2-methylcitrate cycle

A propionate-assimilation pathway that activates propionate to propionyl-CoA, condenses propionyl-CoA with oxaloacetate to form 2-methylcitrate, converts 2-methylcitrate to 2-methylisocitrate through alternative dehydration/isomerization implementations, and cleaves 2-methylisocitrate to succinate and pyruvate. The direct PrpD route is distinguished from the two-component AcnD/PrpF route, and the common aconitase-family hydration step is represented separately, with AcnB- and AcnA-family implementations. The pathway is widespread in proteobacteria and actinobacteria and is also present in fungal mitochondria.

MODULE:methylcitrate_cycleCOMPLETECONCRETEMetabolic Pathwaymodules/methylcitrate_cycle.yaml
propionate catabolic processGO:0019543
GO:0019543
propionate catabolic process
GO:0019543 provides the biological-process scope for catabolism of propionate through propionyl-CoA and the 2-methylcitrate pathway.
PMID:9325432
Propionate oxidation in Escherichia coli: evidence for operation of a methylcitrate cycle in bacteria.
Establishes that E. coli oxidises propionate to pyruvate through the methylcitrate cycle first described in fungi, with PrpC as the 2-methylcitrate synthase.
PMID:12473114
Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase.
Resolves the isomerization of 2-methylcitrate to 2-methylisocitrate in E. coli into the PrpD dehydration and AcnB hydration steps, and reports that acetyl-CoA synthetase can replace PrpE for propionate activation.
PMID:11294638
In vitro conversion of propionate to pyruvate by Salmonella enterica enzymes: 2-methylcitrate dehydratase (PrpD) and aconitase Enzymes catalyze the conversion of 2-methylcitrate to 2-methylisocitrate.
Reconstitutes the complete cycle in vitro from homogeneous PrpE, PrpC, PrpD, AcnA and PrpB, and shows that AcnA and AcnB are redundant for the hydration step.
PMID:14702315
The acnD genes of Shewenella oneidensis and Vibrio cholerae encode a new Fe/S-dependent 2-methylcitrate dehydratase enzyme that requires prpF function in vivo.
Defines the AcnD/PrpF alternative to PrpD: together, but not separately, AcnD and PrpF restore growth of a Salmonella prpD mutant on propionate.
PMID:29145506
The PrpF protein of Shewanella oneidensis MR-1 catalyzes the isomerization of 2-methyl-cis-aconitate during the catabolism of propionate via the AcnD-dependent 2-methylcitric acid cycle.
Shows that PrpF isomerizes the AcnD product into 2-methyl-cis-aconitate, the substrate of the housekeeping aconitase, and assigns 4-methylaconitate as the probable AcnD product.
PMID:11422389
2-Methylisocitrate lyases from the bacterium Escherichia coli and the filamentous fungus Aspergillus nidulans: characterization and comparison of both enzymes.
Identifies E. coli PrpB as the 2-methylisocitrate lyase that cleaves threo-2-methylisocitrate to succinate and pyruvate.
file:PSEPK/prpC/prpC-ai-review.yaml
PSEPK prpC gene review
The curated KT2440 review identifies Q88KF5 as the 2-methylcitrate synthase rather than the housekeeping TCA citrate synthase.
file:PSEPK/acnB/acnB-ai-review.yaml
PSEPK acnB gene review
The curated KT2440 review identifies Q88KF1 as a bifunctional aconitase with a core 2-methylisocitrate dehydratase/hydratase role in propionate assimilation.
file:PSEPK/prpD/prpD-uniprot.txt
UniProtKB entry Q88KF2 for PSEPK PrpD
UniProt records the direct 2-methylcitrate to 2-methyl-cis-aconitate dehydration reaction for Q88KF2.
file:PSEPK/prpF/prpF-uniprot.txt
UniProtKB entry Q88KF3 for PSEPK PrpF
UniProt places the PrpF-family aconitate isomerase Q88KF3 in propionate degradation.
file:projects/P_PUTIDA/deep-research/PSEPK__methylcitrate_cycle__ppu00640-deep-research-openscientist.md
OpenScientist PSEPK 2-methylcitrate-cycle pathway report
The pathway-level family and locus analysis resolves PP_2336 as AcnD, confirms that both dehydration implementations coexist in KT2440, and identifies both AcnA-I and AcnB as candidate enzymes for the common hydration step.
file:modules/methylcitrate_cycle-deep-research-openscientist.md
OpenScientist review of the 2-methylcitrate cycle
The generic module review supports modeling the direct PrpD and two-component AcnD/PrpF routes as alternative implementations that converge before a shared aconitase step. It also cautions that the exact AcnD product structure is not established uniformly across systems.
12Nodes
7Parts
2Variant Sets
4Variants
8Annotons
5Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • methylcitrate_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.

