2FYC | pdb_00002fyc

Crystal structure of the catalytic domain of bovine beta1,4-galactosyltransferase-I in complex with alpha-lactalbumin, Ca and UDP-galactose

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2fyca_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	C-type lysozyme	alpha-Lactalbumin	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d2fycc_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	C-type lysozyme	alpha-Lactalbumin	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d2fycb1	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	beta 1,4 galactosyltransferase (b4GalT1)	beta 1,4 galactosyltransferase (b4GalT1)	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
D	d2fycd_	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	beta 1,4 galactosyltransferase (b4GalT1)	automated matches	cattle (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Lysozyme-like	8034893	3001879	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lysozyme-like	8034893	3001879	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8043892	3000077	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8043892	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		e2fycA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
C		e2fycC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
B		e2fycB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	F:	ECOD (20:10:01)
D		e2fycD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
C	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		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)
D	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, C	PF00062	C-type lysozyme/alpha-lactalbumin family (Lys)	C-type lysozyme/alpha-lactalbumin family	Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bac ...	Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bacterial cell walls. Structure is a multi-domain, mixed alpha and beta fold, containing four conserved disulfide bonds.	Domain
B, D	PF02709	N-terminal domain of galactosyltransferase (Glyco_transf_7C)	N-terminal domain of galactosyltransferase	-	Family
B, D	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, C	Alpha-lactalbumin	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity lactose synthase activity UDP-glycosyltransferase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity lactose synthase activity UDP-glycosyltransferase activity glycosyltransferase activity transferase activity galactosyltransferase activity hexosyltransferase activity UDP-galactosyltransferase activity	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus defense response to Gram-negative bacterium response to biotic stimulus defense response to bacterium response to bacterium response to stress response to external biotic stimulus carbohydrate metabolic process carbohydrate biosynthetic process oligosaccharide metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus defense response to Gram-negative bacterium response to biotic stimulus defense response to bacterium response to bacterium response to stress response to external biotic stimulus carbohydrate metabolic process carbohydrate biosynthetic process oligosaccharide metabolic process primary metabolic process disaccharide metabolic process lactose metabolic process disaccharide biosynthetic process biosynthetic process oligosaccharide biosynthetic process metabolic process cellular process lactose biosynthetic process defense response to Gram-positive bacterium	cellular anatomical structure extracellular region protein-containing complex
B, D	beta-1,4-galactosyltransferase	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 beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity beta-tubulin binding N-acetyllactosamine synthase activity identical protein binding	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 defense response inflammatory response acute inflammatory response 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 multicellular organism development multicellular organismal process reproductive process sex differentiation anatomical structure development developmental process involved in reproduction development of secondary sexual characteristics primary metabolic process metabolic process lipid metabolic process positive regulation of circulating fibrinogen levels regulation of biological quality regulation of circulating fibrinogen levels carbohydrate derivative biosynthetic process biosynthetic process carbohydrate derivative metabolic process multi-multicellular organism process sexual reproduction fertilization multicellular organismal reproductive process penetration of zona pellucida single fertilization glycoprotein biosynthetic process glycoprotein metabolic process protein N-linked glycosylation macromolecule biosynthetic process protein metabolic process macromolecule metabolic process leukocyte migration immune system process mononuclear cell migration myeloid leukocyte migration macrophage migration cell migration cell motility 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 sperm-egg recognition cell-cell recognition binding of sperm to zona pellucida cell recognition blood vessel morphogenesis tube development angiogenesis involved in wound healing angiogenesis vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development system development epithelium development epithelial cell development cellular developmental process cell differentiation cell development tissue development epithelial cell differentiation monosaccharide metabolic process hexose metabolic process small molecule metabolic process galactose metabolic process disaccharide metabolic process lactose metabolic process disaccharide biosynthetic process lactose biosynthetic process	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane Golgi trans cisterna membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment Golgi cisterna cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane Golgi trans cisterna membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment Golgi cisterna intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle Golgi stack cytoplasm Golgi cisterna membrane organelle membrane basal part of cell basal plasma membrane plasma membrane region basolateral plasma membrane protein-containing complex cell-cell junction anchoring junction desmosome cell junction brush border membrane cluster of actin-based cell projections plasma membrane bounded cell projection brush border cell projection apical part of cell apical plasma membrane cell projection membrane extracellular region extracellular space actin-based cell projection filopodium

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR001916	Glycoside hydrolase, family 22	Family
A, C	IPR019799	Glycoside hydrolase family 22 domain	Domain
A, C	IPR000545	Lactalbumin	Family
A, C	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
B, D	IPR027995	Galactosyltransferase, N-terminal	Domain
B, D	IPR027791	Galactosyltransferase, C-terminal	Domain
B, D	IPR003859	Beta-1,4-galactosyltransferase	Family
B, D	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily

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.