1ONW

Crystal structure of Isoaspartyl Dipeptidase from E. coli

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1onwa1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Isoaspartyl dipeptidase	Isoaspartyl dipeptidase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1onwa2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Isoaspartyl dipeptidase, catalytic domain	Isoaspartyl dipeptidase, catalytic domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1onwb1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Isoaspartyl dipeptidase	Isoaspartyl dipeptidase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1onwb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Isoaspartyl dipeptidase, catalytic domain	Isoaspartyl dipeptidase, catalytic domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8034166	3000176	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metallo-dependent hydrolases	8034168	3000428	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8034166	3000176	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8034166	3000176	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-dependent hydrolases	8034168	3000428	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8034166	3000176	SCOP2B (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	F_UNCLASSIFIED	e1onwA1	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: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e1onwA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e1onwB1	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: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e1onwB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: F_UNCLASSIFIED	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	Isoaspartyl dipeptidase	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds omega peptidase activity threonine-type peptidase activity beta-aspartyl-peptidase activity cation binding transition metal ion binding zinc ion binding ion binding binding peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds omega peptidase activity threonine-type peptidase activity beta-aspartyl-peptidase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006680	Amidohydrolase-related	Domain
A, B	IPR011059	Metal-dependent hydrolase, composite domain superfamily	Homologous Superfamily
A, B	IPR032466	Metal-dependent hydrolase	Homologous Superfamily
A, B	IPR010229	Peptidase M38, beta-aspartyl dipeptidase	Family
A, B	IPR033826	Isoaspartyl-dipeptidase	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	isoaspartyl dipeptidase M-CSA #172	Isoaspartyl dipeptidase (IAD) from Escherichia coli is a member of the amidohydrolase superfamily. It catalyses the hydrolysis of dipeptides containing a peptide bond to the beta-carboxylate group of aspartic acid. The apparent physiological role of IAD is to prevent the accumulation of beta-aspartyl dipeptides after proteolysis of these proteins. IAD shows little activity towards the hydrolysis of tripeptides or gamma-glutamyl dipeptides.	Defined by 6 residues: HIS:A-68HIS:A-70LYS:A-162HIS:A-201HIS:A-230ASP:A-285 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.4.19 (PDB Primary Data) Search M-CSA Motif + EC 3.4.19

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.