1OFD

Glutamate Synthase from Synechocystis sp in complex with 2-Oxoglutarate at 2.0 Angstrom 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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ofda1	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	(Synechocystis sp. PCC 6803 ) [TaxId: 1148 ],	SCOPe (2.08)
A	d1ofda2	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	(Synechocystis sp. PCC 6803 ) [TaxId: 1148 ],	SCOPe (2.08)
A	d1ofda3	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	(Synechocystis sp. PCC 6803 ) [TaxId: 1148 ],	SCOPe (2.08)
B	d1ofdb1	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	(Synechocystis sp. PCC 6803 ) [TaxId: 1148 ],	SCOPe (2.08)
B	d1ofdb2	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	(Synechocystis sp. PCC 6803 ) [TaxId: 1148 ],	SCOPe (2.08)
B	d1ofdb3	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	(Synechocystis sp. PCC 6803 ) [TaxId: 1148 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	GltS central region-like	8003242	4003980	SCOP2 (2022-06-29)
A	SCOP2 Family	GXGXG-motif containing domain	8003318	4000235	SCOP2 (2022-06-29)
A	SCOP2 Family	Alpha subunit of glutamate synthase, GAT domain-like	8003377	4000340	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FMN-linked oxidoreductases	8003316	3000014	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GXGXG domain-like	8003319	3000109	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Class II glutamine amidotransferases	8003378	3000131	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Class II glutamine amidotransferases	8003378	3000131	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GXGXG domain-like	8003319	3000109	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FMN-linked oxidoreductases	8003316	3000014	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	GXGXG	e1ofdA2	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Alpha subunit of glutamate synthase-C (From Topology)	T: Alpha subunit of glutamate synthase-C	F: GXGXG	ECOD (1.6)
A	GATase_2_2nd	e1ofdA1	A: a+b two layers	X: Alpha-beta plaits	H: Alpha subunit of glutamate synthase, insertion domain (From Topology)	T: Alpha subunit of glutamate synthase, insertion domain	F: GATase_2_2nd	ECOD (1.6)
A	GATase_2_1st	e1ofdA3	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Class II glutamine amidotransferases	F: GATase_2_1st	ECOD (1.6)
A	Glu_synthase	e1ofdA5	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glu_synthase	ECOD (1.6)
A	Glu_syn_central	e1ofdA4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glu_syn_central	ECOD (1.6)
B	GXGXG	e1ofdB2	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Alpha subunit of glutamate synthase-C (From Topology)	T: Alpha subunit of glutamate synthase-C	F: GXGXG	ECOD (1.6)
B	GATase_2_2nd	e1ofdB1	A: a+b two layers	X: Alpha-beta plaits	H: Alpha subunit of glutamate synthase, insertion domain (From Topology)	T: Alpha subunit of glutamate synthase, insertion domain	F: GATase_2_2nd	ECOD (1.6)
B	GATase_2_1st	e1ofdB3	A: a+b four layers	X: Ntn/PP2C	H: Ntn	T: Class II glutamine amidotransferases	F: GATase_2_1st	ECOD (1.6)
B	Glu_synthase	e1ofdB4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glu_synthase	ECOD (1.6)
B	Glu_syn_central	e1ofdB5	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Glu_syn_central	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	2.160.20.60	Mainly Beta	3 Solenoid	Pectate Lyase C-like	Glutamate synthase, alpha subunit, C-terminal domain	CATH (4.3.0)
B	3.60.20.10	Alpha Beta	4-Layer Sandwich	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1	Aminohydrolase, N-terminal nucleophile (Ntn) domain	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	2.160.20.60	Mainly Beta	3 Solenoid	Pectate Lyase C-like	Glutamate synthase, alpha subunit, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01645	Conserved region in glutamate synthase (Glu_synthase)	Conserved region in glutamate synthase	This family represents a region of the glutamate synthase protein. This region is expressed as a separate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organisms. The aligned regi ...	This family represents a region of the glutamate synthase protein. This region is expressed as a separate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organisms. The aligned region of these proteins contains a putative FMN binding site and Fe-S cluster.	Domain
A, B	PF01493	GXGXG motif (GXGXG)	GXGXG motif	-	Family