Function consistency and core coverage

15 gene-function check(s) reflected in core functions · 0 conflict(s) · 2 evidence or coverage gap(s) (23 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
propionate_coa_ligase PrpE (ECOLI)
UniProtKB:P77495
Family Representative 		propionate-CoA ligase activity
GO:0050218 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
propionate_coa_ligase PrpE (PSEPK)
UniProtKB:Q88KD9
Family Representative 		propionate-CoA ligase activity
GO:0050218 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
methylcitrate_synthase PrpC (ECOLI)
UniProtKB:P31660
Family Representative 		2-methylcitrate synthase activity
GO:0050440 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
methylcitrate_synthase PrpC (PSEPK)
UniProtKB:Q88KF5
Family Representative 		2-methylcitrate synthase activity
GO:0050440 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
prpD_methylcitrate_dehydratase PrpD (ECOLI)
UniProtKB:P77243
Family Representative 		2-methylcitrate dehydratase activity
GO:0047547 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
prpD_methylcitrate_dehydratase PrpD (PSEPK)
UniProtKB:Q88KF2
Family Representative 		2-methylcitrate dehydratase activity
GO:0047547 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
acnD_pathway_dehydratase AcnD (SHEON)
UniProtKB:Q8EJW3
Family Representative 		hydro-lyase activity
GO:0016836 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
acnD_pathway_dehydratase AcnD (PSEPK)
UniProtKB:Q88KF4
Family Representative 		hydro-lyase activity
GO:0016836 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
prpF_aconitate_isomerase PrpF (SHEON)
UniProtKB:Q8EJW4
Family Representative 		intramolecular oxidoreductase activity, transposing C=C bonds
GO:0016863 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
prpF_aconitate_isomerase PrpF (PSEPK)
UniProtKB:Q88KF3
Family Representative 		intramolecular oxidoreductase activity, transposing C=C bonds
GO:0016863 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
acnB_methylisocitrate_hydratase AcnB (ECOLI)
UniProtKB:P36683
Family Representative 		2-methylisocitrate dehydratase activity
GO:0047456 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
acnB_methylisocitrate_hydratase AcnB (PSEPK)
UniProtKB:Q88KF1
Family Representative 		2-methylisocitrate dehydratase activity
GO:0047456 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
acnA_methylisocitrate_hydratase AcnA (SALTY)
UniProtKB:Q8ZP52
Family Representative 		2-methylisocitrate dehydratase activity
GO:0047456 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
methylisocitrate_lyase PrpB (ECOLI)
UniProtKB:P77541
Family Representative 		methylisocitrate lyase activity
GO:0046421 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
methylisocitrate_lyase PrpB (PSEPK)
UniProtKB:Q88KF6
Family Representative 		methylisocitrate lyase activity
GO:0046421 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
propionate_coa_ligase PrpE-family propionate-CoA ligases
PANTHER:PTHR43347
Family 		propionate-CoA ligase activity
GO:0050218 		Family Supported
Family review supports GO:0050218 FAMILY_WIDE. Experimental propionate activation in both major lineages (PrpE and ACSS3) and a PAINT IBD at their common node support the activity across the family. Substrate promiscuity toward acetate does not contradict it.
methylcitrate_synthase PrpC-type 2-methylcitrate synthases
PANTHER:PTHR11739:SF25
Family 		2-methylcitrate synthase activity
GO:0050440 		Family Supported
Family review supports GO:0050440 for PANTHER:PTHR11739:SF25. 2-Methylcitrate synthase: PrpC (SF25) and dual-specificity CIT3 (SF15).
prpD_methylcitrate_dehydratase PrpD 2-methylcitrate dehydratases
PANTHER:PTHR16943:SF8
Family 		2-methylcitrate dehydratase activity
GO:0047547 		Family Supported
Family review supports GO:0047547 for PANTHER:PTHR16943:SF8. Established biochemically for bacterial PrpD (E. coli, Salmonella) in SF8, and probable for the fungal PDH1-type proteins in SF16. PAINT asserts no node for this activity. The fungal cis-aconitate decarboxylases (CAD1, oryM) inside SF8 are exceptions, so the term should be transferred only to SF8 members with PrpD-type operon or pathway context.
acnD_pathway_dehydratase AcnD-family 2-methylcitrate dehydratases
NCBIfam:TIGR02333
Family 		hydro-lyase activity
GO:0016836 		Family Review Missing
No supported structured family review is available for NCBIfam:TIGR02333.
prpF_aconitate_isomerase PrpF methylaconitate isomerases
PANTHER:PTHR43709:SF2
Family 		intramolecular oxidoreductase activity, transposing C=C bonds
GO:0016863 		Family Supported
Family review supports GO:0016863 for PANTHER:PTHR43709:SF2. C=C-transposing isomerase activity holds for the PrpF-type members of SF2 and for the LigU-type allylic isomerase of SF3. It does not hold for the GalD-type keto-enol tautomerases in SF3, listed as a member exception. The specific reaction and substrate differ by member and are not family-wide.
acnB_methylisocitrate_hydratase AcnB-family aconitate hydratases with methylisocitrate activity
PANTHER:PTHR43160:SF4
Family 		2-methylisocitrate dehydratase activity
GO:0047456 		Family Supported
Family review supports GO:0047456 for PANTHER:PTHR43160:SF4. Demonstrated for bacterial AcnB (E. coli, Salmonella) and asserted by PAINT only at the bacterial node; eukaryotic mitochondrial aconitases are not covered by this evidence.
acnA_methylisocitrate_hydratase AcnA-family aconitate hydratases with methylisocitrate activity
NCBIfam:TIGR01341
Family 		2-methylisocitrate dehydratase activity
GO:0047456 		Family Review Missing
No supported structured family review is available for NCBIfam:TIGR01341.
methylisocitrate_lyase PrpB 2-methylisocitrate lyases
PANTHER:PTHR42905:SF5
Family 		methylisocitrate lyase activity
GO:0046421 		Family Supported
Family review supports GO:0046421 for PANTHER:PTHR42905:SF5. Experimentally established for the PrpB enzymes of SF5 only; the other subfamilies catalyse different reactions.

