Bacterial L-carnitine catabolism through 3-dehydrocarnitine

A four-part aerobic bacterial pathway in which a Cbc-type ABC importer supplies L-carnitine, L-carnitine dehydrogenase forms 3-dehydrocarnitine, CdhC transfers a betainyl group to acetyl-CoA while releasing acetoacetate, and CdhB hydrolyzes betainyl-CoA to glycine betaine. The oxygenolytic CntAB route, anaerobic Cai reduction, compatible-solute retention, and downstream glycine-betaine demethylation are outside this boundary.

MODULE:bacterial_l_carnitine_catabolismDRAFTCONCRETEMetabolic Pathwaymodules/bacterial_l_carnitine_catabolism.yaml
carnitine catabolic processGO:0042413
PMID:19919675
The ATP-binding cassette transporter Cbc (choline/betaine/carnitine) recruits multiple substrate-binding proteins with strong specificity for distinct quaternary ammonium compounds.
Establishes CbcWV as a shared core importer and CaiX as the carnitine-specific substrate-binding protein required for carnitine uptake.
PMID:3058208
Purification and properties of carnitine dehydrogenase from Pseudomonas putida.
Directly establishes NAD-dependent L-carnitine oxidation in P. putida.
PMID:19406895
Identification of genes required for Pseudomonas aeruginosa carnitine catabolism.
Genetic evidence establishes the dehydrogenase locus, downstream cleavage genes, and glycine-betaine catabolism as required for carnitine utilization.
PMID:24240508
Revealing the hidden functional diversity of an enzyme family.
Biochemical screening establishes the exact CdhC and CdhB reactions used to convert 3-dehydrocarnitine to glycine betaine.
file:projects/P_PUTIDA/deep-research/PSEPK__bacterial_l_carnitine_catabolism__upa00117-deep-research-openscientist.md
OpenScientist PSEPK carnitine-catabolism synthesis
Species-aware retrieval identifies the conserved PP_0301-PP_0304 locus around lcdH, the adjacent CbcWV core, and the remaining uncertainty in KT2440 transporter specificity while distinguishing alternative carnitine fates.
file:modules/bacterial_l_carnitine_catabolism-exemplar-verification.md
UniProt accession verification for carnitine-catabolism exemplars
Records the official UniProt identities of PA5388/Q9HTH6, CdhC/Q9HTH7, and CdhB/Q9HTH9 and distinguishes accession identity from experimental functional evidence.

In KT2440, Q88R40/Q88R39 form the shared CbcWV core and Q88R30 is the carnitine-selective CaiX component; Q88R38 CbcX is instead the choline-binding component and is not required to define carnitine-specific uptake. The CdhC and CdhB assignments of Q88R31 and Q88R33 are strong orthology and conserved-locus transfers from the experimentally characterized P. aeruginosa proteins Q9HTH7 and Q9HTH9, but the KT2440 proteins remain untested directly.

5Nodes
4Parts
0Variant Sets
0Variants
4Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • bacterial_l_carnitine_catabolism-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 (5/8 grounded genes reviewed)

5 complete review(s) · 5 with deep research · 3 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
cbcV Q88R40 ✓ ✓ ✓
cbcW Q88R39 ✓ ✓ ✓
lcdH Q88R32 ✓ ✓ ✓
PP_0301 Q88R33 ✓ ✓ ✓
PP_0303 Q88R31 ✓ ✓ ✓
Pseudomonas aeruginosa PA5388 CaiX exemplar Q9HTH6 ✗ — —
Pseudomonas aeruginosa CdhC Q9HTH7 ✗ — —
Pseudomonas aeruginosa CdhB Q9HTH9 ✗ — —

Details

Bacterial L-carnitine catabolism through 3-dehydrocarnitineMetabolic Pathwaybacterial_l_carnitine_catabolism
carnitine catabolic processGO:0042413

Connections

cbc_carnitine_uptake -> lcdh_oxidation Provides Input For
lcdh_oxidation -> cdhc_cleavage Provides Input For
cdhc_cleavage -> cdhb_hydrolysis Provides Input For
Part 1: L-carnitine uptake
CaiX-CbcWV L-carnitine uptakeTransport Stepcbc_carnitine_uptake

