1VKN | pdb_00001vkn

Crystal structure of N-acetyl-gamma-glutamyl-phosphate reductase (TM1782) from Thermotoga maritima at 1.80 A resolution

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	d1vknd1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	N-acetyl-gamma-glutamyl-phosphate reductase ArgC	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
D	d1vknd2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	N-acetyl-gamma-glutamyl-phosphate reductase ArgC	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
C	d1vknc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	N-acetyl-gamma-glutamyl-phosphate reductase ArgC	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
C	d1vknc2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	N-acetyl-gamma-glutamyl-phosphate reductase ArgC	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1vknb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	N-acetyl-gamma-glutamyl-phosphate reductase ArgC	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1vknb2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	N-acetyl-gamma-glutamyl-phosphate reductase ArgC	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1vknb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1vkna1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	N-acetyl-gamma-glutamyl-phosphate reductase ArgC	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1vkna2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	GAPDH-like	N-acetyl-gamma-glutamyl-phosphate reductase ArgC	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1vkna3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	GAPDH-like	8056092	3000043	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GAPDH-like	8056092	3000043	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAPDH-like	8056092	3000043	SCOP2B (2022-06-29)
A	SCOP2 Family	Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like	8056091	4000077	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GAPDH-like	8056092	3000043	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)
D	YceM-like_C	e1vknD1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
D	FAD_binding_3	e1vknD2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
C	YceM-like_C	e1vknC1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
C	FAD_binding_3	e1vknC2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
B	YceM-like_C	e1vknB1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: YceM-like_C	ECOD (develop294)
B	FAD_binding_3	e1vknB2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
A	Semialdhyde_dhC	e1vknA1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: Semialdhyde_dhC	ECOD (develop294)
A	GFO_IDH_MocA	e1vknA2	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GFO_IDH_MocA	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01118	Semialdehyde dehydrogenase, NAD binding domain (Semialdhyde_dh)	Semialdehyde dehydrogenase, NAD binding domain	This Pfam entry contains the following members: N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) Aspartate-semialdehyde dehydrogenase	Domain
A, B, C, D	PF22698	Semialdehyde dehydrogenase, dimerisation domain (Semialdhyde_dhC_1)	Semialdehyde dehydrogenase, dimerisation domain	This entry represents the dimerisation domain found in N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) and related sequences not included in Pfam:PF02774 [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	N-acetyl-gamma-glutamyl-phosphate reductase	NADP+ binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding NADP binding small molecule binding NAD binding oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors NADP+ binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding NADP binding small molecule binding NAD binding oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors N-acetyl-gamma-glutamyl-phosphate reductase activity catalytic activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	L-arginine biosynthetic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process L-amino acid biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process arginine metabolic process proteinogenic amino acid metabolic process L-arginine biosynthetic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process L-amino acid biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process arginine metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process small molecule metabolic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR023013	N-acetyl-gamma-glutamyl-phosphate reductase, active site	Active Site
A, B, C, D	IPR058924	N-acetyl-gamma-glutamyl-phosphate reductase, dimerisation domain	Domain
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR050085	N-acetyl-gamma-glutamyl-phosphate reductase	Family
A, B, C, D	IPR000706	N-acetyl-gamma-glutamyl-phosphate reductase, type 1	Family
A, B, C, D	IPR000534	Semialdehyde dehydrogenase, NAD-binding	Domain

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.