3M1H

Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys-gingipain (Kgp) from Porphyromonas gingivalis w83

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)
C	Cleaved_Adhesin	e3m1hC1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Cleaved_Adhesin	ECOD (1.6)
D	Cleaved_Adhesin	e3m1hD1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Cleaved_Adhesin	ECOD (1.6)
A	Cleaved_Adhesin	e3m1hA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Cleaved_Adhesin	ECOD (1.6)
B	Cleaved_Adhesin	e3m1hB1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Cleaved_Adhesin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
A	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF07675	Cleaved Adhesin Domain (Cleaved_Adhesin)	Cleaved Adhesin Domain	This is a family of bacterial protein modules thought to function in various roles including cell adhesion, cell lysis and carbohydrate binding [1]. A tandem repeat of these modules (either two or three repeats) constitute the haemagglutinin/adhesin ...	This is a family of bacterial protein modules thought to function in various roles including cell adhesion, cell lysis and carbohydrate binding [1]. A tandem repeat of these modules (either two or three repeats) constitute the haemagglutinin/adhesin (HA) regions of the gingipains, RgpA, Swiss:Q51816 and Kgp, Swiss:P72194 and Swiss:P72197 [3] expressed by Porphyromonas gingivalis (Bacteroides gingivalis) [2]. They form components of the major extracellular virulence complex RgpA-Kgp - a mixture of proteinases and adhesin domains [4]. The adhesin domains in this complex are found in proteinase-cleaved forms when isolated from the cell surface [5]. Haemagglutinin genes of P. gingivalis [6] (hagA1 HAGA1_PORGI - Swiss:P59915 - and hagA2 HAGA2_PORGI - Swiss:Q51845) suggest that such proteins are composed of eight to ten tandem repeats of these adhesin modules [1]. Genomic data predicts that homologous protein modules are also expressed by a number of other bacteria and form part of putative multi-domain proteins, eg. Swiss:Q26BR9 and Swiss:B0VGL6. These domains may be acting in concert with other adhesion modules thought to be part of these multi-domain proteins such as fibronectin type III, Pfam:PF00041, and Meprin, A5, mu (MAM), Pfam:PF00629, domains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Lysine specific cysteine protease	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity	hemolysis in another organism biological process involved in interspecies interaction between organisms cytolysis in another organism cellular process disruption of cell in another organism disruption of anatomical structure in another organism cytolysis killing of cells of another organism cell killing proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029030	Caspase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR039392	Gingipain, N-terminal	Domain
A, B, C, D	IPR005536	Peptidase C25, Ig-like domain	Domain
A, B, C, D	IPR012600	Gingipain propeptide	Domain
A, B, C, D	IPR038490	Gingipain propeptide superfamily	Homologous Superfamily
A, B, C, D	IPR018832	Peptidase C25, gingipain, C-terminal	Domain
A, B, C, D	IPR001769	Gingipain	Domain
A, B, C, D	IPR029031	Gingipain, N-terminal superfamily	Homologous Superfamily
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR011628	Cleaved adhesin	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.