2P50 | pdb_00002p50

Crystal structure of N-acetyl-D-Glucosamine-6-Phosphate deacetylase liganded with Zn

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)
D	d2p50d1	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)
D	d2p50d2	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)
C	d2p50c1	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)
C	d2p50c2	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)
B	d2p50b1	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	d2p50b2	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	d2p50a1	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	d2p50a2	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)
D	SCOP2B Superfamily	Metallo-dependent hydrolases	8035376	3000428	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8035374	3000176	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8035374	3000176	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metallo-dependent hydrolases	8035376	3000428	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8035374	3000176	SCOP2B (2022-06-29)
C	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)
B	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8035374	3000176	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8035374	3000176	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metallo-dependent hydrolases	8035376	3000428	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8035374	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)
D	NagA_N	e2p50D1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: NagA_N	ECOD (v294.1)
D	DUF711	e2p50D2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
C	NagA_N	e2p50C1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: NagA_N	ECOD (v294.1)
C	DUF711	e2p50C2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
B	NagA_N	e2p50B1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: NagA_N	ECOD (v294.1)
B	DUF711	e2p50B2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
A	NagA_N	e2p50A1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: NagA_N	ECOD (v294.1)
A	DUF711	e2p50A2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
D	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
C	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
C	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)
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, C, D	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, C, D	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 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 deacylase activity hydrolase activity 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 identical protein binding protein binding	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 process cellular component organization or biogenesis N-acetylglucosamine catabolic process carbohydrate derivative catabolic process 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 process cellular component organization or biogenesis N-acetylglucosamine catabolic process carbohydrate derivative catabolic process catabolic process amino sugar catabolic process amino sugar metabolic process carbohydrate derivative metabolic process metabolic process N-acetylglucosamine metabolic process glucosamine-containing compound catabolic process N-acetylneuraminate catabolic process oxoacid metabolic process carboxylic acid metabolic process organic acid catabolic process organic acid metabolic process carboxylic acid catabolic process small molecule metabolic process small molecule catabolic process N-acetylneuraminate metabolic process	protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR003764	N-acetylglucosamine-6-phosphate deacetylase	Family
A, B, C, D	IPR006680	Amidohydrolase-related	Domain
A, B, C, D	IPR011059	Metal-dependent hydrolase, composite domain superfamily	Homologous Superfamily
A, B, C, D	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.