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 malate/oxaloacetate node and pyruvate carboxylase as an anaplerotic input to oxaloacetate.

MODULE:tca_cycleDRAFTMetabolic 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 is modeled as an 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.

13Nodes
12Parts
0Variant Sets
0Variants
12Annotons
0Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

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

Leaf nodes lacking representative members

11 leaf node(s) with no concrete protein grounding:

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (0/0 grounded genes reviewed)

No concrete UniProt-grounded genes in this module.

Details

Context
cytosolGO:0005829 plasma membraneGO:0005886
Tricarboxylic acid cycleMetabolic Pathwaytca_cycle
tricarboxylic acid cycleGO:0006099
Context
cytosolGO:0005829 plasma membraneGO:0005886
Part 1: acetyl-CoA entry
Citrate synthaseReactioncitrate_synthase_step

Annotons

Citrate synthase
citrate_synthase_activity
Participant: Any With Function: citrate synthase activity
Required Function:
citrate synthase activityGO:0036440

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: Any With Function: aconitate hydratase activity
Required Function:
aconitate hydratase activityGO:0003994

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: Any With Function: isocitrate dehydrogenase (NADP+) activity
Required Function:
isocitrate dehydrogenase (NADP+) activityGO:0004450

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: Any With Function: oxoglutarate dehydrogenase (succinyl-transferring) activity
Required Function:
oxoglutarate dehydrogenase (succinyl-transferring) activityGO:0004591

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: Any With Function: dihydrolipoyllysine-residue succinyltransferase activity
Required Function:
dihydrolipoyllysine-residue succinyltransferase activityGO:0004149

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: Any With Function: dihydrolipoyl dehydrogenase (NADH) activity
Required Function:
dihydrolipoyl dehydrogenase (NADH) activityGO:0004148

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: Any With Function: succinate-CoA ligase (ADP-forming) activity
Required Function:
succinate-CoA ligase (ADP-forming) activityGO:0004775

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: Any With Function: succinate dehydrogenase (quinone) activity
Required Function:
succinate dehydrogenase (quinone) activityGO:0008177

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: Any With Function: fumarate hydratase activity
Required Function:
fumarate hydratase activityGO:0004333

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: Any With Function: L-malate dehydrogenase (NAD+) activity
Required Function:
L-malate dehydrogenase (NAD+) activityGO:0030060

Function

L-malate dehydrogenase (NAD+) activityGO:0030060
Substrates: (S)-malate NAD+
Products: oxaloacetate NADH
L-malate dehydrogenase (quinone)
malate_dehydrogenase_quinone_activity
Participant: Any With Function: L-malate dehydrogenase (quinone) activity
Required Function:
L-malate dehydrogenase (quinone) activityGO:0008924

Function

L-malate dehydrogenase (quinone) activityGO:0008924
Substrates: (S)-malate quinone
Products: oxaloacetate quinol
Part 9: anaplerotic oxaloacetate input
Pyruvate carboxylaseReactionpyruvate_carboxylase_step

Annotons

Pyruvate carboxylase
pyruvate_carboxylase_activity
Participant: Any With Function: pyruvate carboxylase activity
Required Function:
pyruvate carboxylase activityGO:0004736

Function

pyruvate carboxylase activityGO:0004736
Substrates: pyruvate bicarbonate ATP
Products: oxaloacetate ADP phosphate

An anaplerotic entry into the oxaloacetate pool rather than a strict cyclic TCA reaction.