2VDC | pdb_00002vdc

THE 9.5 A RESOLUTION STRUCTURE OF GLUTAMATE SYNTHASE FROM CRYO-ELECTRON MICROSCOPY AND ITS OLIGOMERIZATION BEHAVIOR IN SOLUTION: FUNCTIONAL IMPLICATIONS.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d2vdca1	All beta proteins	Single-stranded right-handed beta-helix	Alpha subunit of glutamate synthase, C-terminal domain	Alpha subunit of glutamate synthase, C-terminal domain	Alpha subunit of glutamate synthase, C-terminal domain	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
A	d2vdca2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Alpha subunit of glutamate synthase, central and FMN domains	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
A	d2vdca3	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Class II glutamine amidotransferases	Alpha subunit of glutamate synthase, N-terminal domain	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
C	d2vdcc1	All beta proteins	Single-stranded right-handed beta-helix	Alpha subunit of glutamate synthase, C-terminal domain	Alpha subunit of glutamate synthase, C-terminal domain	Alpha subunit of glutamate synthase, C-terminal domain	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
C	d2vdcc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Alpha subunit of glutamate synthase, central and FMN domains	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
C	d2vdcc3	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Class II glutamine amidotransferases	Alpha subunit of glutamate synthase, N-terminal domain	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
D	d2vdcd1	All beta proteins	Single-stranded right-handed beta-helix	Alpha subunit of glutamate synthase, C-terminal domain	Alpha subunit of glutamate synthase, C-terminal domain	Alpha subunit of glutamate synthase, C-terminal domain	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
D	d2vdcd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Alpha subunit of glutamate synthase, central and FMN domains	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
D	d2vdcd3	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Class II glutamine amidotransferases	Alpha subunit of glutamate synthase, N-terminal domain	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
E	d2vdce1	All beta proteins	Single-stranded right-handed beta-helix	Alpha subunit of glutamate synthase, C-terminal domain	Alpha subunit of glutamate synthase, C-terminal domain	Alpha subunit of glutamate synthase, C-terminal domain	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
E	d2vdce2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Alpha subunit of glutamate synthase, central and FMN domains	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
E	d2vdce3	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Class II glutamine amidotransferases	Alpha subunit of glutamate synthase, N-terminal domain	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
F	d2vdcf1	All beta proteins	Single-stranded right-handed beta-helix	Alpha subunit of glutamate synthase, C-terminal domain	Alpha subunit of glutamate synthase, C-terminal domain	Alpha subunit of glutamate synthase, C-terminal domain	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
F	d2vdcf2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Alpha subunit of glutamate synthase, central and FMN domains	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
F	d2vdcf3	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Class II glutamine amidotransferases	Alpha subunit of glutamate synthase, N-terminal domain	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
B	d2vdcb1	All beta proteins	Single-stranded right-handed beta-helix	Alpha subunit of glutamate synthase, C-terminal domain	Alpha subunit of glutamate synthase, C-terminal domain	Alpha subunit of glutamate synthase, C-terminal domain	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
B	d2vdcb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Alpha subunit of glutamate synthase, central and FMN domains	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)
B	d2vdcb3	Alpha and beta proteins (a+b)	Ntn hydrolase-like	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Class II glutamine amidotransferases	Alpha subunit of glutamate synthase, N-terminal domain	(Azospirillum brasilense ) [TaxId: 192 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Class II glutamine amidotransferases	8056846	3000131	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FMN-linked oxidoreductases	8056848	3000014	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GXGXG domain-like	8056850	3000109	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class II glutamine amidotransferases	8056846	3000131	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GXGXG domain-like	8056850	3000109	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	FMN-linked oxidoreductases	8056848	3000014	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Class II glutamine amidotransferases	8056846	3000131	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	FMN-linked oxidoreductases	8056848	3000014	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GXGXG domain-like	8056850	3000109	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	GXGXG domain-like	8056850	3000109	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Class II glutamine amidotransferases	8056846	3000131	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	FMN-linked oxidoreductases	8056848	3000014	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	FMN-linked oxidoreductases	8056848	3000014	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	GXGXG domain-like	8056850	3000109	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Class II glutamine amidotransferases	8056846	3000131	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FMN-linked oxidoreductases	8056848	3000014	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GXGXG domain-like	8056850	3000109	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II glutamine amidotransferases	8056846	3000131	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)
G		e2vdcG1	A: alpha bundles	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F:	ECOD (develop294)
H	Peptidase_M49	e2vdcH5	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
