7POG | pdb_00007pog

High-resolution structure of native toxin A from Clostridioides difficile

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8099200	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	CW_binding_1	e7pogA7	A: beta duplicates or obligate multimers	X: beta-hairpin stack (From Topology)	H: beta-hairpin stack (From Topology)	T: beta-hairpin stack	F: CW_binding_1	ECOD (1.6)
A	TcdA_TcdB_pore_2nd	e7pogA1	A: beta duplicates or obligate multimers	X: Toxin A (TcdA) delivery domain (From Topology)	H: Toxin A (TcdA) delivery domain (From Topology)	T: Toxin A (TcdA) delivery domain	F: TcdA_TcdB_pore_2nd	ECOD (1.6)
A	TcdA_TcdB_pore_1st	e7pogA5	A: alpha arrays	X: Toxin A (TcdA) helical domain (From Topology)	H: Toxin A (TcdA) helical domain (From Topology)	T: Toxin A (TcdA) helical domain	F: TcdA_TcdB_pore_1st	ECOD (1.6)
A	MLD	e7pogA6	A: alpha bundles	X: Bromodomain-like	H: PMT helical bundle domain-like	T: PMT helical bundle domain-like	F: MLD	ECOD (1.6)
A	TcdA_TcdB	e7pogA2	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: TcdA_TcdB	ECOD (1.6)
A	Peptidase_C80	e7pogA3	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C80	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.1780	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (utative)
A	3.40.50.11050	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	MARTX cysteine protease (CPD) domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF12919	TcdA/TcdB catalytic glycosyltransferase domain (TcdA_TcdB)	TcdA/TcdB catalytic glycosyltransferase domain	This domain represents the N-terminal glycosyltransferase from a set of toxins found in some bacteria. This domain in TcdB glycosylates the host RhoA protein.	Domain
A	PF12918	TcdB toxin N-terminal helical domain (TcdB_N)	TcdB toxin N-terminal helical domain	This is a short helical bundle domain found associated with the catalytic domain of the TcdB toxin from C. difficile [1]. The function of this domain is unknown, but it may be involved in substrate recognition.	Domain
A	PF01473	Putative cell wall binding repeat (Choline_bind_1)	Putative cell wall binding repeat	-	Repeat
A	PF19127	Choline-binding repeat (Choline_bind_3)	Choline-binding repeat	-	Repeat
A	PF11713	Peptidase C80 family (Peptidase_C80)	Peptidase C80 family	This family belongs to cysteine peptidase family C80.	Domain
A	PF12920	TcdA/TcdB pore forming domain (TcdA_TcdB_pore)	TcdA/TcdB pore forming domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Toxin A	glycosyltransferase activity transferase activity catalytic activity binding lipid binding toxin activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity cation binding ion binding metal ion binding small molecule binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure membrane extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome cellular anatomical structure membrane extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region host cell plasma membrane host cell cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR038383	CGT/MARTX, cysteine protease (CPD) domain superfamily	Homologous Superfamily
A	IPR024772	TcdA/TcdB toxin, N-terminal helical domain	Domain
A	IPR020974	CGT/MARTX, cysteine protease (CPD) domain	Domain
A	IPR024769	TcdA/TcdB toxin, pore forming domain	Domain
A	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
A	IPR024770	TcdA/TcdB toxin, catalytic glycosyltransferase domain	Domain
A	IPR018337	Cell wall/choline-binding repeat	Repeat

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.