6RIM | pdb_00006rim

Crystal structure of the catalytic domain of the Weissela oryzae botulinum like toxin

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
H	tRNA-synt_2b	e6rimH1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: tRNA-synt_2b	ECOD (v294.1)
G	tRNA-synt_2b	e6rimG1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: tRNA-synt_2b	ECOD (v294.1)
F	tRNA-synt_2b	e6rimF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: tRNA-synt_2b	ECOD (v294.1)
E	tRNA-synt_2b	e6rimE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: tRNA-synt_2b	ECOD (v294.1)
D	tRNA-synt_2b	e6rimD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: tRNA-synt_2b	ECOD (v294.1)
C	tRNA-synt_2b	e6rimC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: tRNA-synt_2b	ECOD (v294.1)
B	tRNA-synt_2b	e6rimB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: tRNA-synt_2b	ECOD (v294.1)
A	tRNA-synt_2b	e6rimA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: tRNA-synt_2b	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF26320	Botulinum-like neurotoxin Wo, peptidase domain (Peptidase_M27_Wo)	Botulinum-like neurotoxin Wo, peptidase domain	This entry represents the peptidase domain of the botulinum neurotoxin-like protein from Weissella oryzae (BoNT/Wo). This domain is responsible for the zinc-dependent proteolytic activity of the toxin, specifically cleaving the VAMP2 protein between ...	This entry represents the peptidase domain of the botulinum neurotoxin-like protein from Weissella oryzae (BoNT/Wo). This domain is responsible for the zinc-dependent proteolytic activity of the toxin, specifically cleaving the VAMP2 protein between Trp89 and Trp90. The domain contains the conserved HExxH zinc-binding motif characteristic of the M27 metalloproteases family, but features a wider, more open and negatively charged catalytic pocket compared to other botulinum neurotoxins. It also contains a unique beta-hairpin motif (residues 31-60) and an unusually interrupted alpha-helix (residues 309-350) with an extended loop. The crystal structure revealed an additional calcium ion near the active site that may be involved in substrate binding.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Putative botulinum-like toxin Wo	cation binding ion binding binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR058850	Botulinum-like neurotoxin Wo, peptidase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011065	Kunitz inhibitor STI-like superfamily	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.