1CVR

Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1cvra1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	Gingipain R (RgpB), C-terminal domain	Gingipain R (RgpB), C-terminal domain	(Porphyromonas gingivalis ) [TaxId: 837 ],	SCOPe (2.08)
A	d1cvra2	Alpha and beta proteins (a/b)	Caspase-like	Caspase-like	Gingipain R (RgpB), N-terminal domain	Gingipain R (RgpB), N-terminal domain	(Porphyromonas gingivalis ) [TaxId: 837 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Gingipain R (RgpB), N-terminal domain	8031625	4003597	SCOP2 (2022-06-29)
A	SCOP2 Family	Gingipain R (RgpB), C-terminal domain	8055052	4007522	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Caspase-like	8044003	3001096	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	E set domains	8055053	3000070	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	Peptidase_C25_C	e1cvrA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C25_C	ECOD (1.6)
A	Peptidase_C25_cat	e1cvrA3	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C25_cat	ECOD (1.6)
A	Peptidase_C25_N	e1cvrA4	A: a/b three-layered sandwiches	X: Gingipain R extra N-terminal alpha/beta domain (From Topology)	H: Gingipain R extra N-terminal alpha/beta domain (From Topology)	T: Gingipain R extra N-terminal alpha/beta domain	F: Peptidase_C25_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Gingipain r	CATH (4.3.0)
A	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03785	Peptidase family C25, C terminal ig-like domain (Peptidase_C25_C)	Peptidase family C25, C terminal ig-like domain	-	Domain
A	PF01364	Peptidase family C25 (Peptidase_C25)	Peptidase family C25	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	GINGIPAIN R	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding cysteine-type peptidase activity peptidase activity calcium-dependent cysteine-type endopeptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity	proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR026444	Secretion system C-terminal sorting domain	Domain
A	IPR029030	Caspase-like domain superfamily	Homologous Superfamily
A	IPR039392	Gingipain, N-terminal	Domain
A	IPR005536	Peptidase C25, Ig-like domain	Domain
A	IPR012600	Gingipain propeptide	Domain
A	IPR038490	Gingipain propeptide superfamily	Homologous Superfamily
A	IPR041333	Peptidase M60, C-terminal	Domain
A	IPR001769	Gingipain	Domain
A	IPR029031	Gingipain, N-terminal superfamily	Homologous Superfamily
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR014756	Immunoglobulin E-set	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	gingipain R M-CSA #806	Gingipains are key virulence factors of Porphyromonas gingivalis. They are cysteine proteinases with a high specificity for Arg-Xaa or Lys-Xaa. These proteins are single polypeptides with two domains that show homology to the caspases. Gingipain R is implicated in tissue inflammation associated with periodontal diseases. Elucidation of a chemical mechanism for the active site of gingipain R may be useful in design of drugs in the fight against peridontal diseases.	Defined by 4 residues: GLU:A-152HIS:A-211GLY:A-212CYS:A-244 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.4.22.37 (PDB Primary Data) Search M-CSA Motif + EC 3.4.22.37

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.