1XOV

The crystal structure of the listeria monocytogenes bacteriophage PSA endolysin PlyPSA

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1xova1	All beta proteins	SH3-like barrel	Prokaryotic SH3-related domain	Ply C-terminal domain-like	Endolysin Ply, C-terminal domain	(Listeria phage PSA ) [TaxId: 171618 ],	SCOPe (2.08)
A	d1xova2	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	N-acetylmuramoyl-L-alanine amidase-like	Endolysin Ply, catalytic domain	(Listeria phage PSA ) [TaxId: 171618 ],	SCOPe (2.08)
A	d1xova3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Listeria phage PSA ) [TaxId: 171618 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Ply C-terminal domain-like	8021467	4001718	SCOP2 (2022-06-29)
A	SCOP2 Family	N-acetylmuramoyl-L-alanine amidase-like	8021470	4001130	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Prokaryotic SH3-related domain	8033847	3001455	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Zn-dependent exopeptidases	8033850	3000662	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	CwlA_1st	e1xovA4	A: beta barrels	X: SH3	H: SH3	T: SH3	F: CwlA_1st	ECOD (1.6)
A	CwlA_2nd	e1xovA3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: CwlA_2nd	ECOD (1.6)
A	Amidase_3	e1xovA2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: Amidase_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.630.40	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn-dependent exopeptidases	CATH (4.3.0)
A	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18341	PSA endolysin C-terminal cell wall binding domain (PSA_CBD)	PSA endolysin C-terminal cell wall binding domain	This is the C-terminal domain of bacteriophage PSA endolysin. The C-terminal domain is the cell wall-binding domain (CBD) which is composed of two structurally homologous subdomains. CBD comprises two copies of a beta-barrel-like folds, which are hel ...	This is the C-terminal domain of bacteriophage PSA endolysin. The C-terminal domain is the cell wall-binding domain (CBD) which is composed of two structurally homologous subdomains. CBD comprises two copies of a beta-barrel-like folds, which are held together by means of swapped beta-strands. The observed structure of the CBD sub-domains from Listeriaphage endolysin (N-acetyl-muramoyl-l-alanine amidase), could be the result of either a gene duplication during evolution of the CBD or the pick-up of another functionally equivalent coding sequence, followed by swapping of the respective ancestral leading beta-strands [1].	Domain
A	PF01520	N-acetylmuramoyl-L-alanine amidase (Amidase_3)	N-acetylmuramoyl-L-alanine amidase	This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ply protein	catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity cation binding ion binding binding metal ion binding small molecule binding peptidoglycan muralytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity cation binding ion binding binding metal ion binding small molecule binding peptidoglycan muralytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity N-acetylmuramoyl-L-alanine amidase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	methylation metabolic process organonitrogen compound catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process organic substance metabolic process aminoglycan metabolic process methylation metabolic process organonitrogen compound catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process organic substance metabolic process aminoglycan metabolic process peptidoglycan metabolic process macromolecule metabolic process organic substance catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR041341	PSA endolysin, cell wall binding domain	Domain
A	IPR002508	N-acetylmuramoyl-L-alanine amidase, catalytic domain	Domain

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.