2VDC

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


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad2vdca1 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)
Ad2vdca2 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)
Ad2vdca3 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)
Bd2vdcb1 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)
Bd2vdcb2 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)
Bd2vdcb3 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)
Dd2vdcd1 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)
Dd2vdcd2 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)
Dd2vdcd3 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)
Fd2vdcf1 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)
Fd2vdcf2 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)
Fd2vdcf3 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)
Cd2vdcc1 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)
Cd2vdcc2 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)
Cd2vdcc3 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)
Ed2vdce1 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)
Ed2vdce2 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)
Ed2vdce3 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

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyClass II glutamine amidotransferases8056846 3000131 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyFMN-linked oxidoreductases8056848 3000014 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyGXGXG domain-like8056850 3000109 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyFMN-linked oxidoreductases8056848 3000014 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyGXGXG domain-like8056850 3000109 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyClass II glutamine amidotransferases8056846 3000131 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyClass II glutamine amidotransferases8056846 3000131 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyFMN-linked oxidoreductases8056848 3000014 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyGXGXG domain-like8056850 3000109 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyFMN-linked oxidoreductases8056848 3000014 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyGXGXG domain-like8056850 3000109 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyClass II glutamine amidotransferases8056846 3000131 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyClass II glutamine amidotransferases8056846 3000131 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyGXGXG domain-like8056850 3000109 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyFMN-linked oxidoreductases8056848 3000014 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyGXGXG domain-like8056850 3000109 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyFMN-linked oxidoreductases8056848 3000014 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyClass II glutamine amidotransferases8056846 3000131 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APF01493e2vdcA2 A: beta duplicates or obligate multimersX: Single-stranded right-handed beta-helixH: Alpha subunit of glutamate synthase-C (From Topology)T: Alpha subunit of glutamate synthase-CF: PF01493ECOD (1.6)
APF00310e2vdcA1 A: a+b two layersX: Alpha-beta plaitsH: Alpha subunit of glutamate synthase, insertion domain (From Topology)T: Alpha subunit of glutamate synthase, insertion domainF: PF00310ECOD (1.6)
APF00310e2vdcA3 A: a+b four layersX: Ntn/PP2CH: NtnT: Class II glutamine amidotransferasesF: PF00310ECOD (1.6)
APF01645e2vdcA4 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: PF01645ECOD (1.6)
APF04898e2vdcA5 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: PF04898ECOD (1.6)
BPF01493e2vdcB2 A: beta duplicates or obligate multimersX: Single-stranded right-handed beta-helixH: Alpha subunit of glutamate synthase-C (From Topology)T: Alpha subunit of glutamate synthase-CF: PF01493ECOD (1.6)
BPF00310e2vdcB1 A: a+b two layersX: Alpha-beta plaitsH: Alpha subunit of glutamate synthase, insertion domain (From Topology)T: Alpha subunit of glutamate synthase, insertion domainF: PF00310ECOD (1.6)
BPF00310e2vdcB3 A: a+b four layersX: Ntn/PP2CH: NtnT: Class II glutamine amidotransferasesF: PF00310ECOD (1.6)
BPF01645e2vdcB4 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: PF01645ECOD (1.6)
BPF04898e2vdcB5 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: PF04898ECOD (1.6)
DPF01493e2vdcD2 A: beta duplicates or obligate multimersX: Single-stranded right-handed beta-helixH: Alpha subunit of glutamate synthase-C (From Topology)T: Alpha subunit of glutamate synthase-CF: PF01493ECOD (1.6)
DPF00310e2vdcD1 A: a+b two layersX: Alpha-beta plaitsH: Alpha subunit of glutamate synthase, insertion domain (From Topology)T: Alpha subunit of glutamate synthase, insertion domainF: PF00310ECOD (1.6)
DPF00310e2vdcD3 A: a+b four layersX: Ntn/PP2CH: NtnT: Class II glutamine amidotransferasesF: PF00310ECOD (1.6)
DPF01645e2vdcD4 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: PF01645ECOD (1.6)
DPF04898e2vdcD5 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: PF04898ECOD (1.6)
FPF01493e2vdcF2 A: beta duplicates or obligate multimersX: Single-stranded right-handed beta-helixH: Alpha subunit of glutamate synthase-C (From Topology)T: Alpha subunit of glutamate synthase-CF: PF01493ECOD (1.6)
FPF00310e2vdcF1 A: a+b two layersX: Alpha-beta plaitsH: Alpha subunit of glutamate synthase, insertion domain (From Topology)T: Alpha subunit of glutamate synthase, insertion domainF: PF00310ECOD (1.6)
FPF00310e2vdcF3 A: a+b four layersX: Ntn/PP2CH: NtnT: Class II glutamine amidotransferasesF: PF00310ECOD (1.6)
FPF01645e2vdcF4 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: PF01645ECOD (1.6)
FPF04898e2vdcF5 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: PF04898ECOD (1.6)
