2P53

Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetylase D273N mutant complexed with N-acetyl phosphonamidate-d-glucosamine-6-phosphate

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	d2p53b1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	N-acetylglucosamine-6-phosphate deacetylase, NagA	N-acetylglucosamine-6-phosphate deacetylase, NagA	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2p53b2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain	N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d2p53a1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	N-acetylglucosamine-6-phosphate deacetylase, NagA	N-acetylglucosamine-6-phosphate deacetylase, NagA	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d2p53a2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain	N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8035374	3000176	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8035374	3000176	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-dependent hydrolases	8035376	3000428	SCOP2B (2022-06-29)
A	SCOP2 Family	N-acetylglucosamine-6-phosphate deacetylase NagA	8022994	4002805	SCOP2 (2022-06-29)
A	SCOP2 Family	N-acetylglucosamine-6-phosphate deacetylase NagA catalytic domain	8022996	4002851	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Composite domain of metallo-dependent hydrolases	8035374	3000176	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Metallo-dependent hydrolases	8035376	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)
B	PF22643	e2p53B1	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: PF22643	ECOD (1.6)
B	PF01979	e2p53B2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF01979	ECOD (1.6)
A	PF22643	e2p53A1	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: PF22643	ECOD (1.6)
A	PF01979	e2p53A2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF01979	ECOD (1.6)

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)
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, 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	N-acetylglucosamine-6-phosphate deacetylase	deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides N-acetylglucosamine-6-phosphate deacetylase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds N-acetylgalactosamine-6-phosphate deacetylase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides N-acetylglucosamine-6-phosphate deacetylase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds N-acetylgalactosamine-6-phosphate deacetylase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process catabolic process oxoacid metabolic process carbohydrate derivative metabolic process organic acid catabolic process organic acid metabolic process cellular catabolic process carboxylic acid catabolic process amino sugar metabolic process small molecule metabolic process amide metabolic process carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process catabolic process oxoacid metabolic process carbohydrate derivative metabolic process organic acid catabolic process organic acid metabolic process cellular catabolic process carboxylic acid catabolic process amino sugar metabolic process small molecule metabolic process amide metabolic process N-acetylneuraminate metabolic process organonitrogen compound catabolic process N-acetylneuraminate catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process cellular metabolic process carboxylic acid metabolic process amino sugar catabolic process cellular process small molecule catabolic process organic substance catabolic process protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis N-acetylglucosamine metabolic process glucosamine-containing compound catabolic process N-acetylglucosamine catabolic process glucosamine-containing compound metabolic process	protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003764	N-acetylglucosamine-6-phosphate deacetylase	Family
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

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.