A, B	PF00310	Glutamine amidotransferases class-II (GATase_2)	Glutamine amidotransferases class-II	-	Domain
A, B	PF04898	Glutamate synthase central domain (Glu_syn_central)	Glutamate synthase central domain	The central domain of glutamate synthase connects the amino terminal amidotransferase domain with the FMN-binding domain and has an alpha / beta overall topology [1]. This domain appears to be a rudimentary form of the FMN-binding TIM barrel accordi ...	The central domain of glutamate synthase connects the amino terminal amidotransferase domain with the FMN-binding domain and has an alpha / beta overall topology [1]. This domain appears to be a rudimentary form of the FMN-binding TIM barrel according to SCOP.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	FERREDOXIN-DEPENDENT GLUTAMATE SYNTHASE 2	oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity, acting on the CH-NH2 group of donors, iron-sulfur protein as acceptor oxidoreductase activity catalytic activity glutamate synthase (ferredoxin) activity glutamate synthase activity iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding glutamate synthase (NADH) activity cation binding ion binding oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity, acting on the CH-NH2 group of donors, iron-sulfur protein as acceptor oxidoreductase activity catalytic activity glutamate synthase (ferredoxin) activity glutamate synthase activity iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding glutamate synthase (NADH) activity cation binding ion binding metal ion binding	response to nutrient levels response to stimulus oxoacid metabolic process homeostatic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process glutamate metabolic process intracellular nitrogen homeostasis intracellular chemical homeostasis small molecule metabolic process glutamine metabolic process dicarboxylic acid metabolic process response to nutrient levels response to stimulus oxoacid metabolic process homeostatic process amino acid metabolic process organic acid metabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process glutamate metabolic process intracellular nitrogen homeostasis intracellular chemical homeostasis small molecule metabolic process glutamine metabolic process dicarboxylic acid metabolic process nitrogen utilization carboxylic acid metabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process cellular homeostasis chemical homeostasis ammonia assimilation cycle metabolic process cellular process glutamine family amino acid biosynthetic process organic acid biosynthetic process L-glutamate biosynthetic process carboxylic acid biosynthetic process dicarboxylic acid biosynthetic process small molecule biosynthetic process L-amino acid biosynthetic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process glutamate biosynthetic process alpha-amino acid biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029055	Nucleophile aminohydrolases, N-terminal	Homologous Superfamily
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B	IPR036485	Glutamate synthase, alpha subunit, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR006982	Glutamate synthase, central-N	Domain
A, B	IPR002489	Glutamate synthase, alpha subunit, C-terminal	Domain
A, B	IPR017932	Glutamine amidotransferase type 2 domain	Domain
A, B	IPR002932	Glutamate synthase domain	Domain
A, B	IPR050711	Electron transfer and nitrogen metabolism enzyme	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	glutamate synthase (ferredoxin) M-CSA #111	Binds a [3Fe-4S] cluster as well as FAD and FMN. The protein is composed of two domains, one hydrolysing L-glutamine to ammonia and L-glutamate (cf. EC 3.5.1.2, glutaminase), the other combines the produced ammonia with 2-oxoglutarate to produce a second molecule of L-glutamate. The ammonia is channelled through a tunnel in the active protein. This tunnel provides a micro-environment that prevents the protonation of the ammonia, crucial as the enzyme will not function with ammonium as the nitrogen source. The hydrolysis reaction only occurs when ferredoxin and 2-oxoglutarate are bound to the protein.	Defined by 9 residues: CYS:A-1ARG:A-31PHE:A-207ASN:A-227GLY:A-228GLU:A-903GLN:A-969LYS:A-972GLN:A-978 \| Explore in 3D: M-CSA Motif Definition Extent of motif is too large to support Structure Motif searching. EC: 1.4.7.1 (PDB Primary Data)

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.