3GIQ | pdb_00003giq

Crystal structure of N-acyl-D-Glutamate Deacylase from Bordetella Bronchiseptica complexed with zinc and phosphonate inhibitor, a mimic of the reaction tetrahedral intermediate.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d3giqb1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	automated matches	automated matches	Alcaligenes bronchisepticus (Bordetella bronchiseptica ) [TaxId: 518 ],	SCOPe (2.08)
B	d3giqb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	automated matches	automated matches	Alcaligenes bronchisepticus (Bordetella bronchiseptica ) [TaxId: 518 ],	SCOPe (2.08)
A	d3giqa1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	automated matches	automated matches	Alcaligenes bronchisepticus (Bordetella bronchiseptica ) [TaxId: 518 ],	SCOPe (2.08)
A	d3giqa2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	automated matches	automated matches	Alcaligenes bronchisepticus (Bordetella bronchiseptica ) [TaxId: 518 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	DHquinase_I	e3giqB2	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: DHquinase_I	ECOD (v294.1)
A	DHquinase_I	e3giqA2	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: DHquinase_I	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
B	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
B	3.30.1490.130	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
A	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
A	3.30.1490.130	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	N-acyl-D-glutamate deacylase	cation binding ion binding binding metal ion binding small molecule binding N-acyl-D-glutamate deacylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR013108	Amidohydrolase 3	Domain
A, B	IPR023100	D-aminoacylase, insert domain superfamily	Homologous Superfamily
A, B	IPR011059	Metal-dependent hydrolase, composite domain superfamily	Homologous Superfamily
A, B	IPR032466	Metal-dependent hydrolase	Homologous Superfamily

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.