2Q09 | pdb_00002q09

Crystal structure of Imidazolonepropionase from environmental sample with bound inhibitor 3-(2,5-Dioxo-imidazolidin-4-yl)-propionic acid

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	d2q09a1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Imidazolonepropionase-like	Probable 4-imidazolone-5-propanoate amidohydrolase GOS_1928421	(unidentified ) [TaxId: 32644 ],	SCOPe (2.08)
A	d2q09a2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Imidazolonepropionase-like	Probable 4-imidazolone-5-propanoate amidohydrolase GOS_1928421	(unidentified ) [TaxId: 32644 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Imidazolonepropionase-like	8023801	4001967	SCOP2 (2022-06-29)
A	SCOP2 Family	Imidazolonepropionase-like	8023802	4002020	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Composite domain of metallo-dependent hydrolases	8036181	3000176	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Metallo-dependent hydrolases	8036182	3000428	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	PRK09356	e2q09A1	A: beta sandwiches	X: Composite domain of metallo-dependent hydrolases (From Topology)	H: Composite domain of metallo-dependent hydrolases (From Topology)	T: Composite domain of metallo-dependent hydrolases	F: PRK09356	ECOD (1.6)
A	Amidohydro_1_N	e2q09A2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01979	Amidohydrolase family (Amidohydro_1)	Amidohydrolase family	This family of enzymes are a a large metal dependent hydrolase superfamily [1]. The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisatio ...	This family of enzymes are a a large metal dependent hydrolase superfamily [1]. The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisation as a purine and also as a nitrogen source [2]. This family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases, EC:3.5.1.25 These enzymes catalyse the reaction N-acetyl-D-glucosamine 6-phosphate + H2O <=> D-glucosamine 6-phosphate + acetate. This family includes the catalytic domain of urease alpha subunit [3]. Dihydroorotases (EC:3.5.2.3) are also included [4-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Imidazolonepropionase	imidazolonepropionase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding iron ion binding	catabolic process oxoacid metabolic process aromatic amino acid family catabolic process amino acid metabolic process organic acid metabolic process organic acid catabolic process imidazole-containing compound metabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process carboxylic acid catabolic process glutamate metabolic process small molecule metabolic process amino acid catabolic process aromatic amino acid metabolic process catabolic process oxoacid metabolic process aromatic amino acid family catabolic process amino acid metabolic process organic acid metabolic process organic acid catabolic process imidazole-containing compound metabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process carboxylic acid catabolic process glutamate metabolic process small molecule metabolic process amino acid catabolic process aromatic amino acid metabolic process L-histidine catabolic process to glutamate and formate L-histidine metabolic process imidazole-containing compound 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 L-histidine catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process formate metabolic process L-histidine catabolic process to glutamate and formamide amide catabolic process amide metabolic process formamide metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR005920	Imidazolonepropionase	Family
A	IPR006680	Amidohydrolase-related	Domain
A	IPR011059	Metal-dependent hydrolase, composite domain superfamily	Homologous Superfamily
A	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.