Annotations: 1YSJ

Crystal Structure of Bacillus Subtilis YXEP Protein (APC1829), a Dinuclear Metal Binding Peptidase from M20 Family

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)
B	d1ysjb1	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	Bacterial dinuclear zinc exopeptidases	Protein YxeP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1ysjb2	Alpha and beta proteins (a+b)	Ferredoxin-like	Bacterial exopeptidase dimerisation domain	Bacterial exopeptidase dimerisation domain	Protein YxeP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1ysja1	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	Bacterial dinuclear zinc exopeptidases	Protein YxeP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1ysja2	Alpha and beta proteins (a+b)	Ferredoxin-like	Bacterial exopeptidase dimerisation domain	Bacterial exopeptidase dimerisation domain	Protein YxeP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Zn-dependent exopeptidases	8034925	3000662	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bacterial exopeptidase dimerisation domain	8034927	3001194	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Zn-dependent exopeptidases	8034925	3000662	SCOP2B (2022-06-29)
A	SCOP2 Family	Bacterial dinuclear zinc exopeptidases	8022545	4000587	SCOP2 (2022-06-29)
A	SCOP2 Family	Bacterial exopeptidase dimerisation domain	8022547	4001271	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Zn-dependent exopeptidases	8034925	3000662	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Bacterial exopeptidase dimerisation domain	8034927	3001194	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)
B	RNase_P_Rpp14	e1ysjB1	A: beta barrels	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.2)
B	HGTP_anticodon	e1ysjB2	A: beta barrels	X: HTH	H: HTH	T: winged helix domain	F: HGTP_anticodon	ECOD (v294.2)
A	M20_dimer	e1ysjA1	A: a+b two layers	X: Alpha-beta plaits	H: Bacterial exopeptidase dimerisation domain	T: Bacterial exopeptidase dimerisation domain	F: M20_dimer	ECOD (v294.2)
A	Peptidase_M28	e1ysjA2	A: beta barrels	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Peptidase_M28	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
B	3.30.70.360	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
A	3.30.70.360	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01546	Peptidase family M20/M25/M40 (Peptidase_M20)	Peptidase family M20/M25/M40	-	Family
A, B	PF07687	Peptidase dimerisation domain (M20_dimer)	Peptidase dimerisation domain	This domain consists of 4 beta strands and two alpha helices which make up the dimerisation surface of members of the M20 family of peptidases [1]. This family includes a range of zinc metallopeptidases belonging to several families in the peptidase ...	This domain consists of 4 beta strands and two alpha helices which make up the dimerisation surface of members of the M20 family of peptidases [1]. This family includes a range of zinc metallopeptidases belonging to several families in the peptidase classification [2]. Family M20 are Glutamate carboxypeptidases. Peptidase family M25 contains X-His dipeptidases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	protein yxeP	hydrolase activity catalytic activity deacetylase activity N-acetyldiaminopimelate deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides deacylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding ion binding binding metal ion binding small molecule binding	oxoacid metabolic process sulfur amino acid metabolic process L-cysteine biosynthetic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process sulfur compound metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process oxoacid metabolic process sulfur amino acid metabolic process L-cysteine biosynthetic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process sulfur compound metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process serine family amino acid biosynthetic process sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002933	Peptidase M20	Family
A, B	IPR033846	YxeP peptidase-like	Family
A, B	IPR017439	Amidohydrolase	Family
A, B	IPR036264	Bacterial exopeptidase dimerisation domain	Homologous Superfamily
A, B	IPR011650	Peptidase M20, dimerisation domain	Domain

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.