Tricarboxylic acid cycle

A taxon-neutral module for the oxidative tricarboxylic acid (TCA) cycle, covering acetyl-CoA entry through citrate synthase, citrate/isocitrate interconversion, oxidative decarboxylation to succinyl-CoA, succinate-level phosphorylation, succinate oxidation through respiratory complex II, fumarate hydration, and malate oxidation to regenerate oxaloacetate. The module also records common bacterial alternatives at the aconitase, isocitrate dehydrogenase, fumarase, and malate/oxaloacetate steps.

MODULE:tca_cycleDRAFTCONCRETEMetabolic Pathwaymodules/tca_cycle.yaml
tricarboxylic acid cycleGO:0006099
GO:0006099
tricarboxylic acid cycle
GO represents the TCA cycle as the pathway that oxidizes acetyl-CoA to CO2 while generating reducing equivalents and regenerating oxaloacetate.
file:genes/PSEPK/gltA/gltA-ai-review.yaml
PSEPK gltA gene review
PSEPK GltA is a curated citrate synthase and marks acetyl-CoA entry into the KT2440 TCA cycle.
file:genes/PSEPK/sdhA/sdhA-ai-review.yaml
PSEPK sdhA gene review
PSEPK SdhA is curated as the catalytic flavoprotein subunit of succinate dehydrogenase, connecting the TCA cycle to the respiratory quinone pool.
file:modules/tca_cycle-deep-research-openscientist.md
OpenScientist module research for the TCA cycle
The generic module-level research supports the oxidative TCA-cycle boundary, including bacterial variants at fumarase and malate oxidation and treating pyruvate carboxylase as an anaplerotic input rather than a cyclic reaction.
file:projects/P_PUTIDA/deep-research/PSEPK__tca_cycle__ppu00020-deep-research-openscientist.md
OpenScientist PSEPK/ppu00020 TCA-cycle research
The P. putida KT2440 pathway report concludes that the oxidative TCA cycle is satisfiable, with quinone-linked MQO as the primary malate oxidation branch and with scpC/prpC treated as methylcitrate or CoA-transferase boundary cases rather than core SCS/citrate synthase replacements.

Reusable boundary: this module describes the oxidative TCA cycle and its immediate bacterial alternatives, not every KEGG ppu00020 neighbor. Pyruvate dehydrogenase supplies acetyl-CoA upstream, pyruvate carboxylase supplies an external anaplerotic oxaloacetate input, and methylcitrate/propionyl-CoA CoA-transferase proteins should be treated as adjacent propionate-metabolism context unless direct evidence places them in the main cyclic flux. The PSEPK instantiation is satisfiable with gltA/Q88FA4, acnB/Q88KF1 plus acnA-I/Q88L24, icd/Q88FS2 plus idh/Q88FS1, sucA/Q88FA9-sucB/Q88FB0 with lpdG/Q88FB1 or related E3 components, sucD/Q88FB3-sucC/Q88FB2, sdhABCD/Q88FA7-Q88FA8-Q88FA5-Q88FA6, fumarase paralogs including the class-I enzyme PP_0897/Q88PF3 and the class-II enzymes fumC/Q88M20 and fumC-I/Q88PA6, and malate oxidation by mqo1/Q88PU7, mqo2/Q88NF9, mqo3/Q88IS4, and/or mdh/Q88Q44.

12Nodes
11Parts
0Variant Sets
0Variants
11Annotons
0Connections

Derived QC

Recommended-field compliance

55.6% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)

Module deep research

✓ present

  • tca_cycle-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.

Gene-review completeness (21/21 grounded genes reviewed)

21 complete review(s) · 21 with deep research · 0 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
acnA-I Q88L24 ✓ ✓ ✓
acnB Q88KF1 ✓ ✓ ✓
fumC Q88M20 ✓ ✓ ✓
fumC-I Q88PA6 ✓ ✓ ✓
gltA Q88FA4 ✓ ✓ ✓
icd Q88FS2 ✓ ✓ ✓
idh Q88FS1 ✓ ✓ ✓
lpdG Q88FB1 ✓ ✓ ✓
mdh Q88Q44 ✓ ✓ ✓
mqo1 Q88PU7 ✓ ✓ ✓
mqo2 Q88NF9 ✓ ✓ ✓
mqo3 Q88IS4 ✓ ✓ ✓
PP_0897 Q88PF3 ✓ ✓ ✓
sdhA Q88FA7 ✓ ✓ ✓
sdhB Q88FA8 ✓ ✓ ✓
sdhC Q88FA5 ✓ ✓ ✓
sdhD Q88FA6 ✓ ✓ ✓
sucA Q88FA9 ✓ ✓ ✓
sucB Q88FB0 ✓ ✓ ✓
sucC Q88FB2 ✓ ✓ ✓
sucD Q88FB3 ✓ ✓ ✓

