Bacterial NADPH-dependent GS–GOGAT ammonia assimilation

Glutamine synthetase and a two-chain NADPH-dependent glutamate synthase couple ammonium incorporation to net L-glutamate synthesis. GS uses ATP to amidate L-glutamate; GOGAT transfers the glutamine amide nitrogen to 2-oxoglutarate using NADPH, yielding two glutamates. One glutamate replenishes the GS substrate pool, giving one net glutamate per turn. This chemistry occurs in Pseudomonas putida, Escherichia coli, Bacillus subtilis and Azospirillum brasilense, with differences in enzyme families, regulation, assembly and physiological dependence.

MODULE:bacterial_ammonia_assimilationCOMPLETECONCRETEMetabolic Pathwaymodules/bacterial_ammonia_assimilation.yaml
ammonia assimilation cycleGO:0019676
PMID:24158439
Primary GS substrate structures ground the first reaction.
The glutamate substrate peptide carboxyl and amide groups interact with Arg 298 and His 245 , whereas its side chain carboxyl interacts with a Mg 2+ ion.
PMID:10785395
Primary GOGAT biochemistry grounds the second reaction.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:34931064
Native Bacillus structure independently corroborates complementary subunit chemistry.
The higher resolution did permit unambiguous assignment of two 4Fe-4S clusters in GltB, and a 3Fe-4S clusters and FMN in GltA.
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The review supplies an explicit cyclic synthesis and network-boundary interpretation.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.

Direct GDH assimilation is an alternative in E. coli and some other bacteria, not a third required step or a universal property of every GDH. Native B. subtilis RocG/GudB physiology is primarily catabolic under the studied conditions, while C. glutamicum GOGAT is dispensable in tested regimes. High-affinity language and numeric kinetic values are not generalized from conserved chemistry. Ferredoxin- and NADH-linked GOGAT, transport, nitrogen fixation/reduction, PII/Ntr signaling, GlnA adenylylation and GlnR/TnrA regulation are outside the minimal catalytic requirement; their actual gene functions remain in the member reviews. The broader nitrogen_cycle module is a coarse neighboring view. No ancestral PTN is asserted: the old broad nodes are unnecessary for exact-product requirements and do not establish NADPH specificity or universal localization. Family reviews exist for every family the members use: PTHR43407 (GlnA-alpha), PTHR43785 (GlnA-beta and gamma-glutamyl-amine ligases), PTHR11938 (GOGAT catalytic chain plus adrenodoxin reductase), PTHR42783 (GltD-type small chains) and PTHR43100 (Gram-positive small chain and eukaryotic NADH-GOGAT). PTHR43785:SF12 is kept on B. subtilis GlnA as a verified membership record even though its family review leaves glutamine synthetase activity UNRESOLVED: SF12 mixes ammonium-using glutamine synthetases with PuuA, GlnA3, GlnA4, Gms and IpuC, so the activity rests on the protein's own biochemistry, not on the family, and the FAMILY_FUNCTION_UNREVIEWED warning reflects that. The large-chain glutaminase assertions record the subunit-level glutamine-hydrolysing partial reaction; NADPH specificity is carried only by the assembled complex.

13Nodes
8Parts
1Variant Sets
4Variants
8Annotons
8Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • bacterial_ammonia_assimilation-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

