2G9D | pdb_00002g9d

Crystal Structure of Succinylglutamate desuccinylase from Vibrio cholerae, Northeast Structural Genomics Target VcR20

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	d2g9da1	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Zn-dependent exopeptidases	AstE/AspA-like	Succinylglutamate desuccinylase AstE	(Vibrio cholerae MO10 ) [TaxId: 345072 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	AstE/AspA-like	8029367	4003075	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Zn-dependent exopeptidases	8041746	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	AstE_AspA_C_1	e2g9dA3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: Succinylglutamate desuccinylase / Aspartoacylase C-terminal domain (From Topology)	T: Succinylglutamate desuccinylase / Aspartoacylase C-terminal domain	F: AstE_AspA_C_1	ECOD (1.6)
A	AstE_AspA_N	e2g9dA2	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: AstE_AspA_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
A	2.40.50.630	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04952	AstE/AspA barrel-sandwich hybrid domain (AstE_AspA_hybrid)	AstE/AspA barrel-sandwich hybrid domain	This entry represents the barrel-sandwich hybrid domain found in Succinylglutamate desuccinylase (AstE), aspartoacylase (AspA) and related enzymes. AstE catalyses the fifth and last step in arginine catabolism by the arginine succinyltransferase path ...	This entry represents the barrel-sandwich hybrid domain found in Succinylglutamate desuccinylase (AstE), aspartoacylase (AspA) and related enzymes. AstE catalyses the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway whereas AspA cleaves acylaspartate into a fatty acid and aspartate. Mutations in human AspA lead to Canavan disease disease [1]. The domain represented by this entry has similarity to known barrel-sandwich domains that are defined by sandwich of half-barrel shaped beta-sheets. This domain is also described as shielding domain as it was found to cover the enzyme active site and thus limiting its accessibility [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Succinylglutamate desuccinylase	hydrolase activity, acting on ester bonds hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds succinylglutamate desuccinylase activity	catabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process arginine metabolic process L-arginine catabolic process carboxylic acid catabolic process glutamate metabolic process L-arginine catabolic process to L-glutamate small molecule metabolic process amino acid catabolic process catabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process arginine metabolic process L-arginine catabolic process carboxylic acid catabolic process glutamate metabolic process L-arginine catabolic process to L-glutamate small molecule metabolic process amino acid catabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process small molecule catabolic process succinate metabolic process L-arginine catabolic process to succinate	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007036	AstE/AspA barrel-sandwich hybrid domain	Domain
A	IPR016681	Succinylglutamate desuccinylase	Family
A	IPR050178	AspA/AstE family	Family
A	IPR055438	Succinylglutamate desuccinylase/Aspartoacylase, catalytic 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.