Details

Tricarboxylic acid cycleMetabolic Pathwaytca_cycle
tricarboxylic acid cycleGO:0006099
Part 1: acetyl-CoA entry
Citrate synthaseReactioncitrate_synthase_step

Annotons

Citrate synthase
citrate_synthase_activity
Participant: Family: bacterial citrate synthase family
Family:
bacterial citrate synthase family
Representative Members: PSEPK GltA exemplarUniProtKB:Q88FA4

Function

citrate synthase activityGO:0036440
Substrates: acetyl-CoA oxaloacetate H2O
Products: citrate CoA

Condenses acetyl-CoA and oxaloacetate to form citrate, the committed entry step of the cycle.

Part 2: citrate to isocitrate
Aconitate hydrataseReactionaconitate_hydratase_step

Annotons

Aconitase
aconitate_hydratase_activity
Participant: Family: bacterial aconitate hydratase families
Family:
bacterial aconitate hydratase families
Representative Members: PSEPK AcnA-I exemplarUniProtKB:Q88L24 PSEPK AcnB exemplarUniProtKB:Q88KF1

Function

aconitate hydratase activityGO:0003994
Substrates: citrate
Products: isocitrate

Reversibly isomerizes citrate to isocitrate through cis-aconitate.

Part 3: isocitrate oxidation
Isocitrate dehydrogenaseReactionisocitrate_dehydrogenase_step

Annotons

NADP-dependent isocitrate dehydrogenase
isocitrate_dehydrogenase_nadp_activity
Participant: Family: bacterial NADP-dependent isocitrate dehydrogenase families
Family:
bacterial NADP-dependent isocitrate dehydrogenase families
Representative Members: PSEPK Icd exemplarUniProtKB:Q88FS2 PSEPK Idh exemplarUniProtKB:Q88FS1

Function

isocitrate dehydrogenase (NADP+) activityGO:0004450
Substrates: isocitrate NADP+
Products: 2-oxoglutarate CO2 NADPH

Oxidatively decarboxylates isocitrate to 2-oxoglutarate while reducing NADP+ in many bacteria.

Part 4: 2-oxoglutarate oxidation
2-oxoglutarate dehydrogenase complexMetabolic Pathwayoxoglutarate_dehydrogenase_complex_step

Multienzyme oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA by E1, E2, and E3 components.

Part 1: E1 decarboxylation
2-oxoglutarate dehydrogenase E1Reactionoxoglutarate_dehydrogenase_e1_step

Annotons

2-oxoglutarate dehydrogenase
oxoglutarate_dehydrogenase_activity
Participant: Family: bacterial SucA E1 family
Family:
bacterial SucA E1 family
Representative Members: PSEPK SucA exemplarUniProtKB:Q88FA9

Function

oxoglutarate dehydrogenase (succinyl-transferring) activityGO:0004591
Substrates: 2-oxoglutarate
Products: succinyl-dihydrolipoamide
Part 2: E2 succinyltransferase
Dihydrolipoyllysine-residue succinyltransferaseReactiondihydrolipoyl_succinyltransferase_step

Annotons

Dihydrolipoyllysine-residue succinyltransferase
dihydrolipoyl_succinyltransferase_activity
Participant: Family: bacterial SucB E2 family
Family:
bacterial SucB E2 family
Representative Members: PSEPK SucB exemplarUniProtKB:Q88FB0

Function

dihydrolipoyllysine-residue succinyltransferase activityGO:0004149
Substrates: succinyl-dihydrolipoamide CoA
Products: succinyl-CoA
Part 3: E3 lipoamide dehydrogenase
Dihydrolipoyl dehydrogenaseReactiondihydrolipoyl_dehydrogenase_step

Annotons

Dihydrolipoyl dehydrogenase
dihydrolipoyl_dehydrogenase_activity
Participant: Family: bacterial Lpd E3 family
Family:
bacterial Lpd E3 family
Representative Members: PSEPK LpdG provisional exemplarUniProtKB:Q88FB1

Function

dihydrolipoyl dehydrogenase (NADH) activityGO:0004148
Substrates: dihydrolipoamide NAD+
Products: lipoamide NADH
Part 5: succinyl-CoA to succinate
Succinate-CoA ligaseReactionsuccinate_coa_ligase_step

Annotons

ADP-forming succinate-CoA ligase
succinate_coa_ligase_adp_activity
Participant: Protein Complex: bacterial SucCD succinate-CoA ligase complex
Protein Complex:
bacterial SucCD succinate-CoA ligase complexGO:0009361
Active units:
SucC beta subunit
Participant: Family: bacterial SucC family
Family:
bacterial SucC family
Representative Members: PSEPK SucC exemplarUniProtKB:Q88FB2
Role: Nucleotide-binding beta subunit of the heteromeric ligase.
SucD alpha subunit
Participant: Family: bacterial SucD family
Family:
bacterial SucD family
Representative Members: PSEPK SucD exemplarUniProtKB:Q88FB3
Role: CoA- and phosphate-handling alpha subunit of the heteromeric ligase.