12 gene-function check(s) reflected in core functions · 0 conflict(s) · 1 evidence or coverage gap(s) (28 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
psepk_gs_activity glnA
UniProtKB:Q88CY3
Gene 		glutamine synthetase activity
GO:0004356 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
psepk_gogat_activity PROTEIN_COMPLEX
Gene 		glutamate synthase (NADPH) activity
GO:0004355 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
psepk_gogat_activity/psepk_large_unit gltB
UniProtKB:Q88CV4
Complex Unit 		glutaminase activity
GO:0004359 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
psepk_gogat_activity/psepk_small_unit gltD
UniProtKB:Q88CV5
Complex Unit 		oxidoreductase activity, acting on NAD(P)H
GO:0016651 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ecoli_gs_activity glnA
UniProtKB:P0A9C5
Gene 		glutamine synthetase activity
GO:0004356 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ecoli_gogat_activity PROTEIN_COMPLEX
Gene 		glutamate synthase (NADPH) activity
GO:0004355 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
ecoli_gogat_activity/ecoli_large_unit gltB
UniProtKB:P09831
Complex Unit 		glutaminase activity
GO:0004359 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ecoli_gogat_activity/ecoli_small_unit gltD
UniProtKB:P09832
Complex Unit 		oxidoreductase activity, acting on NAD(P)H
GO:0016651 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
bacsu_gs_activity glnA
UniProtKB:P12425
Gene 		glutamine synthetase activity
GO:0004356 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
bacsu_gogat_activity PROTEIN_COMPLEX
Gene 		glutamate synthase (NADPH) activity
GO:0004355 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
bacsu_gogat_activity/bacsu_large_unit gltA
UniProtKB:P39812
Complex Unit 		glutaminase activity
GO:0004359 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
bacsu_gogat_activity/bacsu_small_unit gltB
UniProtKB:O34399
Complex Unit 		oxidoreductase activity, acting on NAD(P)H
GO:0016651 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
azobr_gs_activity glnA
UniProtKB:P10583
Gene 		glutamine synthetase activity
GO:0004356 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
azobr_gogat_activity PROTEIN_COMPLEX
Gene 		glutamate synthase (NADPH) activity
GO:0004355 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
azobr_gogat_activity/azobr_large_unit gltB
UniProtKB:Q05755
Complex Unit 		glutaminase activity
GO:0004359 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
azobr_gogat_activity/azobr_small_unit gltD
UniProtKB:Q05756
Complex Unit 		oxidoreductase activity, acting on NAD(P)H
GO:0016651 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
psepk_gs_activity glnA exact-product family classification
PANTHER:PTHR43407:SF2
Family 		glutamine synthetase activity
GO:0004356 		Family Supported
Family review supports GO:0004356 FAMILY_WIDE. Shared by all bacterial and archaeal members of both subfamilies; vertebrate lengsin is the recorded exception.
psepk_large_unit gltB exact-product family classification
PANTHER:PTHR11938:SF148
Family 		glutaminase activity
GO:0004359 		Family Supported
Family review supports GO:0004359 for PANTHER:PTHR11938:SF148. The N-terminal Ntn-type amidotransferase domain that hydrolyses glutamine to release ammonia into the tunnel is a feature of every GOGAT catalytic chain and is missing from the SF91 adrenodoxin reductases. This is the partial activity the module assigns to the large chain. The applicable subfamilies are the same GOGAT-named set as for glutamate synthase activity, with the uncharacterized SF134 and SF145 left out for the same reason. GOGAT gates this site so that glutamine is not hydrolysed without an acceptor, and GOA carries the term on no GOGAT large chain; the scope records the domain's partial reaction, not an uncoupled glutaminase.
psepk_small_unit gltD exact-product family classification
PANTHER:PTHR42783:SF3
Family 		oxidoreductase activity, acting on NAD(P)H
GO:0016651 		Family Supported
Family review supports GO:0016651 for PANTHER:PTHR42783:SF3. Rule shared with PTHR43100: the scope covers only subfamilies with a characterized NAD(P)H-oxidising member. SF3 qualifies, because GltD, SfrB (NADPH-Fe(3+) oxidoreductase) and FdhB (NADP(+)-dependent formate dehydrogenase) are recorded as NADPH-linked. SF1 (AegA) keeps the FAD/NAD(P)-binding domain but has no donor assay in the cached sources, so it is left out. The scope rests on the domain and the characterized members, not on the root IBD, which is taxon-restricted to Bacteria and does not reach archaeal SudA. This is the activity the module assigns to the GltD small chains.
ecoli_gs_activity glnA exact-product family classification
PANTHER:PTHR43407:SF2
Family 		glutamine synthetase activity
GO:0004356 		Family Supported
Family review supports GO:0004356 FAMILY_WIDE. Shared by all bacterial and archaeal members of both subfamilies; vertebrate lengsin is the recorded exception.
ecoli_large_unit gltB exact-product family classification
PANTHER:PTHR11938:SF148
Family 		glutaminase activity
GO:0004359 		Family Supported
Family review supports GO:0004359 for PANTHER:PTHR11938:SF148. The N-terminal Ntn-type amidotransferase domain that hydrolyses glutamine to release ammonia into the tunnel is a feature of every GOGAT catalytic chain and is missing from the SF91 adrenodoxin reductases. This is the partial activity the module assigns to the large chain. The applicable subfamilies are the same GOGAT-named set as for glutamate synthase activity, with the uncharacterized SF134 and SF145 left out for the same reason. GOGAT gates this site so that glutamine is not hydrolysed without an acceptor, and GOA carries the term on no GOGAT large chain; the scope records the domain's partial reaction, not an uncoupled glutaminase.
ecoli_small_unit gltD exact-product family classification
PANTHER:PTHR42783:SF3
Family 		oxidoreductase activity, acting on NAD(P)H
GO:0016651 		Family Supported
Family review supports GO:0016651 for PANTHER:PTHR42783:SF3. Rule shared with PTHR43100: the scope covers only subfamilies with a characterized NAD(P)H-oxidising member. SF3 qualifies, because GltD, SfrB (NADPH-Fe(3+) oxidoreductase) and FdhB (NADP(+)-dependent formate dehydrogenase) are recorded as NADPH-linked. SF1 (AegA) keeps the FAD/NAD(P)-binding domain but has no donor assay in the cached sources, so it is left out. The scope rests on the domain and the characterized members, not on the root IBD, which is taxon-restricted to Bacteria and does not reach archaeal SudA. This is the activity the module assigns to the GltD small chains.
bacsu_gs_activity glnA exact-product family classification
PANTHER:PTHR43785:SF12
Family 		glutamine synthetase activity
GO:0004356 		Family Function Unreviewed
Family review leaves GO:0004356 UNRESOLVED. Glutamine synthetase activity is a member-level property in this family. The ammonium-using GlnA enzymes and the gamma-glutamyl-amine ligases (PuuA, GlnA3, GlnA4, Gms, IpuC) are mixed within SF12, and no curated residue site separating them has been established here. Family or SF12 membership is therefore not evidence of GS activity; B. subtilis GlnA has it from its own biochemistry.
bacsu_large_unit gltA exact-product family classification
PANTHER:PTHR11938:SF133
Family 		glutaminase activity
GO:0004359 		Family Supported
Family review supports GO:0004359 for PANTHER:PTHR11938:SF133. The N-terminal Ntn-type amidotransferase domain that hydrolyses glutamine to release ammonia into the tunnel is a feature of every GOGAT catalytic chain and is missing from the SF91 adrenodoxin reductases. This is the partial activity the module assigns to the large chain. The applicable subfamilies are the same GOGAT-named set as for glutamate synthase activity, with the uncharacterized SF134 and SF145 left out for the same reason. GOGAT gates this site so that glutamine is not hydrolysed without an acceptor, and GOA carries the term on no GOGAT large chain; the scope records the domain's partial reaction, not an uncoupled glutaminase.
bacsu_small_unit gltB exact-product family classification
PANTHER:PTHR43100:SF1
Family 		oxidoreductase activity, acting on NAD(P)H
GO:0016651 		Family Supported
Family review supports GO:0016651 for PANTHER:PTHR43100:SF1. Rule shared with PTHR42783: the scope covers only subfamilies with a characterized NAD(P)H-oxidising member. The FAD/NAD(P)-binding module that oxidises NADPH (bacterial small chains) or NADH (eukaryotic single-chain GOGATs) defines SF1, the subfamily holding every characterized member. SF2 and SF3 keep the domain but have no characterized member, so they are left out. This is the partial activity the module assigns to B. subtilis GltB.
azobr_gs_activity glnA exact-product family classification
PANTHER:PTHR43407:SF2
Family 		glutamine synthetase activity
GO:0004356 		Family Supported
Family review supports GO:0004356 FAMILY_WIDE. Shared by all bacterial and archaeal members of both subfamilies; vertebrate lengsin is the recorded exception.
azobr_large_unit gltB exact-product family classification
PANTHER:PTHR11938:SF133
Family 		glutaminase activity
GO:0004359 		Family Supported
Family review supports GO:0004359 for PANTHER:PTHR11938:SF133. The N-terminal Ntn-type amidotransferase domain that hydrolyses glutamine to release ammonia into the tunnel is a feature of every GOGAT catalytic chain and is missing from the SF91 adrenodoxin reductases. This is the partial activity the module assigns to the large chain. The applicable subfamilies are the same GOGAT-named set as for glutamate synthase activity, with the uncharacterized SF134 and SF145 left out for the same reason. GOGAT gates this site so that glutamine is not hydrolysed without an acceptor, and GOA carries the term on no GOGAT large chain; the scope records the domain's partial reaction, not an uncoupled glutaminase.
azobr_small_unit gltD exact-product family classification
PANTHER:PTHR42783:SF3
Family 		oxidoreductase activity, acting on NAD(P)H
GO:0016651 		Family Supported
Family review supports GO:0016651 for PANTHER:PTHR42783:SF3. Rule shared with PTHR43100: the scope covers only subfamilies with a characterized NAD(P)H-oxidising member. SF3 qualifies, because GltD, SfrB (NADPH-Fe(3+) oxidoreductase) and FdhB (NADP(+)-dependent formate dehydrogenase) are recorded as NADPH-linked. SF1 (AegA) keeps the FAD/NAD(P)-binding domain but has no donor assay in the cached sources, so it is left out. The scope rests on the domain and the characterized members, not on the root IBD, which is taxon-restricted to Bacteria and does not reach archaeal SudA. This is the activity the module assigns to the GltD small chains.

