PrpD is the 2-methylcitrate dehydratase of Pseudomonas putida KT2440. It catalyzes the cofactor-independent dehydration of (2S,3S)-2-methylcitrate to 2-methyl-cis-aconitate in the methylcitrate cycle for propionate catabolism. A separate aconitase catalyzes the subsequent hydration to 2-methylisocitrate.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0016829 lyase activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: Correct but uninformative parent-level description of the catalytic activity. Reason: PrpD belongs to the NCBIfam TIGR02330 PrpD (2-methylcitrate dehydratase) family with a defined EC 4.2.1.79 reaction. Lyase activity is true but is entailed by the 2-methylcitrate dehydratase activity asserted in this review, matching the E. coli prpD review. Supporting Evidence: file:PSEPK/prpD/prpD-uniprot.txt NCBIfam; TIGR02330; prpD; 1. |
| GO:0019543 propionate catabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: Correct process annotation for the PrpD reaction in the methylcitrate cycle. Reason: The pathway report places Q88KF2 at the direct dehydration step of the 2-methylcitrate cycle of propionate catabolism, and biochemical work on the orthologous pathway identifies PrpD as the dehydratase required for conversion of 2-methylcitrate toward 2-methylisocitrate. Supporting Evidence: file:projects/P_PUTIDA/deep-research/PSEPK__methylcitrate_cycle__ppu00640-deep-research-openscientist.md 3. Dehydration of 2-methylcitrate → **2-methyl-*cis*-aconitate** — PrpD (direct) **or** AcnD+PrpF (two-component). PMID:11294638 This work shows that the prpD gene of the prpBCDE operon of this bacterium encodes a protein with 2-methylcitrate dehydratase enzyme activity. file:PSEPK/prpD/prpD-deep-research-openscientist.md The gene **prpD** (locus tag **PP_2338**; UniProt **Q88KF2**) of *Pseudomonas putida* strain KT2440 encodes **2-methylcitrate dehydratase (EC 4.2.1.79)** |
| GO:0047547 2-methylcitrate dehydratase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Correct and specific core molecular function. Reason: The exact target is classified in the NCBIfam TIGR02330 PrpD 2-methylcitrate dehydratase family (InterPro IPR012705). Purified Salmonella PrpD directly catalyzes the same reaction. Supporting Evidence: file:PSEPK/prpD/prpD-uniprot.txt NCBIfam; TIGR02330; prpD; 1. PMID:11294638 This work shows that the prpD gene of the prpBCDE operon of this bacterium encodes a protein with 2-methylcitrate dehydratase enzyme activity. |
| GO:0051537 2 iron, 2 sulfur cluster binding | IEA GO_REF:0000002 | REMOVE | Summary: Incorrect InterPro-derived cofactor annotation for the PrpD family. Reason: PrpD is mechanistically distinct from aconitases. Purified PrpD was shown not to contain an iron-sulfur center and not to require metal ions or reducing agents, directly contradicting this electronic annotation. Supporting Evidence: PMID:11294638 Homogeneous PrpD enzyme did not contain an iron-sulfur center, displayed no requirements for metal cations or reducing agents for activity |
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Download this section (compressed HTML)Q: Under which carbon sources does KT2440 use PrpD rather than the adjacent AcnD/PrpF-like route for conversion of 2-methylcitrate to 2-methylisocitrate?
Experiment: Compare growth, pathway-intermediate accumulation, and isotope flux in prpD, acnD-like, prpF, and combined mutants during growth on propionate and odd-chain carbon sources.
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