2EBF

Crystal structures reveal a thiol-protease like catalytic triad in the C-terminal region of Pasteurella multocida toxin

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth X]	d2ebfx1	All alpha proteins	PMT central region-like	PMT central region-like	PMT central region-like	Dermonecrotic toxin, ToxA	(Pasteurella multocida ) [TaxId: 747 ],	SCOPe (2.08)
A [auth X]	d2ebfx2	Alpha and beta proteins (a/b)	EreA/ChaN-like	EreA/ChaN-like	PMT domain-like	Dermonecrotic toxin, ToxA	(Pasteurella multocida ) [TaxId: 747 ],	SCOPe (2.08)
A [auth X]	d2ebfx3	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	PMT C-terminal domain like	Dermonecrotic toxin, ToxA	(Pasteurella multocida ) [TaxId: 747 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth X]	SCOP2 Family	PMT central region-like	8021525	4001607	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Family	PMT domain-like	8021527	4002144	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Family	PMT C-terminal domain like	8021528	4002524	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Superfamily	PMT central region-like	8033905	3001977	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Superfamily	EreA/ChaN-like	8033907	3000873	SCOP2 (2022-06-29)
A [auth X]	SCOP2 Superfamily	Cysteine proteinases	8033908	3001808	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 [auth X]	MLD	e2ebfX1	A: alpha bundles	X: Bromodomain-like	H: PMT helical bundle domain-like	T: PMT helical bundle domain-like	F: MLD	ECOD (1.6)
A [auth X]	EUF08248	e2ebfX2	A: alpha complex topology	X: PMT central region-like (From Topology)	H: PMT central region-like (From Topology)	T: PMT central region-like	F: EUF08248	ECOD (1.6)
A [auth X]	Tox-PLDMTX	e2ebfX3	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Tox-PLDMTX	ECOD (1.6)
A [auth X]	EUF08646	e2ebfX4	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)
A [auth X]	3.10.670.10	Alpha Beta	Roll	Secreted effector protein ssei fold	Secreted effector protein ssei.	CATH (4.3.0)
A [auth X]	1.20.140.180	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
A [auth X]	3.40.50.11550	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth X]	PF20900	Pasteurella multocida toxin, C3 domain (PMT_C3)	Pasteurella multocida toxin, C3 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 C-terminal catalytic domain C3, which has a Cys-His-Asp triad known to perform acyl-hydrolysis such as peptidase activity or an acyl-transfer reaction. This domain adopts a typical alpha-beta protein fold with seven beta-strands and eight helices. It is organised into two subdomains that form the the biologically active cleft space [1,2].	Domain
A [auth X]	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 [auth X]	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 [auth X]	Dermonecrotic toxin	hydrolase activity, acting on ester bonds hydrolase activity catalytic activity phospholipase activity lipase activity toxin activity binding phospholipid binding lipid binding	symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host G protein-coupled receptor signal transduction pathway symbiont-mediated perturbation of host receptor-mediated signal transduction symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction cellular process disruption of cell in another organism disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host G protein-coupled receptor signal transduction pathway symbiont-mediated perturbation of host receptor-mediated signal transduction symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction cellular process disruption of cell in another organism disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing	cellular anatomical structure membrane extracellular region host cell plasma membrane host cellular component host cell part host cell membrane intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth X]	IPR046673	Dermonecrotic toxin, N-terminal domain	Domain
A [auth X]	IPR054135	Dermonecrotic toxin, barrel-like domain	Domain
A [auth X]	IPR048460	Dermonecrotic toxin, C3 domain	Domain
A [auth X]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A [auth X]	IPR048461	Dermonecrotic toxin-like, C2 domain	Domain
A [auth X]	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.