Gene-review completeness (12/12 grounded genes reviewed)

12 complete review(s) · 3 with deep research · 0 missing review · 9 reviewed but lacking deep research

Gene Review Complete Deep research
glnA P0A9C5 ✓ ✓ ✗
glnA P10583 ✓ ✓ ✗
glnA P12425 ✓ ✓ ✗
glnA Q88CY3 ✓ ✓ ✓
gltA P39812 ✓ ✓ ✗
gltB O34399 ✓ ✓ ✗
gltB P09831 ✓ ✓ ✗
gltB Q05755 ✓ ✓ ✗
gltB Q88CV4 ✓ ✓ ✓
gltD P09832 ✓ ✓ ✗
gltD Q05756 ✓ ✓ ✗
gltD Q88CV5 ✓ ✓ ✓

Details

Context
BacteriaNCBITaxon:2

The reviewed implementations are Pseudomonas putida KT2440, Escherichia coli K-12, Bacillus subtilis 168 and sequence-defined Azospirillum brasilense products. Bacterial taxon context does not assert presence in every bacterium.

Bacterial NADPH-dependent GS–GOGAT ammonia assimilationMetabolic Pathwaybacterial_ammonia_assimilation
ammonia assimilation cycleGO:0019676
Context
BacteriaNCBITaxon:2

The reviewed implementations are Pseudomonas putida KT2440, Escherichia coli K-12, Bacillus subtilis 168 and sequence-defined Azospirillum brasilense products. Bacterial taxon context does not assert presence in every bacterium.

The activity compiler treats an assembled complex as one atom and does not itself evaluate subunit assembly or cellular context. The accompanying requirement-aware oracle recursively checks the active units and exact products; 4096 subsets test all 12 panel proteins. Presence denotes capacity only, not measurable flux or growth sufficiency.

Variant set: Native-organism implementations by sequence-defined organism and native enzyme pairing (One Or More)

A complete route requires GS and both GOGAT chains from one implementation. Families annotate exact products; they do not authorize mixed-species assemblies or donor substitutions.

PSEPK sequence-defined GS–GOGAT cycleMetabolic Pathwaypsepk_gs_gogat_cycle

Exact products are KT2440. Domain/rule evidence and characterized bacterial homologs establish chemistry; native KT2440 BarSeq corroborates condition-dependent physiology without supplying exact enzyme kinetics or complex stoichiometry.

Context
Pseudomonas putida KT2440NCBITaxon:160488
same-organism intracellular catalytic context

This is a biochemical capacity model, not proof of flux, expression, growth essentiality or identical nitrogen affinity under all conditions.

file:PSEPK/glnA/glnA-uniprot.txt
Independent RuleBase-supported reaction and target GS domains establish conserved chemistry; native KT2440 fitness is separate physiological context.
Reaction=L-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate +
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC2223721/?report=xml
Native KT2440/KT2442-lineage transcriptomics detects nitrogen-regulated glnA expression; target RuleBase and domains establish the catalytic assignment.
We also detected NtrC-dependent activation of the glnA gene coding for glutamine synthetase.
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:35285712
Native KT2440 gene identities and condition-dependent fitness corroborate conserved-domain inference.
GltB (PP_5076) and GltD (PP_5075) comprise the glutamate synthase (GOGAT) of P. putida

Exact products are KT2440. Domain/rule evidence and characterized bacterial homologs establish chemistry; native KT2440 BarSeq corroborates condition-dependent physiology without supplying exact enzyme kinetics or complex stoichiometry.

Connections

GS produces the glutamine consumed by GOGAT.
file:PSEPK/glnA/glnA-uniprot.txt
Independent RuleBase-supported reaction and target GS domains establish conserved chemistry; native KT2440 fitness is separate physiological context.
Reaction=L-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate +
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC2223721/?report=xml
Native KT2440/KT2442-lineage transcriptomics detects nitrogen-regulated glnA expression; target RuleBase and domains establish the catalytic assignment.
We also detected NtrC-dependent activation of the glnA gene coding for glutamine synthetase.
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:35285712
Native KT2440 gene identities and condition-dependent fitness corroborate conserved-domain inference.
GltB (PP_5076) and GltD (PP_5075) comprise the glutamate synthase (GOGAT) of P. putida
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The full E. coli synthesis explicitly describes cyclic net glutamate production and ATP investment.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.
Of the two glutamate products, one replenishes the GS substrate pool; the other is net glutamate synthesis from 2-oxoglutarate.
file:PSEPK/glnA/glnA-uniprot.txt
Independent RuleBase-supported reaction and target GS domains establish conserved chemistry; native KT2440 fitness is separate physiological context.
Reaction=L-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate +
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC2223721/?report=xml
Native KT2440/KT2442-lineage transcriptomics detects nitrogen-regulated glnA expression; target RuleBase and domains establish the catalytic assignment.
We also detected NtrC-dependent activation of the glnA gene coding for glutamine synthetase.
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:35285712
Native KT2440 gene identities and condition-dependent fitness corroborate conserved-domain inference.
GltB (PP_5076) and GltD (PP_5075) comprise the glutamate synthase (GOGAT) of P. putida
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The full E. coli synthesis explicitly describes cyclic net glutamate production and ATP investment.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.
Part 1: ATP-dependent incorporation of ammonium into glutamine
PSEPK GlnA glutamine synthesisReactionpsepk_glutamine_formation
file:PSEPK/glnA/glnA-uniprot.txt
Independent RuleBase-supported reaction and target GS domains establish conserved chemistry; native KT2440 fitness is separate physiological context.
Reaction=L-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate +
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC2223721/?report=xml
Native KT2440/KT2442-lineage transcriptomics detects nitrogen-regulated glnA expression; target RuleBase and domains establish the catalytic assignment.
We also detected NtrC-dependent activation of the glnA gene coding for glutamine synthetase.