Gene-review completeness (15/15 grounded genes reviewed)

15 complete review(s) · 7 with deep research · 0 missing review · 8 reviewed but lacking deep research

Gene Review Complete Deep research
acnA Q8ZP52 ✓ ✓ ✗
acnA-II Q88KF4 ✓ ✓ ✓
acnB P36683 ✓ ✓ ✗
acnB Q88KF1 ✓ ✓ ✓
acnD Q8EJW3 ✓ ✓ ✗
prpB P77541 ✓ ✓ ✗
prpB Q88KF6 ✓ ✓ ✓
prpC P31660 ✓ ✓ ✗
prpC Q88KF5 ✓ ✓ ✓
prpD P77243 ✓ ✓ ✗
prpD Q88KF2 ✓ ✓ ✓
prpE P77495 ✓ ✓ ✗
prpE Q88KD9 ✓ ✓ ✓
prpF Q88KF3 ✓ ✓ ✓
prpF Q8EJW4 ✓ ✓ ✗

Details

2-methylcitrate cycleMetabolic Pathwaymethylcitrate_cycle
propionate catabolic processGO:0019543

The root is deliberately multi-part and taxon-neutral. Representative members are drawn from organisms where each step was characterized biochemically or genetically: Escherichia coli K-12 (PrpE, PrpC, PrpD, AcnB, PrpB), Salmonella enterica LT2 (AcnA), and Shewanella oneidensis MR-1 (AcnD, PrpF), together with Pseudomonas putida KT2440, which encodes both dehydration routes. Family descriptors are grounded at the PANTHER subfamily that holds the pathway enzymes wherever the family review restricts the activity to that subfamily. The fungal mitochondrial cycle (for example, yeast CIT3 in citrate synthase subfamily SF15, and a 2-methylisocitrate lyase of the isocitrate lyase family) uses enzymes outside these bacterial subfamilies, so it is noted but not separately modeled. PrpD and AcnD/PrpF are modeled with ONE_OR_MORE semantics because organisms may encode either or both routes (KT2440 and Ralstonia eutropha encode both; PMID:14702315). The common hydration step likewise allows AcnA- and AcnB-family implementations, which coexist in enteric bacteria and are redundant there. E. coli AcnA is not used as an exemplar because its 2-methylisocitrate dehydratase activity has not been shown directly. KT2440 AcnA-I (Q88L24) is a candidate for the AcnA route only by orthology, so it is also not listed. The AcnD product is represented generically: 4-methylaconitate is the leading assignment, but the exact structure and stereochemistry are not established uniformly across organisms. Propionate activation is not exclusive to PrpE; in E. coli, acetyl-CoA synthetase can substitute.

