4R4Z

Structure of PNGF-II in P21 space group

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	PF22252	e4r4zA2	A: beta meanders	X: Lipoprotein localization factors LolAB	H: Lipoprotein localization factors LolAB (From Topology)	T: Lipoprotein localization factors LolAB	F: PF22252	ECOD (1.6)
A	PF09112	e4r4zA3	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: PF09112	ECOD (1.6)
A	PF09113	e4r4zA1	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: PF09113	ECOD (1.6)
B	PF22252	e4r4zB3	A: beta meanders	X: Lipoprotein localization factors LolAB	H: Lipoprotein localization factors LolAB (From Topology)	T: Lipoprotein localization factors LolAB	F: PF22252	ECOD (1.6)
B	PF09112	e4r4zB1	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: PF09112	ECOD (1.6)
B	PF09113	e4r4zB2	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: PF09113	ECOD (1.6)
D	PF22252	e4r4zD2	A: beta meanders	X: Lipoprotein localization factors LolAB	H: Lipoprotein localization factors LolAB (From Topology)	T: Lipoprotein localization factors LolAB	F: PF22252	ECOD (1.6)
D	PF09112	e4r4zD3	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: PF09112	ECOD (1.6)
D	PF09113	e4r4zD1	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: PF09113	ECOD (1.6)
C	PF22252	e4r4zC1	A: beta meanders	X: Lipoprotein localization factors LolAB	H: Lipoprotein localization factors LolAB (From Topology)	T: Lipoprotein localization factors LolAB	F: PF22252	ECOD (1.6)
C	PF09112	e4r4zC2	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: PF09112	ECOD (1.6)
C	PF09113	e4r4zC3	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: PF09113	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.1570	Mainly Beta	Sandwich	Jelly Rolls	Peptide-N-glycosidase F, N-terminal domain	CATH (4.3.0)
A	2.60.120.230	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	2.60.120.1570	Mainly Beta	Sandwich	Jelly Rolls	Peptide-N-glycosidase F, N-terminal domain	CATH (4.3.0)
B	2.60.120.230	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D	2.60.120.1570	Mainly Beta	Sandwich	Jelly Rolls	Peptide-N-glycosidase F, N-terminal domain	CATH (4.3.0)
D	2.60.120.230	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.60.120.1570	Mainly Beta	Sandwich	Jelly Rolls	Peptide-N-glycosidase F, N-terminal domain	CATH (4.3.0)
C	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, B, C, D	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, B, C, D	PF22252	N-glycanase peptide, N-terminal domain (PNGase_F-II_N)	N-glycanase peptide, N-terminal domain	This domain is found at the N-terminal end of N-glycanase peptide from Elizabethkingia meningoseptica (PNGase F-II) and other bacterial sequences mainly found in flavobacteriales. This is often found associated with Pfam:PF09112 and Pfam:PF09113.	Domain
A, B, C, D	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, B, C, D	PNGF-II	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 cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR008977	PHM/PNGase F domain superfamily	Homologous Superfamily
A, B, C, D	IPR015197	Peptide-N-glycosidase F, C-terminal	Domain
A, B, C, D	IPR014784	Copper type II, ascorbate-dependent monooxygenase-like, C-terminal	Homologous Superfamily
A, B, C, D	IPR043022	Peptide-N-glycosidase F, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR015196	Peptide-N-glycosidase F, N-terminal	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 R01GM133198.