Annotons

PSEPK GlnA activity
psepk_gs_activity
Participant: Gene Product: glnA
Gene Product:
glnAUniProtKB:Q88CY3
Family:
glnA exact-product family classificationPANTHER:PTHR43407:SF2 The family identifies evolutionary membership; the donor specificity and functional partners of this protein depend on its biochemical evidence.
Representative Members: glnAUniProtKB:Q88CY3
Taxon:
Pseudomonas putida KT2440NCBITaxon:160488
This PSEPK gene product acts with the other proteins in the same cellular implementation.

Function

glutamine synthetase activityGO:0004356
Substrates: L-glutamate ammonium ATP
Products: L-glutamine ADP phosphate

Processes

ammonia assimilation cycleGO:0019676
file:PSEPK/glnA/glnA-uniprot.txt
Independent RuleBase-supported reaction and target GS domains establish conserved chemistry; native KT2440 fitness is separate physiological context.
Reaction=L-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate +
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC2223721/?report=xml
Native KT2440/KT2442-lineage transcriptomics detects nitrogen-regulated glnA expression; target RuleBase and domains establish the catalytic assignment.
We also detected NtrC-dependent activation of the glnA gene coding for glutamine synthetase.
Part 2: Glutamine-dependent NADPH-linked glutamate synthesis
PSEPK gltB/gltD glutamate synthesisReactionpsepk_glutamate_formation
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:35285712
Native KT2440 gene identities and condition-dependent fitness corroborate conserved-domain inference.
GltB (PP_5076) and GltD (PP_5075) comprise the glutamate synthase (GOGAT) of P. putida

Annotons

PSEPK assembled NADPH-GOGAT activity
psepk_gogat_activity
Participant: Protein Complex: glutamate synthase complex (NADPH)
Protein Complex:
glutamate synthase complex (NADPH)GO:0009342 Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.
Active units:
gltB large chain1
Participant: Gene Product: gltB
Gene Product:
gltBUniProtKB:Q88CV4
Family:
gltB exact-product family classificationPANTHER:PTHR11938:SF148 The family identifies evolutionary membership; the donor specificity and functional partners of this protein depend on its biochemical evidence.
Representative Members: gltBUniProtKB:Q88CV4
Taxon:
Pseudomonas putida KT2440NCBITaxon:160488
This PSEPK gene product acts with the other proteins in the same cellular implementation.
Role: Hydrolyzes glutamine and channels ammonia to its FMN-associated glutamate-forming center; receives reducing equivalents from the small chain.
Function:
glutaminase activityGO:0004359
PMID:11188694
Large-chain structure connects glutamine hydrolysis and glutamate formation by an ammonia tunnel.
Channeling of the ammonia intermediate is brought about by an internal tunnel of 31 A length, which runs from the site of L-glutamine hydrolysis to the site of L-glutamate synthesis.
PMID:10785395
The FMN/2-oxoglutarate site is located in alpha.
one FMN (at Site 2, the 2-oxoglutarate/L-glutamate site in the alpha subunit)
file:PSEPK/gltB/gltB-uniprot.txt
Target domain architecture corroborates the comparative mechanistic assignment.
InterPro; IPR017932; GATase_2_dom.
Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.
gltD small chain1
Participant: Gene Product: gltD
Gene Product:
gltDUniProtKB:Q88CV5
Family:
gltD exact-product family classificationPANTHER:PTHR42783:SF3 The family identifies evolutionary membership; the donor specificity and functional partners of this protein depend on its biochemical evidence.
Representative Members: gltDUniProtKB:Q88CV5
Taxon:
Pseudomonas putida KT2440NCBITaxon:160488
This PSEPK gene product acts with the other proteins in the same cellular implementation.
Role: Oxidizes NADPH through FAD and the iron-sulfur relay, delivering reducing equivalents to the large-chain synthase center.
Function:
oxidoreductase activity, acting on NAD(P)HGO:0016651
PMID:10785395
The pyridine-nucleotide/FAD site is in beta.
one FAD (at Site 1, the pyridine nucleotide site within the beta subunit)
PMID:31473159
Cryo-EM places both [4Fe–4S] clusters in beta.
allows unequivocal location of the FAD cofactor and of two electron transfer [4Fe-4S]+1,+2 clusters within βGltS.
file:PSEPK/gltD/gltD-uniprot.txt
Target domain architecture corroborates the comparative mechanistic assignment.
Gene3D; 3.50.50.60; FAD/NAD(P)-binding domain; 1.
Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.
Taxon:
Pseudomonas putida KT2440NCBITaxon:160488
Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.

Function

glutamate synthase (NADPH) activityGO:0004355
Substrates: L-glutamine 2-oxoglutarate NADPH
Products: L-glutamate NADP+

Processes

ammonia assimilation cycleGO:0019676
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:35285712
Native KT2440 gene identities and condition-dependent fitness corroborate conserved-domain inference.
GltB (PP_5076) and GltD (PP_5075) comprise the glutamate synthase (GOGAT) of P. putida
ECOLI sequence-defined GS–GOGAT cycleMetabolic Pathwayecoli_gs_gogat_cycle

Exact products are K-12. Native genetic evidence supports the GltB/GltD enzyme; older strainW chemistry and modern A. brasilense/B. subtilis structures are comparative, not K-12 measurements.

Context
Escherichia coli K-12NCBITaxon:83333
same-organism intracellular catalytic context

This is a biochemical capacity model, not proof of flux, expression, growth essentiality or identical nitrogen affinity under all conditions.

file:ECOLI/glnA/glnA-uniprot.txt
Curated target catalytic reaction and the native biochemical literature support GS chemistry; comparative structures do not supply exact K-12 kinetic constants.
Reaction=L-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate +
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The full E. coli synthesis describes the ATP-requiring GS–GOGAT cycle.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:2448295
Native complementation links the GOGAT large-chain gene to enzyme activity without assigning the polar regulatory phenotype to catalysis.
By contrast, plasmids carrying gltB+ only complemented cells for glutamate synthase activity.

Exact products are K-12. Native genetic evidence supports the GltB/GltD enzyme; older strainW chemistry and modern A. brasilense/B. subtilis structures are comparative, not K-12 measurements.

