1KN9

CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD MECHANISM.

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
Membrane Protein Annotation: OPM
Membrane Protein Annotation: mpstruc

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1kn9a_	All beta proteins	LexA/Signal peptidase	LexA/Signal peptidase	Type 1 signal peptidase	Type 1 signal peptidase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d1kn9b_	All beta proteins	LexA/Signal peptidase	LexA/Signal peptidase	Type 1 signal peptidase	Type 1 signal peptidase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d1kn9c_	All beta proteins	LexA/Signal peptidase	LexA/Signal peptidase	Type 1 signal peptidase	Type 1 signal peptidase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d1kn9d_	All beta proteins	LexA/Signal peptidase	LexA/Signal peptidase	Type 1 signal peptidase	Type 1 signal peptidase	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	LexA/Signal peptidase-like	8043153	3000103	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	LexA/Signal peptidase-like	8043153	3000103	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	LexA/Signal peptidase-like	8043153	3000103	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	LexA/Signal peptidase-like	8043153	3000103	SCOP2B (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_S24_1	e1kn9A1	A: beta barrels	X: SH3	H: LexA/Signal peptidase (From Topology)	T: LexA/Signal peptidase	F: Peptidase_S24_1	ECOD (1.6)
B	Peptidase_S24_1	e1kn9B1	A: beta barrels	X: SH3	H: LexA/Signal peptidase (From Topology)	T: LexA/Signal peptidase	F: Peptidase_S24_1	ECOD (1.6)
C	Peptidase_S24_1	e1kn9C1	A: beta barrels	X: SH3	H: LexA/Signal peptidase (From Topology)	T: LexA/Signal peptidase	F: Peptidase_S24_1	ECOD (1.6)
D	Peptidase_S24_1	e1kn9D2	A: beta barrels	X: SH3	H: LexA/Signal peptidase (From Topology)	T: LexA/Signal peptidase	F: Peptidase_S24_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.10.109.10	Mainly Beta	Ribbon	Umud Fragment, subunit A	Umud Fragment, subunit A	CATH (4.3.0)
A	2.170.230.10	Mainly Beta	Beta Complex	Signal Peptidase I	Chain: A, domain 2	CATH (4.3.0)
B	2.10.109.10	Mainly Beta	Ribbon	Umud Fragment, subunit A	Umud Fragment, subunit A	CATH (4.3.0)
B	2.170.230.10	Mainly Beta	Beta Complex	Signal Peptidase I	Chain: A, domain 2	CATH (4.3.0)
C	2.10.109.10	Mainly Beta	Ribbon	Umud Fragment, subunit A	Umud Fragment, subunit A	CATH (4.3.0)
C	2.170.230.10	Mainly Beta	Beta Complex	Signal Peptidase I	Chain: A, domain 2	CATH (4.3.0)
D	2.10.109.10	Mainly Beta	Ribbon	Umud Fragment, subunit A	Umud Fragment, subunit A	CATH (4.3.0)
D	2.170.230.10	Mainly Beta	Beta Complex	Signal Peptidase I	Chain: A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF10502	Signal peptidase, peptidase S26 (Peptidase_S26)	Signal peptidase, peptidase S26	This is a family of membrane signal serine endopeptidases which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal, signal peptides as proteins are translocated across membranes. The ...	This is a family of membrane signal serine endopeptidases which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal, signal peptides as proteins are translocated across membranes. The active site residues take the form of a catalytic dyad that is Ser, Lys in subfamily S26A; the Ser is the nucleophile in catalysis, and the Lys is the general base.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Signal peptidase I	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process signal peptide processing primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process biosynthetic process proteolysis organic substance biosynthetic process protein processing metabolic process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process signal peptide processing primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process biosynthetic process proteolysis organic substance biosynthetic process protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process peptide metabolic process	cell periphery plasma membrane membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR019533	Peptidase S26	Domain
A, B, C, D	IPR019766	Signal peptidase I, all-beta subdomain	Homologous Superfamily
A, B, C, D	IPR019756	Peptidase S26A, signal peptidase I, serine active site	Active Site
A, B, C, D	IPR019758	Peptidase S26A, signal peptidase I, conserved site	Conserved Site
A, B, C, D	IPR019757	Peptidase S26A, signal peptidase I, lysine active site	Active Site
A, B, C, D	IPR036286	LexA/Signal peptidase-like superfamily	Homologous Superfamily
A, B, C, D	IPR000223	Peptidase S26A, signal peptidase I	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM	Transmembrane	Alpha-helical polytopic	Peptidase SF	Peptidase S26

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	MONOTOPIC MEMBRANE PROTEINS	Peptidases	LepB Signal Peptidase (SPase), apoprotein

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.