Connections

Propionyl-CoA is the acyl donor for 2-methylcitrate synthesis.
2-methylcitrate enters either dehydration implementation.
Both alternatives converge on 2-methyl-cis-aconitate.
2-methylisocitrate is the substrate cleaved by PrpB.
Part 1: propionate activation
Propionate activation to propionyl-CoAReactionpropionate_activation

Annotons

Propionate-CoA ligase
propionate_coa_ligase
Participant: Family: PrpE-family propionate-CoA ligases
Family:
PrpE-family propionate-CoA ligasesPANTHER:PTHR43347
Representative Members: PrpE (ECOLI)UniProtKB:P77495 PrpE (PSEPK)UniProtKB:Q88KD9

Function

propionate-CoA ligase activityGO:0050218
Substrates: propionate CoA ATP
Products: propionyl-CoA AMP diphosphate

Supplies the propionyl-CoA substrate used by 2-methylcitrate synthase. Nonorthologous activation routes, such as acetyl-CoA synthetase in E. coli, require separate pathway-instance adjudication.

Part 2: 2-methylcitrate formation
2-methylcitrate synthesisReactionmethylcitrate_synthesis

Annotons

2-methylcitrate synthase
methylcitrate_synthase
Participant: Family: PrpC-type 2-methylcitrate synthases
Family:
PrpC-type 2-methylcitrate synthasesPANTHER:PTHR11739:SF25 Bacterial PrpC enzymes form PANTHER subfamily SF25 of the citrate synthase family (PANTHER's subfamily name notwithstanding). The dual-specificity fungal mitochondrial CIT3-type enzymes (SF15) are a separate eukaryotic implementation and are not grounded here.
Representative Members: PrpC (ECOLI)UniProtKB:P31660 PrpC (PSEPK)UniProtKB:Q88KF5

Function

2-methylcitrate synthase activityGO:0050440
Substrates: propionyl-CoA oxaloacetate H2O
Products: 2-methylcitrate CoA

Condenses propionyl-CoA and oxaloacetate to commit carbon to the cycle.

Part 3: 2-methyl-cis-aconitate generation
Conversion of 2-methylcitrate to 2-methyl-cis-aconitateMetabolic Pathwaymethylaconitate_generation

Alternative direct and two-component implementations produce the 2-methyl-cis-aconitate substrate used by the common hydration step.

Variant set: 2-methylcitrate dehydration implementations by reaction mechanism (One Or More)
Direct PrpD routeReactionprpD_direct_route

Annotons

PrpD 2-methylcitrate dehydratase
prpD_methylcitrate_dehydratase
Participant: Family: PrpD 2-methylcitrate dehydratases
Family:
PrpD 2-methylcitrate dehydratasesPANTHER:PTHR16943:SF8 PrpD enzymes form PANTHER subfamily SF8 of the MmgE/PrpD family, which also contains cis-aconitate decarboxylases; family membership alone does not establish this activity.
Representative Members: PrpD (ECOLI)UniProtKB:P77243 PrpD (PSEPK)UniProtKB:Q88KF2

Function

2-methylcitrate dehydratase activityGO:0047547
Substrates: 2-methylcitrate
Products: 2-methyl-cis-aconitate H2O

Directly dehydrates (2S,3S)-2-methylcitrate to 2-methyl-cis-aconitate by a syn elimination.

Two-component AcnD/PrpF routeMetabolic PathwayacnD_prpF_route

An aconitase-family dehydratase first forms a positional methylaconitate isomer, which PrpF rearranges to 2-methyl-cis-aconitate.

Connections

acnD_dehydration -> prpF_isomerization Provides Input For
The AcnD product is the substrate rearranged by PrpF.
Part 1: AcnD-dependent dehydration
AcnD-family 2-methylcitrate dehydrationReactionacnD_dehydration

Annotons

AcnD 2-methylcitrate dehydratase
acnD_pathway_dehydratase
Participant: Family: AcnD-family 2-methylcitrate dehydratases
Family:
AcnD-family 2-methylcitrate dehydratasesNCBIfam:TIGR02333 AcnD forms a diverged lineage within the AcnA-type aconitase family (PANTHER PTHR11670), lacking isocitrate and 2-methylisocitrate activity despite the NCBIfam model name. PTHR11670 assigns no subfamilies and also contains the canonical aconitases and iron-regulatory proteins, so the AcnD-specific NCBIfam model is used to ground this role.
Representative Members: AcnD (SHEON)UniProtKB:Q8EJW3 AcnD (PSEPK)UniProtKB:Q88KF4

Function

hydro-lyase activityGO:0016836
Substrates: 2-methylcitrate
Products: AcnD-derived methylaconitate isomer H2O
Cofactors: 4 iron, 4 sulfur cluster

Dehydrates 2-methylcitrate to the methylaconitate isomer used by PrpF. GO lacks an AcnD-specific product-resolved molecular-function term, so the available hydro-lyase parent is used.