Connections

GS produces the glutamine consumed by GOGAT.
file:ECOLI/glnA/glnA-uniprot.txt
Curated target catalytic reaction and the native biochemical literature support GS chemistry; comparative structures do not supply exact K-12 kinetic constants.
Reaction=L-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate +
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The full E. coli synthesis describes the ATP-requiring GS–GOGAT cycle.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:2448295
Native complementation links the GOGAT large-chain gene to enzyme activity without assigning the polar regulatory phenotype to catalysis.
By contrast, plasmids carrying gltB+ only complemented cells for glutamate synthase activity.
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The full E. coli synthesis explicitly describes cyclic net glutamate production and ATP investment.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.
Of the two glutamate products, one replenishes the GS substrate pool; the other is net glutamate synthesis from 2-oxoglutarate.
file:ECOLI/glnA/glnA-uniprot.txt
Curated target catalytic reaction and the native biochemical literature support GS chemistry; comparative structures do not supply exact K-12 kinetic constants.
Reaction=L-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate +
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The full E. coli synthesis describes the ATP-requiring GS–GOGAT cycle.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:2448295
Native complementation links the GOGAT large-chain gene to enzyme activity without assigning the polar regulatory phenotype to catalysis.
By contrast, plasmids carrying gltB+ only complemented cells for glutamate synthase activity.
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The full E. coli synthesis explicitly describes cyclic net glutamate production and ATP investment.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.
Part 1: ATP-dependent incorporation of ammonium into glutamine
ECOLI GlnA glutamine synthesisReactionecoli_glutamine_formation
file:ECOLI/glnA/glnA-uniprot.txt
Curated target catalytic reaction and the native biochemical literature support GS chemistry; comparative structures do not supply exact K-12 kinetic constants.
Reaction=L-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate +
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The full E. coli synthesis describes the ATP-requiring GS–GOGAT cycle.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.

Annotons

ECOLI GlnA activity
ecoli_gs_activity
Participant: Gene Product: glnA
Gene Product:
glnAUniProtKB:P0A9C5
Family:
glnA exact-product family classificationPANTHER:PTHR43407:SF2 The family identifies evolutionary membership; the donor specificity and functional partners of this protein depend on its biochemical evidence.
Representative Members: glnAUniProtKB:P0A9C5
Taxon:
Escherichia coli K-12NCBITaxon:83333
This ECOLI gene product acts with the other proteins in the same cellular implementation.

Function

glutamine synthetase activityGO:0004356
Substrates: L-glutamate ammonium ATP
Products: L-glutamine ADP phosphate

Processes

ammonia assimilation cycleGO:0019676
file:ECOLI/glnA/glnA-uniprot.txt
Curated target catalytic reaction and the native biochemical literature support GS chemistry; comparative structures do not supply exact K-12 kinetic constants.
Reaction=L-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate +
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The full E. coli synthesis describes the ATP-requiring GS–GOGAT cycle.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.
Part 2: Glutamine-dependent NADPH-linked glutamate synthesis
ECOLI gltB/gltD glutamate synthesisReactionecoli_glutamate_formation
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:2448295
Native complementation links the GOGAT large-chain gene to enzyme activity without assigning the polar regulatory phenotype to catalysis.
By contrast, plasmids carrying gltB+ only complemented cells for glutamate synthase activity.

Annotons

ECOLI assembled NADPH-GOGAT activity
ecoli_gogat_activity
Participant: Protein Complex: glutamate synthase complex (NADPH)
Protein Complex:
glutamate synthase complex (NADPH)GO:0009342 Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.
Active units:
gltB large chain1
Participant: Gene Product: gltB
Gene Product:
gltBUniProtKB:P09831
Family:
gltB exact-product family classificationPANTHER:PTHR11938:SF148 The family identifies evolutionary membership; the donor specificity and functional partners of this protein depend on its biochemical evidence.
Representative Members: gltBUniProtKB:P09831
Taxon:
Escherichia coli K-12NCBITaxon:83333
This ECOLI gene product acts with the other proteins in the same cellular implementation.
Role: Hydrolyzes glutamine and channels ammonia to its FMN-associated glutamate-forming center; receives reducing equivalents from the small chain.
Function:
glutaminase activityGO:0004359
PMID:11188694
Large-chain structure connects glutamine hydrolysis and glutamate formation by an ammonia tunnel.
Channeling of the ammonia intermediate is brought about by an internal tunnel of 31 A length, which runs from the site of L-glutamine hydrolysis to the site of L-glutamate synthesis.
PMID:10785395
The FMN/2-oxoglutarate site is located in alpha.
one FMN (at Site 2, the 2-oxoglutarate/L-glutamate site in the alpha subunit)
file:ECOLI/gltB/gltB-uniprot.txt
Target domain architecture corroborates the comparative mechanistic assignment.
InterPro; IPR017932; GATase_2_dom.
Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.
gltD small chain1
Participant: Gene Product: gltD
Gene Product:
gltDUniProtKB:P09832
Family:
gltD exact-product family classificationPANTHER:PTHR42783:SF3 The family identifies evolutionary membership; the donor specificity and functional partners of this protein depend on its biochemical evidence.
Representative Members: gltDUniProtKB:P09832
Taxon:
Escherichia coli K-12NCBITaxon:83333
This ECOLI gene product acts with the other proteins in the same cellular implementation.
Role: Oxidizes NADPH through FAD and the iron-sulfur relay, delivering reducing equivalents to the large-chain synthase center.
Function:
oxidoreductase activity, acting on NAD(P)HGO:0016651
PMID:10785395
The pyridine-nucleotide/FAD site is in beta.
one FAD (at Site 1, the pyridine nucleotide site within the beta subunit)
PMID:31473159
Cryo-EM places both [4Fe–4S] clusters in beta.
allows unequivocal location of the FAD cofactor and of two electron transfer [4Fe-4S]+1,+2 clusters within βGltS.
file:ECOLI/gltD/gltD-uniprot.txt
Target domain architecture corroborates the comparative mechanistic assignment.
InterPro; IPR006006; GltD-like.
Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.
Taxon:
Escherichia coli K-12NCBITaxon:83333
Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.

Function

glutamate synthase (NADPH) activityGO:0004355
Substrates: L-glutamine 2-oxoglutarate NADPH
Products: L-glutamate NADP+

Processes

ammonia assimilation cycleGO:0019676
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:2448295
Native complementation links the GOGAT large-chain gene to enzyme activity without assigning the polar regulatory phenotype to catalysis.
By contrast, plasmids carrying gltB+ only complemented cells for glutamate synthase activity.
BACSU sequence-defined GS–GOGAT cycleMetabolic Pathwaybacsu_gs_gogat_cycle

Exact products are strain 168. Native-species structural evidence is from NCIB3610; conserved catalytic transfer is supported by target domains, whereas active GudB counter-enzyme regulation is not transferred to cryptic-gudB strain 168 physiology.