CPF01493e2vdcC2 A: beta duplicates or obligate multimersX: Single-stranded right-handed beta-helixH: Alpha subunit of glutamate synthase-C (From Topology)T: Alpha subunit of glutamate synthase-CF: PF01493ECOD (1.6)
CPF00310e2vdcC1 A: a+b two layersX: Alpha-beta plaitsH: Alpha subunit of glutamate synthase, insertion domain (From Topology)T: Alpha subunit of glutamate synthase, insertion domainF: PF00310ECOD (1.6)
CPF00310e2vdcC3 A: a+b four layersX: Ntn/PP2CH: NtnT: Class II glutamine amidotransferasesF: PF00310ECOD (1.6)
CPF01645e2vdcC4 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: PF01645ECOD (1.6)
CPF04898e2vdcC5 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: PF04898ECOD (1.6)
EPF01493e2vdcE2 A: beta duplicates or obligate multimersX: Single-stranded right-handed beta-helixH: Alpha subunit of glutamate synthase-C (From Topology)T: Alpha subunit of glutamate synthase-CF: PF01493ECOD (1.6)
EPF00310e2vdcE1 A: a+b two layersX: Alpha-beta plaitsH: Alpha subunit of glutamate synthase, insertion domain (From Topology)T: Alpha subunit of glutamate synthase, insertion domainF: PF00310ECOD (1.6)
EPF00310e2vdcE3 A: a+b four layersX: Ntn/PP2CH: NtnT: Class II glutamine amidotransferasesF: PF00310ECOD (1.6)
EPF01645e2vdcE4 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: PF01645ECOD (1.6)
EPF04898e2vdcE5 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: PF04898ECOD (1.6)
HPF14691e2vdcH5 A: alpha arraysX: alpha-helical ferredoxin-likeH: alpha-helical ferredoxin (From Topology)T: alpha-helical ferredoxinF: PF14691ECOD (1.6)
HPF07992e2vdcH7 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: PF07992ECOD (1.6)
HPF13450e2vdcH6 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: PF13450ECOD (1.6)
IPF14691e2vdcI5 A: alpha arraysX: alpha-helical ferredoxin-likeH: alpha-helical ferredoxin (From Topology)T: alpha-helical ferredoxinF: PF14691ECOD (1.6)
IPF07992e2vdcI7 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: PF07992ECOD (1.6)
IPF13450e2vdcI6 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: PF13450ECOD (1.6)
LPF14691e2vdcL5 A: alpha arraysX: alpha-helical ferredoxin-likeH: alpha-helical ferredoxin (From Topology)T: alpha-helical ferredoxinF: PF14691ECOD (1.6)
LPF07992e2vdcL7 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: PF07992ECOD (1.6)
LPF13450e2vdcL6 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: PF13450ECOD (1.6)
GPF14691e2vdcG1 A: alpha arraysX: alpha-helical ferredoxin-likeH: alpha-helical ferredoxin (From Topology)T: alpha-helical ferredoxinF: PF14691ECOD (1.6)
GPF07992e2vdcG3 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: PF07992ECOD (1.6)
GPF13450e2vdcG2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: PF13450ECOD (1.6)
JPF14691e2vdcJ5 A: alpha arraysX: alpha-helical ferredoxin-likeH: alpha-helical ferredoxin (From Topology)T: alpha-helical ferredoxinF: PF14691ECOD (1.6)
JPF07992e2vdcJ7 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: PF07992ECOD (1.6)
JPF13450e2vdcJ6 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: PF13450ECOD (1.6)
KPF14691e2vdcK5 A: alpha arraysX: alpha-helical ferredoxin-likeH: alpha-helical ferredoxin (From Topology)T: alpha-helical ferredoxinF: PF14691ECOD (1.6)
KPF07992e2vdcK7 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: PF07992ECOD (1.6)
KPF13450e2vdcK6 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: FAD/NAD(P)-binding domainF: PF13450ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D, E
PF01645Conserved region in glutamate synthase (Glu_synthase)Conserved region in glutamate synthaseThis 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, C, D, E
PF01493GXGXG motif (GXGXG)GXGXG motif- Family
A, B, C, D, E
PF00310Glutamine amidotransferases class-II (GATase_2)Glutamine amidotransferases class-II- Domain
A, B, C, D, E
PF04898Glutamate synthase central domain (Glu_syn_central)Glutamate synthase central domainThe 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
G, H, I, J, K
PF07992Pyridine nucleotide-disulphide oxidoreductase (Pyr_redox_2)Pyridine nucleotide-disulphide oxidoreductaseThis family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.Domain
G, H, I, J, K
PF14691Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster (Fer4_20)Dihydroprymidine dehydrogenase domain II, 4Fe-4S clusterDomain II of the enzyme dihydroprymidine dehydrogenase binds FAD. Dihydroprymidine dehydrogenase catalyses the first and rate-limiting step of pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds [1]. This doma ...Domain II of the enzyme dihydroprymidine dehydrogenase binds FAD. Dihydroprymidine dehydrogenase catalyses the first and rate-limiting step of pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds [1]. This domain carries two Fe4-S4 clusters.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C, D, E
GLUTAMATE SYNTHASE [NADPH] LARGE CHAIN -
G, H, I, J, K
GLUTAMATE SYNTHASE [NADPH] SMALL CHAIN -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D, E
IPR029055Nucleophile aminohydrolases, N-terminalHomologous Superfamily
A, B, C, D, E
IPR036485Glutamate synthase, alpha subunit, C-terminal domain superfamilyHomologous Superfamily
A, B, C, D, E
IPR006982Glutamate synthase, central-NDomain
A, B, C, D, E
IPR002489Glutamate synthase, alpha subunit, C-terminalDomain
A, B, C, D, E
IPR013785Aldolase-type TIM barrelHomologous Superfamily
A, B, C, D, E
IPR017932Glutamine amidotransferase type 2 domainDomain
A, B, C, D, E
IPR002932Glutamate synthase domainDomain
G, H, I, J, K
IPR028261Dihydroprymidine dehydrogenase domain IIDomain
G, H, I, J, K
IPR006006Glutamate synthase NADPH small chain-likeFamily
G, H, I, J, K
IPR023753FAD/NAD(P)-binding domainDomain
G, H, I, J, K
IPR036188FAD/NAD(P)-binding domain superfamilyHomologous Superfamily
G, H, I, J, K
IPR009051Alpha-helical ferredoxinHomologous Superfamily