Part 2: methylaconitate isomerization
PrpF methylaconitate isomerizationReactionprpF_isomerization

Annotons

PrpF aconitate isomerase
prpF_aconitate_isomerase
Participant: Family: PrpF methylaconitate isomerases
Family:
PrpF methylaconitate isomerasesPANTHER:PTHR43709:SF2
Representative Members: PrpF (SHEON)UniProtKB:Q8EJW4 PrpF (PSEPK)UniProtKB:Q88KF3

Function

intramolecular oxidoreductase activity, transposing C=C bondsGO:0016863
Substrates: AcnD-derived methylaconitate isomer
Products: 2-methyl-cis-aconitate

Converts the AcnD product (probably 4-methyl-cis-aconitate) to 2-methyl-cis-aconitate by moving the C=C bond. GO lacks a methylaconitate-specific isomerase term (a 'methylaconitate isomerase activity' term is proposed in the PrpF gene reviews), so the C=C-transposing parent is used.

Part 4: 2-methylisocitrate formation
2-methyl-cis-aconitate hydrationReactionmethylisocitrate_formation
Variant set: Aconitase-family hydration implementations by aconitase paralog family (One Or More)
AcnB-family hydrationReactionacnB_hydration_route

Annotons

AcnB-family 2-methylisocitrate hydratase
acnB_methylisocitrate_hydratase
Participant: Family: AcnB-family aconitate hydratases with methylisocitrate activity
Family:
AcnB-family aconitate hydratases with methylisocitrate activityPANTHER:PTHR43160:SF4
Representative Members: AcnB (ECOLI)UniProtKB:P36683 AcnB (PSEPK)UniProtKB:Q88KF1

Function

2-methylisocitrate dehydratase activityGO:0047456
Substrates: 2-methyl-cis-aconitate H2O
Products: 2-methylisocitrate
Cofactors: 4 iron, 4 sulfur cluster

Uses the reversible aconitase-family reaction in the hydration direction to form the PrpB substrate.

AcnA-family hydrationReactionacnA_hydration_route

Annotons

AcnA-family 2-methylisocitrate hydratase
acnA_methylisocitrate_hydratase
Participant: Family: AcnA-family aconitate hydratases with methylisocitrate activity
Family:
AcnA-family aconitate hydratases with methylisocitrate activityNCBIfam:TIGR01341 AcnA-type aconitases (NCBIfam TIGR01341) within PANTHER PTHR11670. The PANTHER family is not used here because it has no subfamilies and also contains AcnD and the iron-regulatory proteins. Hydration of 2-methyl-cis-aconitate is shown for Salmonella AcnA and should be transferred only with organism-specific evidence.
Representative Members: AcnA (SALTY)UniProtKB:Q8ZP52

Function

2-methylisocitrate dehydratase activityGO:0047456
Substrates: 2-methyl-cis-aconitate H2O
Products: 2-methylisocitrate
Cofactors: 4 iron, 4 sulfur cluster

Provides a second aconitase-family implementation of the reversible hydration step where AcnA retains this substrate range.

Part 5: carbon-carbon cleavage
2-methylisocitrate cleavageReactionmethylisocitrate_cleavage

Annotons

2-methylisocitrate lyase
methylisocitrate_lyase
Participant: Family: PrpB 2-methylisocitrate lyases
Family:
PrpB 2-methylisocitrate lyasesPANTHER:PTHR42905:SF5 PrpB enzymes form PANTHER subfamily SF5 of the isocitrate lyase/PEP mutase family PTHR42905 (PANTHER's family and subfamily names notwithstanding); other subfamilies are oxaloacetate decarboxylases and PEP phosphomutases.
Representative Members: PrpB (ECOLI)UniProtKB:P77541 PrpB (PSEPK)UniProtKB:Q88KF6

Function

methylisocitrate lyase activityGO:0046421
Substrates: 2-methylisocitrate
Products: succinate pyruvate
Cofactors: magnesium ion

Cleaves 2-methylisocitrate to succinate and pyruvate, returning the oxaloacetate-derived carbon skeleton to central metabolism.