Context
Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308
same-organism intracellular catalytic context

This is a biochemical capacity model, not proof of flux, expression, growth essentiality or identical nitrogen affinity under all conditions.

PMID:23535029
Native GS ligates ammonium to glutamate using ATP.
GS catalyses the ATP-dependent synthesis of glutamine from glutamate and ammonium.
PMID:24158439
Native substrate/metal structures corroborate the catalytic mechanism.
The glutamate substrate peptide carboxyl and amide groups interact with Arg 298 and His 245 , whereas its side chain carboxyl interacts with a Mg 2+ ion.
PMID:34931064
Native species structure and NADPH assays establish GltA/GltB chemistry; the assayed NCIB3610 background is distinguished from the sequence-defined 168 exemplars.
These co-factors play a key role is shuttling electrons from the GltB-bound NADPH to 2-iminoglurate that is formed in the synthase domain of GltA
PMID:18326565
Native physiology separates anabolic GOGAT from catabolic GDH.
Both RocG and GudB1 were unable to catalyze the anabolic reaction, most probably because of their very high K(m) values for ammonium.

Exact products are strain 168. Native-species structural evidence is from NCIB3610; conserved catalytic transfer is supported by target domains, whereas active GudB counter-enzyme regulation is not transferred to cryptic-gudB strain 168 physiology.

Connections

GS produces the glutamine consumed by GOGAT.
PMID:23535029
Native GS ligates ammonium to glutamate using ATP.
GS catalyses the ATP-dependent synthesis of glutamine from glutamate and ammonium.
PMID:24158439
Native substrate/metal structures corroborate the catalytic mechanism.
The glutamate substrate peptide carboxyl and amide groups interact with Arg 298 and His 245 , whereas its side chain carboxyl interacts with a Mg 2+ ion.
PMID:34931064
Native species structure and NADPH assays establish GltA/GltB chemistry; the assayed NCIB3610 background is distinguished from the sequence-defined 168 exemplars.
These co-factors play a key role is shuttling electrons from the GltB-bound NADPH to 2-iminoglurate that is formed in the synthase domain of GltA
PMID:18326565
Native physiology separates anabolic GOGAT from catabolic GDH.
Both RocG and GudB1 were unable to catalyze the anabolic reaction, most probably because of their very high K(m) values for ammonium.
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The full E. coli synthesis explicitly describes cyclic net glutamate production and ATP investment.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.
Of the two glutamate products, one replenishes the GS substrate pool; the other is net glutamate synthesis from 2-oxoglutarate.
PMID:23535029
Native GS ligates ammonium to glutamate using ATP.
GS catalyses the ATP-dependent synthesis of glutamine from glutamate and ammonium.
PMID:24158439
Native substrate/metal structures corroborate the catalytic mechanism.
The glutamate substrate peptide carboxyl and amide groups interact with Arg 298 and His 245 , whereas its side chain carboxyl interacts with a Mg 2+ ion.
PMID:34931064
Native species structure and NADPH assays establish GltA/GltB chemistry; the assayed NCIB3610 background is distinguished from the sequence-defined 168 exemplars.
These co-factors play a key role is shuttling electrons from the GltB-bound NADPH to 2-iminoglurate that is formed in the synthase domain of GltA
PMID:18326565
Native physiology separates anabolic GOGAT from catabolic GDH.
Both RocG and GudB1 were unable to catalyze the anabolic reaction, most probably because of their very high K(m) values for ammonium.
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The full E. coli synthesis explicitly describes cyclic net glutamate production and ATP investment.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.
Part 1: ATP-dependent incorporation of ammonium into glutamine
BACSU GlnA glutamine synthesisReactionbacsu_glutamine_formation
PMID:23535029
Native GS ligates ammonium to glutamate using ATP.
GS catalyses the ATP-dependent synthesis of glutamine from glutamate and ammonium.
PMID:24158439
Native substrate/metal structures corroborate the catalytic mechanism.
The glutamate substrate peptide carboxyl and amide groups interact with Arg 298 and His 245 , whereas its side chain carboxyl interacts with a Mg 2+ ion.

Annotons

BACSU GlnA activity
bacsu_gs_activity
Participant: Gene Product: glnA
Gene Product:
glnAUniProtKB:P12425
Family:
glnA exact-product family classificationPANTHER:PTHR43785:SF12 The family identifies evolutionary membership; the donor specificity and functional partners of this protein depend on its biochemical evidence.
Representative Members: glnAUniProtKB:P12425
Taxon:
Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308
This BACSU gene product acts with the other proteins in the same cellular implementation.

Function

glutamine synthetase activityGO:0004356
Substrates: L-glutamate ammonium ATP
Products: L-glutamine ADP phosphate

Processes

ammonia assimilation cycleGO:0019676
PMID:23535029
Native GS ligates ammonium to glutamate using ATP.
GS catalyses the ATP-dependent synthesis of glutamine from glutamate and ammonium.
PMID:24158439
Native substrate/metal structures corroborate the catalytic mechanism.
The glutamate substrate peptide carboxyl and amide groups interact with Arg 298 and His 245 , whereas its side chain carboxyl interacts with a Mg 2+ ion.
Part 2: Glutamine-dependent NADPH-linked glutamate synthesis
BACSU gltA/gltB glutamate synthesisReactionbacsu_glutamate_formation
PMID:34931064
Native species structure and NADPH assays establish GltA/GltB chemistry; the assayed NCIB3610 background is distinguished from the sequence-defined 168 exemplars.
These co-factors play a key role is shuttling electrons from the GltB-bound NADPH to 2-iminoglurate that is formed in the synthase domain of GltA
PMID:18326565
Native physiology separates anabolic GOGAT from catabolic GDH.
Both RocG and GudB1 were unable to catalyze the anabolic reaction, most probably because of their very high K(m) values for ammonium.