I	Peptidase_M49	e2vdcI5	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
K	Peptidase_M49	e2vdcK5	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
L	Peptidase_M49	e2vdcL5	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
J	Peptidase_M49	e2vdcJ5	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (develop294)
A	GATase_2	e2vdcA1	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: GATase_2	ECOD (develop294)
A	Hexapep,Acetyltransf_11	e2vdcA2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Hexapep,Acetyltransf_11	ECOD (develop294)
A	GATase_2	e2vdcA3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: GATase_2	ECOD (develop294)
A	YkuD	e2vdcA4	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)
C	GATase_2	e2vdcC1	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: GATase_2	ECOD (develop294)
C	Hexapep,Acetyltransf_11	e2vdcC2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Hexapep,Acetyltransf_11	ECOD (develop294)
C	GATase_2	e2vdcC3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: GATase_2	ECOD (develop294)
C	YkuD	e2vdcC4	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)
D	GATase_2	e2vdcD1	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: GATase_2	ECOD (develop294)
D	Hexapep,Acetyltransf_11	e2vdcD2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Hexapep,Acetyltransf_11	ECOD (develop294)
D	GATase_2	e2vdcD3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: GATase_2	ECOD (develop294)
D	YkuD	e2vdcD4	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)
E	GATase_2	e2vdcE1	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: GATase_2	ECOD (develop294)
E	Hexapep,Acetyltransf_11	e2vdcE2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Hexapep,Acetyltransf_11	ECOD (develop294)
E	GATase_2	e2vdcE3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: GATase_2	ECOD (develop294)
E	YkuD	e2vdcE4	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)
F	GATase_2	e2vdcF1	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: GATase_2	ECOD (develop294)
F	Hexapep,Acetyltransf_11	e2vdcF2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Hexapep,Acetyltransf_11	ECOD (develop294)
F	GATase_2	e2vdcF3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: GATase_2	ECOD (develop294)
F	YkuD	e2vdcF4	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)
B	GATase_2	e2vdcB1	A: alpha bundles	X: EGF-like	H: General secretion pathway protein M (EpsM) periplasmic domain-related	T: General secretion pathway protein M (EpsM) periplasmic domain-related	F: GATase_2	ECOD (develop294)
B	Hexapep,Acetyltransf_11	e2vdcB2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Hexapep,Acetyltransf_11	ECOD (develop294)
B	GATase_2	e2vdcB3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: GATase_2	ECOD (develop294)
B	YkuD	e2vdcB4	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: YkuD	ECOD (develop294)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, I, J, K G, H, I, J, K, L	GLUTAMATE SYNTHASE [NADPH] SMALL CHAIN	iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity glutamate synthase (NADPH) activity catalytic activity glutamate synthase activity cation binding ion binding metal ion binding	oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process L-glutamate biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process carboxylic acid biosynthetic process glutamate metabolic process small molecule metabolic process dicarboxylic acid biosynthetic process small molecule biosynthetic process dicarboxylic acid metabolic process carboxylic acid metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process L-glutamate biosynthetic process alpha-amino acid metabolic process L-glutamine family amino acid biosynthetic process carboxylic acid biosynthetic process glutamate metabolic process small molecule metabolic process dicarboxylic acid biosynthetic process small molecule biosynthetic process dicarboxylic acid metabolic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process	-
A, B, C, D, E A, B, C, D, E, F	GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN	oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity glutamate synthase (NADPH) activity catalytic activity glutamate synthase activity iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	glutamine metabolic process response to nutrient levels response to stimulus oxoacid metabolic process homeostatic process dicarboxylic acid metabolic process nitrogen utilization carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process cellular homeostasis chemical homeostasis glutamate metabolic process glutamine metabolic process response to nutrient levels response to stimulus oxoacid metabolic process homeostatic process dicarboxylic acid metabolic process nitrogen utilization carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process cellular homeostasis chemical homeostasis glutamate metabolic process intracellular nitrogen homeostasis ammonia assimilation cycle intracellular chemical homeostasis small molecule metabolic process metabolic process cellular process organic acid biosynthetic process L-glutamate biosynthetic process L-glutamine family amino acid biosynthetic process carboxylic acid biosynthetic process dicarboxylic acid biosynthetic process small molecule biosynthetic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G, H, I, J, K G, H, I, J, K, L	IPR028261	Dihydroprymidine dehydrogenase domain II	Domain
G, H, I, J, K G, H, I, J, K, L	IPR006006	Glutamate synthase NADPH small chain-like	Family
G, H, I, J, K G, H, I, J, K, L	IPR023753	FAD/NAD(P)-binding domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR029055	Nucleophile aminohydrolases, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR036485	Glutamate synthase, alpha subunit, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006982	Glutamate synthase, central-N	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002489	Glutamate synthase, alpha subunit, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR017932	Glutamine amidotransferase type 2 domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002932	Glutamate synthase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050711	Electron transfer and nitrogen metabolism enzyme	Family