4NUY | pdb_00004nuy

Crystal structure of EndoS, an endo-beta-N-acetyl-glucosaminidase from Streptococcus pyogenes

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	F5_F8_type_C_1	e4nuyA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: F5_F8_type_C_1	ECOD (1.6)
A	EUF07803	e4nuyA5	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Ig-like domain in endo-beta-N-acetylglucosaminidase F2 (From Topology)	T: Ig-like domain in endo-beta-N-acetylglucosaminidase F2	F: EUF07803	ECOD (1.6)
A	LRR_8_3,RHH_6	e4nuyA4	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: LRR_8_3,RHH_6	ECOD (1.6)
A	EUF08143	e4nuyA3	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 (From Topology)	T: Helical bundle domain in endo-beta-N-acetylglucosaminidase F2	F: EUF08143	ECOD (1.6)
A	Glyco_hydro_18_1	e4nuyA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glyco_hydro_18_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF23952	Endo-beta-N-acetylglucosaminidase EndoS LRR domain (LRR_EndoS)	Endo-beta-N-acetylglucosaminidase EndoS LRR domain	-	Repeat
A	PF20746	Endo-beta-N-acetylglucosaminidase F2, Ig-like domain (EndoS_Ig-like)	Endo-beta-N-acetylglucosaminidase F2, Ig-like domain	This domain is found in Endo-beta-N-acetylglucosaminidase F2 (EndoS) from Streptococcus pyogenes (Swiss:Q48RM3) and similar sequences predominantly found in Firmicutes. EndoS is an immunomodulatory enzyme secreted by the bacteria to remove carbohydra ...	This domain is found in Endo-beta-N-acetylglucosaminidase F2 (EndoS) from Streptococcus pyogenes (Swiss:Q48RM3) and similar sequences predominantly found in Firmicutes. EndoS is an immunomodulatory enzyme secreted by the bacteria to remove carbohydrates from IgG antibodies in a highly specific manner, which gives the pathogen a survival advantage over its host. This protein is composed of five distinct protein domains. The domain located at the base of the V-shaped EndoS structure (this entry), also named hybrid Ig domain, is composed of two subdomains. The smaller one is inserted within the loop that connects the LRR domain to the second and third beta strands of the larger subdomain. The latter is a typical Ig domain structurally similar to the interleukin-4 receptor [1,2,3].	Domain
A	PF23916	Endo-beta-N-acetylglucosaminidase EndoS TIM-barrel domain (TIM-barrel_EndoS)	Endo-beta-N-acetylglucosaminidase EndoS TIM-barrel domain	This entry represents the TIM barrel domain found in Endo-beta-N-acetylglucosaminidase EndoS from Streptococcus spp. EndoS is a secreted protein that catalyses the hydrolysis of the N-linked oligosaccharides on opsonizing immunoglobulin G [1], thus c ...	This entry represents the TIM barrel domain found in Endo-beta-N-acetylglucosaminidase EndoS from Streptococcus spp. EndoS is a secreted protein that catalyses the hydrolysis of the N-linked oligosaccharides on opsonizing immunoglobulin G [1], thus contributing to immune response evasion and increased survival of the bacteria in patients [2]. This domain binds to complex-type N-glycans and has enzymatic activity [3,4].	Domain
A	PF22382	Endo-beta-N-acetylglucosaminidase, helical bundle (EndoS_helical)	Endo-beta-N-acetylglucosaminidase, helical bundle	This entry represents a three-helix bundle domain of EndoS from Streptococcus pyogenes and similar bacterial proteins. EndoS is involved in immune evasion mechanisms and possesses a specific endoglycosidase activity that targets IgG antibodies [1,2]. ...	This entry represents a three-helix bundle domain of EndoS from Streptococcus pyogenes and similar bacterial proteins. EndoS is involved in immune evasion mechanisms and possesses a specific endoglycosidase activity that targets IgG antibodies [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Endo-beta-N-acetylglucosaminidase F2	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding toxin activity mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity	symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated response to host defenses response to external stimulus biological process involved in interaction with host response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated perturbation of host process response to host immune response symbiont-mediated evasion of host immune response response to host symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated response to host defenses response to external stimulus biological process involved in interaction with host response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated perturbation of host process response to host immune response symbiont-mediated evasion of host immune response response to host response to external biotic stimulus modulation of process of another organism carbohydrate metabolic process primary metabolic process metabolic process cellular process	cellular anatomical structure extracellular region host extracellular space host cellular component other organism part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR057016	Endo-beta-N-acetylglucosaminidase EndoS/F2-like, TIM-barrel domain	Domain
A	IPR001579	Glycosyl hydrolase family 18, active site	Active Site
A	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A	IPR049410	Endo-beta-N-acetylglucosaminidase EndoS-like, Ig-like domain	Domain
A	IPR055024	Endo-beta-N-acetylglucosaminidase EndoS, helical bundle	Domain

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.