Annotons

BACSU assembled NADPH-GOGAT activity
bacsu_gogat_activity
Participant: Protein Complex: glutamate synthase complex (NADPH)
Protein Complex:
glutamate synthase complex (NADPH)GO:0009342 Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.
Active units:
gltA large chain1
Participant: Gene Product: gltA
Gene Product:
gltAUniProtKB:P39812
Family:
gltA exact-product family classificationPANTHER:PTHR11938:SF133 The family identifies evolutionary membership; the donor specificity and functional partners of this protein depend on its biochemical evidence.
Representative Members: gltAUniProtKB:P39812
Taxon:
Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308
This BACSU gene product acts with the other proteins in the same cellular implementation.
Role: Hydrolyzes glutamine and channels ammonia to its FMN-associated glutamate-forming center; receives reducing equivalents from the small chain.
Function:
glutaminase activityGO:0004359
PMID:11188694
Large-chain structure connects glutamine hydrolysis and glutamate formation by an ammonia tunnel.
Channeling of the ammonia intermediate is brought about by an internal tunnel of 31 A length, which runs from the site of L-glutamine hydrolysis to the site of L-glutamate synthesis.
PMID:10785395
The FMN/2-oxoglutarate site is located in alpha.
one FMN (at Site 2, the 2-oxoglutarate/L-glutamate site in the alpha subunit)
PMID:34931064
Native B. subtilis structure assigns the cofactors and electron flow to the correct chains.
The higher resolution did permit unambiguous assignment of two 4Fe-4S clusters in GltB, and a 3Fe-4S clusters and FMN in GltA.
file:BACSU/gltA/gltA-uniprot.txt
Target domain architecture corroborates the comparative mechanistic assignment.
InterPro; IPR017932; GATase_2_dom.
Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.
gltB small chain1
Participant: Gene Product: gltB
Gene Product:
gltBUniProtKB:O34399
Family:
gltB exact-product family classificationPANTHER:PTHR43100:SF1 The family identifies evolutionary membership; the donor specificity and functional partners of this protein depend on its biochemical evidence.
Representative Members: gltBUniProtKB:O34399
Taxon:
Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308
This BACSU gene product acts with the other proteins in the same cellular implementation.
Role: Oxidizes NADPH through FAD and the iron-sulfur relay, delivering reducing equivalents to the large-chain synthase center.
Function:
oxidoreductase activity, acting on NAD(P)HGO:0016651
PMID:10785395
The pyridine-nucleotide/FAD site is in beta.
one FAD (at Site 1, the pyridine nucleotide site within the beta subunit)
PMID:31473159
Cryo-EM places both [4Fe–4S] clusters in beta.
allows unequivocal location of the FAD cofactor and of two electron transfer [4Fe-4S]+1,+2 clusters within βGltS.
PMID:34931064
Native B. subtilis structure assigns the cofactors and electron flow to the correct chains.
The higher resolution did permit unambiguous assignment of two 4Fe-4S clusters in GltB, and a 3Fe-4S clusters and FMN in GltA.
file:BACSU/gltB/gltB-uniprot.txt
Target domain architecture corroborates the comparative mechanistic assignment.
NCBIfam; TIGR01317; GOGAT_sm_gam; 1.
Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.
Taxon:
Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308
Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.

Function

glutamate synthase (NADPH) activityGO:0004355
Substrates: L-glutamine 2-oxoglutarate NADPH
Products: L-glutamate NADP+

Processes

ammonia assimilation cycleGO:0019676
PMID:34931064
Native species structure and NADPH assays establish GltA/GltB chemistry; the assayed NCIB3610 background is distinguished from the sequence-defined 168 exemplars.
These co-factors play a key role is shuttling electrons from the GltB-bound NADPH to 2-iminoglurate that is formed in the synthase domain of GltA
PMID:18326565
Native physiology separates anabolic GOGAT from catabolic GDH.
Both RocG and GudB1 were unable to catalyze the anabolic reaction, most probably because of their very high K(m) values for ammonium.
AZOBR sequence-defined GS–GOGAT cycleMetabolic Pathwayazobr_gs_gogat_cycle

Sp7 sequence provenance is retained for the three products. Species-level tracer data, native Sp6 purification and strain-unspecified recombinant/cryo-EM work have distinct scopes; this route is a supported sequence-defined implementation, not a claim that all experiments assayed one matched Sp7 preparation.

Context
Azospirillum brasilenseNCBITaxon:192
same-organism intracellular catalytic context

This is a biochemical capacity model, not proof of flux, expression, growth essentiality or identical nitrogen affinity under all conditions.

file:AZOBR/glnA/glnA-uniprot.txt
Curated homology-supported target function plus exact Sp7 sequence and native species-level tracer corroboration.
Catalyzes the ATP-dependent biosynthesis of glutamine from glutamate and ammonia.
PMID:2878685
The Sp7 glnA sequence identifies this target.
PMID:2887545
Native tracer/inhibitor data support its physiological route.
These results imply that the GS-GOGAT pathway is the primary route of NH4+ assimilation by A. brasilense grown with excess or limiting nitrogen
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:2887545
Native species-level tracer/inhibitor evidence establishes GS–GOGAT flow.
These results imply that the GS-GOGAT pathway is the primary route of NH4+ assimilation by A. brasilense grown with excess or limiting nitrogen

Sp7 sequence provenance is retained for the three products. Species-level tracer data, native Sp6 purification and strain-unspecified recombinant/cryo-EM work have distinct scopes; this route is a supported sequence-defined implementation, not a claim that all experiments assayed one matched Sp7 preparation.

Connections

GS produces the glutamine consumed by GOGAT.
file:AZOBR/glnA/glnA-uniprot.txt
Curated homology-supported target function plus exact Sp7 sequence and native species-level tracer corroboration.
Catalyzes the ATP-dependent biosynthesis of glutamine from glutamate and ammonia.
PMID:2878685
The Sp7 glnA sequence identifies this target.
PMID:2887545
Native tracer/inhibitor data support its physiological route.
These results imply that the GS-GOGAT pathway is the primary route of NH4+ assimilation by A. brasilense grown with excess or limiting nitrogen
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:2887545
Native species-level tracer/inhibitor evidence establishes GS–GOGAT flow.
These results imply that the GS-GOGAT pathway is the primary route of NH4+ assimilation by A. brasilense grown with excess or limiting nitrogen
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The full E. coli synthesis explicitly describes cyclic net glutamate production and ATP investment.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.
Of the two glutamate products, one replenishes the GS substrate pool; the other is net glutamate synthesis from 2-oxoglutarate.
file:AZOBR/glnA/glnA-uniprot.txt
Curated homology-supported target function plus exact Sp7 sequence and native species-level tracer corroboration.
Catalyzes the ATP-dependent biosynthesis of glutamine from glutamate and ammonia.
PMID:2878685
The Sp7 glnA sequence identifies this target.
PMID:2887545
Native tracer/inhibitor data support its physiological route.
These results imply that the GS-GOGAT pathway is the primary route of NH4+ assimilation by A. brasilense grown with excess or limiting nitrogen
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:2887545
Native species-level tracer/inhibitor evidence establishes GS–GOGAT flow.
These results imply that the GS-GOGAT pathway is the primary route of NH4+ assimilation by A. brasilense grown with excess or limiting nitrogen
url:https://pmc.ncbi.nlm.nih.gov/articles/PMC3973380/?report=xml
The full E. coli synthesis explicitly describes cyclic net glutamate production and ATP investment.
Net glutamate production from 2-oxoglutarate can hereby be achieved not only by GDH alone but also by GS-GOGAT coupled together. The latter process expends one ATP.
Part 1: ATP-dependent incorporation of ammonium into glutamine
AZOBR GlnA glutamine synthesisReactionazobr_glutamine_formation
file:AZOBR/glnA/glnA-uniprot.txt
Curated homology-supported target function plus exact Sp7 sequence and native species-level tracer corroboration.
Catalyzes the ATP-dependent biosynthesis of glutamine from glutamate and ammonia.
PMID:2878685
The Sp7 glnA sequence identifies this target.
PMID:2887545
Native tracer/inhibitor data support its physiological route.
These results imply that the GS-GOGAT pathway is the primary route of NH4+ assimilation by A. brasilense grown with excess or limiting nitrogen