Function

succinate-CoA ligase (ADP-forming) activityGO:0004775
Substrates: succinyl-CoA ADP phosphate
Products: succinate ATP CoA

Conserves thioester energy by substrate-level phosphorylation; some organisms or annotations also use the GDP-forming term GO:0004776 for the same heteromeric enzyme family.

Part 6: succinate oxidation
Succinate dehydrogenaseReactionsuccinate_dehydrogenase_step

Annotons

Succinate dehydrogenase (quinone)
succinate_dehydrogenase_quinone_activity
Participant: Protein Complex: bacterial SdhABCD succinate dehydrogenase complex
Protein Complex:
bacterial SdhABCD succinate dehydrogenase complexGO:0045273
Active units:
SdhA flavoprotein subunit
Participant: Family: bacterial SdhA family
Family:
bacterial SdhA family
Representative Members: PSEPK SdhA exemplarUniProtKB:Q88FA7
Role: Catalyzes succinate oxidation at the FAD-containing active site.
Function:
succinate dehydrogenase activityGO:0000104
SdhB iron-sulfur subunit
Participant: Family: bacterial SdhB family
Family:
bacterial SdhB family
Representative Members: PSEPK SdhB exemplarUniProtKB:Q88FA8
Role: Relays electrons from SdhA toward the membrane quinone site.
Function:
electron transfer activityGO:0009055
SdhC membrane subunit
Participant: Family: bacterial SdhC family
Family:
bacterial SdhC family
Representative Members: PSEPK SdhC exemplarUniProtKB:Q88FA5
Role: Contributes the cytochrome-b membrane anchor and quinone-interaction domain.
SdhD membrane subunit
Participant: Family: bacterial SdhD family
Family:
bacterial SdhD family
Representative Members: PSEPK SdhD exemplarUniProtKB:Q88FA6
Role: Completes the membrane anchor and contributes to quinone-linked electron transfer.

Function

succinate dehydrogenase (quinone) activityGO:0008177
Substrates: succinate quinone
Products: fumarate quinol

Locations

plasma membraneGO:0005886

Membrane-bound complex II links succinate oxidation in the TCA cycle to respiratory electron transfer through the quinone pool.

Part 7: fumarate hydration
Fumarate hydrataseReactionfumarate_hydratase_step

Annotons

Fumarate hydratase
fumarate_hydratase_activity
Participant: Family: bacterial class-I and class-II fumarate hydratase families
Family:
bacterial class-I and class-II fumarate hydratase families
Representative Members: PSEPK class-I fumarase exemplarUniProtKB:Q88PF3 PSEPK FumC-I exemplarUniProtKB:Q88PA6 PSEPK FumC exemplarUniProtKB:Q88M20

Function

fumarate hydratase activityGO:0004333
Substrates: fumarate H2O
Products: (S)-malate
Part 8: malate oxidation
Malate to oxaloacetateMetabolic Pathwaymalate_to_oxaloacetate_step

Regeneration of oxaloacetate from malate. Organisms may use an NAD-dependent malate dehydrogenase, one or more malate:quinone oxidoreductases, or both.

Annotons

NAD-dependent L-malate dehydrogenase
malate_dehydrogenase_nad_activity
Participant: Family: bacterial NAD-dependent malate dehydrogenase family
Family:
bacterial NAD-dependent malate dehydrogenase family
Representative Members: PSEPK Mdh exemplarUniProtKB:Q88Q44

Function

L-malate dehydrogenase (NAD+) activityGO:0030060
Substrates: (S)-malate NAD+
Products: oxaloacetate NADH
L-malate dehydrogenase (quinone)
malate_dehydrogenase_quinone_activity
Participant: Family: bacterial malate:quinone oxidoreductase family
Family:
bacterial malate:quinone oxidoreductase family
Representative Members: PSEPK Mqo1 exemplarUniProtKB:Q88PU7 PSEPK Mqo2 exemplarUniProtKB:Q88NF9 PSEPK Mqo3 exemplarUniProtKB:Q88IS4

Function

L-malate dehydrogenase (quinone) activityGO:0008924
Substrates: (S)-malate quinone
Products: oxaloacetate quinol