2VHL

The Three-dimensional structure of the N-Acetylglucosamine-6- phosphate deacetylase from Bacillus subtilis

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	d2vhla1	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	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d2vhla2	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	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d2vhlb1	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	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d2vhlb2	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	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	N-acetylglucosamine-6-phosphate deacetylase, NagA	8029542	4002805	SCOP2 (2022-06-29)
A	SCOP2 Family	N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain	8029544	4002851	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Composite domain of metallo-dependent hydrolases	8041921	3000176	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Metallo-dependent hydrolases	8041923	3000428	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8041921	3000176	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-dependent hydrolases	8041923	3000428	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	nagA_1	e2vhlA2	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: nagA_1	ECOD (1.6)
A	Amidohydro_1_N	e2vhlA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Amidohydro_1_N	ECOD (1.6)
B	nagA_1	e2vhlB1	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: nagA_1	ECOD (1.6)
B	Amidohydro_1_N	e2vhlB2	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)
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
A, B	PF22644	BsNagA composite domain (BsNagA_N)	BsNagA composite domain	This entry represents the composite domain of NagA from Bacillus subtilis [1], a N-acetylglucosamine-6-phosphate deacetylase, similar to that from E.coli. However, they have some sequence differences [1].	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 deacylase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding protein binding binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides N-acetylglucosamine-6-phosphate deacetylase activity deacylase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding protein binding binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	carbohydrate derivative catabolic process catabolic process carbohydrate derivative metabolic process N-acetylglucosamine metabolic process glucosamine-containing compound catabolic process N-acetylglucosamine catabolic process amino sugar catabolic process amino sugar metabolic process metabolic process cellular process glucosamine-containing compound metabolic process N-acetylneuraminate catabolic process oxoacid metabolic process carboxylic acid metabolic process carbohydrate derivative catabolic process catabolic process carbohydrate derivative metabolic process N-acetylglucosamine metabolic process glucosamine-containing compound catabolic process N-acetylglucosamine catabolic process amino sugar catabolic process amino sugar metabolic process metabolic process cellular process glucosamine-containing compound metabolic process N-acetylneuraminate catabolic process oxoacid metabolic process carboxylic acid metabolic process organic acid catabolic process organic acid metabolic process cellular catabolic process carboxylic acid catabolic process small molecule metabolic process amide metabolic process small molecule catabolic process N-acetylneuraminate metabolic process	-

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 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.