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) C-terminal domain	8055052	4007522	SCOP2 (2022-06-29)
A	SCOP2 Family	Gingipain R (RgpB) N-terminal domain	8031625	4003597	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	E set domains	8055053	3000070	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Caspase-like	8044003	3001096	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	organic substance metabolic process organonitrogen compound metabolic process 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 National Science Foundation (DBI-1832184), 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 R01GM133198.