6A8J | pdb_00006a8j

Crystal structure of bacterial protein toxins

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)
D	MLD	e6a8jD2	A: alpha bundles	X: Bromodomain-like	H: PMT helical bundle domain-like	T: PMT helical bundle domain-like	F: MLD	ECOD (1.6)
D	UNK_F_TYPE	e6a8jD3	A: alpha complex topology	X: PMT central region-like (From Topology)	H: PMT central region-like (From Topology)	T: PMT central region-like	F: UNK_F_TYPE	ECOD (1.6)
D	EUF08646	e6a8jD1	A: a/b three-layered sandwiches	X: EreA/ChaN-like (From Topology)	H: EreA/ChaN-like (From Topology)	T: EreA/ChaN-like	F: EUF08646	ECOD (1.6)
C	MLD	e6a8jC1	A: alpha bundles	X: Bromodomain-like	H: PMT helical bundle domain-like	T: PMT helical bundle domain-like	F: MLD	ECOD (1.6)
C	UNK_F_TYPE	e6a8jC2	A: alpha complex topology	X: PMT central region-like (From Topology)	H: PMT central region-like (From Topology)	T: PMT central region-like	F: UNK_F_TYPE	ECOD (1.6)
C	EUF08646	e6a8jC3	A: a/b three-layered sandwiches	X: EreA/ChaN-like (From Topology)	H: EreA/ChaN-like (From Topology)	T: EreA/ChaN-like	F: EUF08646	ECOD (1.6)
B	MLD	e6a8jB3	A: alpha bundles	X: Bromodomain-like	H: PMT helical bundle domain-like	T: PMT helical bundle domain-like	F: MLD	ECOD (1.6)
B	UNK_F_TYPE	e6a8jB2	A: alpha complex topology	X: PMT central region-like (From Topology)	H: PMT central region-like (From Topology)	T: PMT central region-like	F: UNK_F_TYPE	ECOD (1.6)
B	EUF08646	e6a8jB1	A: a/b three-layered sandwiches	X: EreA/ChaN-like (From Topology)	H: EreA/ChaN-like (From Topology)	T: EreA/ChaN-like	F: EUF08646	ECOD (1.6)
A	MLD	e6a8jA1	A: alpha bundles	X: Bromodomain-like	H: PMT helical bundle domain-like	T: PMT helical bundle domain-like	F: MLD	ECOD (1.6)
A	UNK_F_TYPE	e6a8jA3	A: alpha complex topology	X: PMT central region-like (From Topology)	H: PMT central region-like (From Topology)	T: PMT central region-like	F: UNK_F_TYPE	ECOD (1.6)
A	EUF08646	e6a8jA2	A: a/b three-layered sandwiches	X: EreA/ChaN-like (From Topology)	H: EreA/ChaN-like (From Topology)	T: EreA/ChaN-like	F: EUF08646	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.140.180	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (utative)
D	3.40.50.11550	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
C	1.20.140.180	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (utative)
C	3.40.50.11550	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
B	1.20.140.180	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (utative)
B	3.40.50.11550	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
A	1.20.140.180	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (utative)
A	3.40.50.11550	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF20899	Pasteurella multocida toxin, C2 domain (PMT_C2)	Pasteurella multocida toxin, C2 domain	Pasteurella multocida toxin (PMT) inhibits osteoblastic differentiation in mammals and birds. Its N-terminal region binds to target cells, while its C-terminal region, with a Trojan horse-like shape, carries the intracellularly active moiety. The lat ...	Pasteurella multocida toxin (PMT) inhibits osteoblastic differentiation in mammals and birds. Its N-terminal region binds to target cells, while its C-terminal region, with a Trojan horse-like shape, carries the intracellularly active moiety. The latter consists of three distinct domains: C1 (Pfam:PF11647), C2 and C3. This entry represents the larger of these domains, the central region C2, which has 18 helices and nine beta-strands and is organised into two subdomains with typical alpha-beta structures characteristic of nucleotide-binding proteins [1]. This domain is also found in the Ras/Rap1-specific endopeptidase (RRSP), an effector domain from the multifunctional-autoprocessing repeats-in- toxin (MARTX) toxin from Vibrio vulnificus responsible for the disruption of host innate immune defenses during infection [2,3].	Domain
A, B, C, D	PF11647	Membrane Localization Domain (MLD)	Membrane Localization Domain	This is a membrane localization domain found in multiple families of bacterial toxins including all of the clostridial glucosyltransferase toxins and various MARTX toxins (multifunctional-autoprocessing RTX toxins) [1,4]. In the Pasteurella multocida ...	This is a membrane localization domain found in multiple families of bacterial toxins including all of the clostridial glucosyltransferase toxins and various MARTX toxins (multifunctional-autoprocessing RTX toxins) [1,4]. In the Pasteurella multocida toxin (PMT) C-terminal fragment, structural analysis have indicated that the C1 domain possesses a signal that leads the toxin to the cell membrane. Furthermore, the C1 domain was found to structurally resemble the phospholipid-binding domain of C. difficile toxin B [2]. Functional studies in Vibrio cholera indicate that the subdomain at the N terminus of RID (Rho-inactivation domain), homologous to the membrane targeting C1 domain of Pasteurella multocida toxin, is a conserved membrane localization domain essential for proper localization [1]. The Rho-inactivation domain (RID) of MARTX (Multifunctional Autoprocessing RTX toxin) is responsible for inactivating the Rho-family of small GTPases in Vibrio cholerae. It is a bacterial toxin that self-process by a cysteine peptidase mechanism [3]. The Vibrio cholerae RTX toxin is an autoprocessing cysteine protease whose activity is stimulated by the intracellular environment [3]. This cysteine peptidase belongs to MEROPS peptidase family G6.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	RTX toxin	toxin activity	-	host cellular component cellular anatomical structure host cell part host cell membrane other organism part membrane extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR048461	Dermonecrotic toxin-like, C2 domain	Domain
A, B, C, D	IPR020972	Dermonecrotic/RTX toxin, membrane localization domain	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.