Annotons

CaiX-CbcWV carnitine importer
cbc_carnitine_importer
Participant: Protein Complex: CaiX-CbcWV ABC importer
Protein Complex:
CaiX-CbcWV ABC importer
Active units:
CaiX carnitine-binding unit1
Participant: Ortholog Of: Pseudomonas aeruginosa PA5388 CaiX exemplar
Ortholog Of:
Pseudomonas aeruginosa PA5388 CaiX exemplarUniProtKB:Q9HTH6 Orthologs of P. aeruginosa PA5388, identified as CaiX by PMID:19919675, that retain CbcWV association.
Role: Captures L-carnitine in the periplasm and presents it to CbcW.
CbcW membrane unit2
Participant: Family: CbcW-like osmolyte ABC permeases
Family:
CbcW-like osmolyte ABC permeasesPANTHER:PTHR47737
Representative Members: PSEPK CbcWUniProtKB:Q88R39
Role: Forms the transmembrane path used by CaiX-bound carnitine.
CbcV ATP-coupling unit2
Participant: Family: CbcV-like osmolyte ABC ATPases
Family:
CbcV-like osmolyte ABC ATPasesPANTHER:PTHR43869
Representative Members: PSEPK CbcVUniProtKB:Q88R40
Role: Couples ATP hydrolysis to substrate import.

Function

carnitine transmembrane transporter activityGO:0015226
Substrates: L-carnitine (outside) ATP water
Products: L-carnitine (inside) ADP phosphate

Processes

carnitine transmembrane transportGO:1902603

Locations

plasma membraneGO:0005886

Imports L-carnitine for intracellular catabolism.

Part 2: L-carnitine oxidation
L-carnitine to 3-dehydrocarnitineReactionlcdh_oxidation

Annotons

L-carnitine dehydrogenase
lcdh_activity
Participant: Ortholog Of: PSEPK L-carnitine dehydrogenase LcdH
Ortholog Of:
PSEPK L-carnitine dehydrogenase LcdHUniProtKB:Q88R32 Orthologs retaining the L-carnitine dehydrogenase active site, NAD specificity, and carnitine-catabolism context.

Function

carnitine 3-dehydrogenase activityGO:0047728
Substrates: L-carnitine NAD+
Products: 3-dehydrocarnitine NADH proton

Processes

carnitine catabolic processGO:0042413

Produces the beta-keto substrate consumed by CdhC.

Part 3: 3-dehydrocarnitine cleavage
3-Dehydrocarnitine and acetyl-CoA to betainyl-CoA and acetoacetateReactioncdhc_cleavage

Annotons

3-Dehydrocarnitine:acetyl-CoA trimethylamine transferase
cdhc_activity
Participant: Family: Functionally heterogeneous BKACE SF2 constrained to CdhC activity
Family:
Functionally heterogeneous BKACE SF2 constrained to CdhC activityPANTHER:PTHR37418:SF2
Representative Members: PSEPK CdhC candidate PP_0303UniProtKB:Q88R31 Pseudomonas aeruginosa CdhCUniProtKB:Q9HTH7
Required Function:
3-dehydrocarnitine:acetyl-CoA trimethylamine transferase activity

Function

3-dehydrocarnitine:acetyl-CoA trimethylamine transferase activityGO:0016747
Substrates: 3-dehydrocarnitine acetyl-CoA
Products: N,N,N-trimethylglycyl-CoA (betainyl-CoA) acetoacetate

Processes

carnitine catabolic processGO:0042413

Couples carbon-chain cleavage to betainyl-CoA formation.

Part 4: glycine-betaine formation
Betainyl-CoA hydrolysis to glycine betaineReactioncdhb_hydrolysis

Annotons

Betainyl-CoA thioesterase
cdhb_activity
Participant: Family: CdhB betainyl-CoA thioesterase subfamily
Family:
CdhB betainyl-CoA thioesterase subfamilyPANTHER:PTHR31793:SF2
Representative Members: PSEPK CdhB candidate PP_0301UniProtKB:Q88R33 Pseudomonas aeruginosa CdhBUniProtKB:Q9HTH9
Required Function:
betainyl-CoA thioesterase activity

Function

betainyl-CoA thioesterase activityGO:0016289
Substrates: N,N,N-trimethylglycyl-CoA (betainyl-CoA) water
Products: glycine betaine CoA proton

Processes

carnitine catabolic processGO:0042413

Releases glycine betaine and regenerates free CoA.