Annotons

AZOBR GlnA activity
azobr_gs_activity
Participant: Gene Product: glnA
Gene Product:
glnAUniProtKB:P10583
Family:
glnA exact-product family classificationPANTHER:PTHR43407:SF2 The family identifies evolutionary membership; the donor specificity and functional partners of this protein depend on its biochemical evidence.
Representative Members: glnAUniProtKB:P10583
Taxon:
Azospirillum brasilenseNCBITaxon:192
This AZOBR gene product acts with the other proteins in the same cellular implementation.

Function

glutamine synthetase activityGO:0004356
Substrates: L-glutamate ammonium ATP
Products: L-glutamine ADP phosphate

Processes

ammonia assimilation cycleGO:0019676
file:AZOBR/glnA/glnA-uniprot.txt
Curated homology-supported target function plus exact Sp7 sequence and native species-level tracer corroboration.
Catalyzes the ATP-dependent biosynthesis of glutamine from glutamate and ammonia.
PMID:2878685
The Sp7 glnA sequence identifies this target.
PMID:2887545
Native tracer/inhibitor data support its physiological route.
These results imply that the GS-GOGAT pathway is the primary route of NH4+ assimilation by A. brasilense grown with excess or limiting nitrogen
Part 2: Glutamine-dependent NADPH-linked glutamate synthesis
AZOBR gltB/gltD glutamate synthesisReactionazobr_glutamate_formation
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:2887545
Native species-level tracer/inhibitor evidence establishes GS–GOGAT flow.
These results imply that the GS-GOGAT pathway is the primary route of NH4+ assimilation by A. brasilense grown with excess or limiting nitrogen

Annotons

AZOBR assembled NADPH-GOGAT activity
azobr_gogat_activity
Participant: Protein Complex: glutamate synthase complex (NADPH)
Protein Complex:
glutamate synthase complex (NADPH)GO:0009342 Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.
Active units:
gltB large chain1
Participant: Gene Product: gltB
Gene Product:
gltBUniProtKB:Q05755
Family:
gltB exact-product family classificationPANTHER:PTHR11938:SF133 The family identifies evolutionary membership; the donor specificity and functional partners of this protein depend on its biochemical evidence.
Representative Members: gltBUniProtKB:Q05755
Taxon:
Azospirillum brasilenseNCBITaxon:192
This AZOBR gene product acts with the other proteins in the same cellular implementation.
Role: Hydrolyzes glutamine and channels ammonia to its FMN-associated glutamate-forming center; receives reducing equivalents from the small chain.
Function:
glutaminase activityGO:0004359
PMID:11188694
Large-chain structure connects glutamine hydrolysis and glutamate formation by an ammonia tunnel.
Channeling of the ammonia intermediate is brought about by an internal tunnel of 31 A length, which runs from the site of L-glutamine hydrolysis to the site of L-glutamate synthesis.
PMID:10785395
The FMN/2-oxoglutarate site is located in alpha.
one FMN (at Site 2, the 2-oxoglutarate/L-glutamate site in the alpha subunit)
file:AZOBR/gltB/gltB-uniprot.txt
Target domain architecture corroborates the comparative mechanistic assignment.
InterPro; IPR017932; GATase_2_dom.
Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.
gltD small chain1
Participant: Gene Product: gltD
Gene Product:
gltDUniProtKB:Q05756
Family:
gltD exact-product family classificationPANTHER:PTHR42783:SF3 The family identifies evolutionary membership; the donor specificity and functional partners of this protein depend on its biochemical evidence.
Representative Members: gltDUniProtKB:Q05756
Taxon:
Azospirillum brasilenseNCBITaxon:192
This AZOBR gene product acts with the other proteins in the same cellular implementation.
Role: Oxidizes NADPH through FAD and the iron-sulfur relay, delivering reducing equivalents to the large-chain synthase center.
Function:
oxidoreductase activity, acting on NAD(P)HGO:0016651
PMID:10785395
The pyridine-nucleotide/FAD site is in beta.
one FAD (at Site 1, the pyridine nucleotide site within the beta subunit)
PMID:31473159
Cryo-EM places both [4Fe–4S] clusters in beta.
allows unequivocal location of the FAD cofactor and of two electron transfer [4Fe-4S]+1,+2 clusters within βGltS.
file:AZOBR/gltD/gltD-uniprot.txt
Target domain architecture corroborates the comparative mechanistic assignment.
Gene3D; 3.50.50.60; FAD/NAD(P)-binding domain; 1.
Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.
Taxon:
Azospirillum brasilenseNCBITaxon:192
Both sequence-defined large and small chains must assemble in the same organism/cell. Presence of one chain, or a mixed-organism pair, does not satisfy this activity. The listed stoichiometries describe one catalytic large/small unit, not the entire higher-order aggregate.

Function

glutamate synthase (NADPH) activityGO:0004355
Substrates: L-glutamine 2-oxoglutarate NADPH
Products: L-glutamate NADP+

Processes

ammonia assimilation cycleGO:0019676
PMID:10785395
Primary recombinant A. brasilense biochemistry establishes the complementary alpha/beta NADPH-GOGAT mechanism.
catalyses the NADPH-dependent reductive transfer of glutamine amide group to the C(2) carbon of 2-oxoglutarate to yield L-glutamate.
PMID:31473159
Primary structural evidence confirms two-glutamate output and the small-chain electron relay.
catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate.
PMID:2887545
Native species-level tracer/inhibitor evidence establishes GS–GOGAT flow.
These results imply that the GS-GOGAT pathway is the primary route of NH4+ assimilation by A. brasilense grown with excess or limiting nitrogen