1OFD
Glutamate Synthase from Synechocystis sp in complex with 2-Oxoglutarate at 2.0 Angstrom resolution
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
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 |
---|---|---|---|---|---|
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 ... | Domain | |
PF01493 | GXGXG motif (GXGXG) | GXGXG motif | - | Family | |
PF00310 | Glutamine amidotransferases class-II (GATase_2) | Glutamine amidotransferases class-II | - | Domain | |
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 ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR029055 | Nucleophile aminohydrolases, N-terminal | Homologous Superfamily | |
IPR013785 | Aldolase-type TIM barrel | Homologous Superfamily | |
IPR036485 | Glutamate synthase, alpha subunit, C-terminal domain superfamily | Homologous Superfamily | |
IPR006982 | Glutamate synthase, central-N | Domain | |
IPR002489 | Glutamate synthase, alpha subunit, C-terminal | Domain | |
IPR017932 | Glutamine amidotransferase type 2 domain | Domain | |
IPR002932 | Glutamate synthase domain | Domain | |
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 |
---|---|---|---|
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 | EC: 1.4.7.1 (PDB Primary Data) |