1PGS

THE THREE-DIMENSIONAL STRUCTURE OF PNGASE F, A GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1pgsa1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	PHM/PNGase F	Glycosyl-asparaginase	Peptide:N-glycosidase F, PNGase F	(Elizabethkingia meningoseptica ) [TaxId: 238 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	glycosyl-asparaginase	8028722	4002410	SCOP2 (2022-06-29)
A	SCOP2 Family	glycosyl-asparaginase	8028724	4002410	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PHM/PNGase F	8041101	3001201	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PHM/PNGase F	8041103	3001201	SCOP2 (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	N-glycanase_C	e1pgsA2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: N-glycanase_C	ECOD (1.6)
A	N-glycanase_N	e1pgsA1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: N-glycanase_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.230	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF09113	Peptide-N-glycosidase F, C terminal (N-glycanase_C)	Peptide-N-glycosidase F, C terminal	Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The doma ...	Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The domain allows the protein to bind sugars and catalyses the complete removal of N-linked oligosaccharide chains from glycoproteins [1].	Domain
A	PF09112	Peptide-N-glycosidase F, N terminal (N-glycanase_N)	Peptide-N-glycosidase F, N terminal	Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The doma ...	Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The domain allows the protein to bind sugars and catalyses the complete removal of N-linked oligosaccharide chains from glycoproteins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL)ASPARAGINE AMIDASE F	oxidoreductase activity monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008977	PHM/PNGase F domain superfamily	Homologous Superfamily
A	IPR015197	Peptide-N-glycosidase F, C-terminal	Domain
A	IPR014784	Copper type II, ascorbate-dependent monooxygenase-like, C-terminal	Homologous Superfamily
A	IPR015196	Peptide-N-glycosidase F, N-terminal	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase M-CSA #878	Peptide aspartylglucosaminidase (PNGase) removes asparagine linked oligosaccharide chains from intact proteins.	Defined by 3 residues: ASP:A-60GLU:A-118GLU:A-206 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.5.1.52 (PDB Primary Data) Search M-CSA Motif + EC 3.5.1.52

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.