N-acetyllactosamine synthase; EC:2.4.1.38, Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and EC:2.4.1.22 Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin EC:2.4.1.90 is the catalysed reaction.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Beta-1,4-galactosyltransferase 1	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding lactose synthase activity UDP-glycosyltransferase activity glycosyltransferase activity transferase activity galactosyltransferase activity hexosyltransferase activity UDP-galactosyltransferase activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding lactose synthase activity UDP-glycosyltransferase activity glycosyltransferase activity transferase activity galactosyltransferase activity hexosyltransferase activity UDP-galactosyltransferase activity catalytic activity cytoskeletal protein binding protein binding tubulin binding alpha-tubulin binding identical protein binding beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity beta-tubulin binding N-acetyllactosamine synthase activity	wound healing regulation of biological process cell population proliferation regulation of cellular process response to stimulus positive regulation of cell population proliferation positive regulation of epithelial cell proliferation biological regulation positive regulation of biological process response to stress regulation of cell population proliferation cellular process regulation of epithelial cell proliferation response to wounding wound healing regulation of biological process cell population proliferation regulation of cellular process response to stimulus positive regulation of cell population proliferation positive regulation of epithelial cell proliferation biological regulation positive regulation of biological process response to stress regulation of cell population proliferation cellular process regulation of epithelial cell proliferation response to wounding epithelial cell proliferation positive regulation of cellular process positive regulation of epithelial cell proliferation involved in wound healing cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death developmental process reproductive process developmental process involved in reproduction development of secondary sexual characteristics multi-multicellular organism process multicellular organismal process sexual reproduction fertilization multicellular organismal reproductive process penetration of zona pellucida single fertilization carbohydrate derivative biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process protein N-linked glycosylation macromolecule biosynthetic process biosynthetic process metabolic process protein metabolic process macromolecule metabolic process carbohydrate metabolic process oligosaccharide biosynthetic process carbohydrate biosynthetic process oligosaccharide metabolic process cell adhesion negative regulation of cell population proliferation negative regulation of biological process negative regulation of cellular process negative regulation of epithelial cell proliferation regulation of reproductive process acrosome reaction regulation of acrosome reaction blood vessel morphogenesis tube development angiogenesis involved in wound healing angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development epithelium development epithelial cell development cellular developmental process cell differentiation cell development tissue development epithelial cell differentiation disaccharide metabolic process lactose metabolic process disaccharide biosynthetic process lactose biosynthetic process defense response inflammatory response acute inflammatory response lipid metabolic process positive regulation of circulating fibrinogen levels regulation of biological quality regulation of circulating fibrinogen levels leukocyte migration immune system process mononuclear cell migration myeloid leukocyte migration macrophage migration cell migration cell motility sperm-egg recognition cell-cell recognition binding of sperm to zona pellucida cell recognition monosaccharide metabolic process hexose metabolic process small molecule metabolic process galactose metabolic process	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle basal part of cell basal plasma membrane plasma membrane region basolateral plasma membrane intracellular organelle intracellular anatomical structure Golgi apparatus cytoplasm intracellular membrane-bounded organelle endomembrane system Golgi membrane bounding membrane of organelle organelle membrane cell-cell junction anchoring junction desmosome cell junction cell projection actin-based cell projection filopodium plasma membrane bounded cell projection Golgi trans cisterna Golgi apparatus subcompartment organelle subcompartment Golgi cisterna Golgi stack intracellular vesicle lytic vacuole vesicle membrane cytoplasmic vesicle lysosome vacuolar membrane azurophil granule vacuole lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane secretory granule primary lysosome secretory vesicle azurophil granule membrane secretory granule membrane Golgi cisterna membrane protein-containing complex brush border membrane cluster of actin-based cell projections brush border apical part of cell apical plasma membrane cell projection membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR027791	Galactosyltransferase, C-terminal	Domain
A, B, C	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
A, B, C	IPR027995	Galactosyltransferase, N-terminal	Domain
A, B, C	IPR003859	Beta-1,4-galactosyltransferase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: P15291	B4GALT1-CDG congenital disorder of glycosylation astrocytic tumor cystic fibrosis intellectual disability lung carcinoma osteosarcoma swine influenza glioblastoma large cell medulloblastoma malignant glioma ovarian cancer inborn errors of metabolism lung cancer malignant mesothelioma B4GALT1-CDG congenital disorder of glycosylation astrocytic tumor cystic fibrosis intellectual disability lung carcinoma osteosarcoma swine influenza glioblastoma large cell medulloblastoma malignant glioma ovarian cancer inborn errors of metabolism lung cancer malignant mesothelioma psoriasis

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.