1VGY | pdb_00001vgy

Crystal structure of succinyl diaminopimelate desuccinylase

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	d1vgyb1	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	Bacterial dinuclear zinc exopeptidases	Succinyl-diaminopimelate desuccinylase, catalytic domain	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
B	d1vgyb2	Alpha and beta proteins (a+b)	Ferredoxin-like	Bacterial exopeptidase dimerisation domain	Bacterial exopeptidase dimerisation domain	Succinyl-diaminopimelate desuccinylase	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
A	d1vgya1	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	Bacterial dinuclear zinc exopeptidases	Succinyl-diaminopimelate desuccinylase, catalytic domain	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
A	d1vgya2	Alpha and beta proteins (a+b)	Ferredoxin-like	Bacterial exopeptidase dimerisation domain	Bacterial exopeptidase dimerisation domain	Succinyl-diaminopimelate desuccinylase	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Bacterial exopeptidase dimerisation domain	8035743	3001194	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Zn-dependent exopeptidases	8035742	3000662	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Zn-dependent exopeptidases	8035742	3000662	SCOP2B (2022-06-29)
A	SCOP2 Family	Bacterial dinuclear zinc exopeptidases	8023362	4000587	SCOP2 (2022-06-29)
A	SCOP2 Family	Bacterial exopeptidase dimerisation domain	8023363	4001271	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Zn-dependent exopeptidases	8035742	3000662	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Bacterial exopeptidase dimerisation domain	8035743	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		e1vgyB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Fer4,DUF3470	F:	ECOD (20:10:01)
B		e1vgyB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_1	F:	ECOD (20:10:01)
A		e1vgyA1	A: Alpha-beta plaits	X: Bacterial exopeptidase dimerisation domain	H: Bacterial exopeptidase dimerisation domain	T: M20_dimer	F:	ECOD (20:10:01)
A		e1vgyA2	A: Phosphorylase/hydrolase-like	X: Zn-dependent exopeptidases	H: Zn-dependent exopeptidases	T: Peptidase_M20	F:	ECOD (20:10:01)

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	succinyl-diaminopimelate desuccinylase	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding deacetylase activity acetylornithine deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides deacylase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding deacetylase activity acetylornithine deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides deacylase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds zinc ion binding succinyl-diaminopimelate desuccinylase activity	diaminopimelate biosynthetic process oxoacid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process lipid biosynthetic process carboxylic acid metabolic process fatty acid derivative biosynthetic process primary metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process fatty acid derivative metabolic process amino acid biosynthetic process biosynthetic process diaminopimelate biosynthetic process oxoacid metabolic process small molecule biosynthetic process dicarboxylic acid metabolic process lipid biosynthetic process carboxylic acid metabolic process fatty acid derivative biosynthetic process primary metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process fatty acid derivative metabolic process amino acid biosynthetic process biosynthetic process metabolic process cellular process small molecule metabolic process dicarboxylic acid biosynthetic process lipid metabolic process L-arginine biosynthetic process L-amino acid biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process L-amino acid metabolic process arginine metabolic process proteinogenic amino acid metabolic process proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process lysine metabolic process L-lysine biosynthetic process aspartate family amino acid biosynthetic process L-lysine biosynthetic process via diaminopimelate	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR005941	Succinyl-diaminopimelate desuccinylase, proteobacteria	Family
A, B	IPR002933	Peptidase M20	Family
A, B	IPR050072	Peptidase M20A family, bacterial cell wall biosynthesis	Family
A, B	IPR036264	Bacterial exopeptidase dimerisation domain	Homologous Superfamily
A, B	IPR011650	Peptidase M20, dimerisation domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.