Q7VZI5 (locus BP0922) encodes a PrpF-family protein in Bordetella pertussis, the causative agent of whooping cough. The protein is predicted to function as a methylitaconate delta-isomerase (EC 5.3.3.6), catalyzing the interconversion of methylitaconate isomers within the 2-methylcitric acid cycle. This cycle enables bacteria to catabolize propionate as a carbon source by converting propionyl-CoA, via 2-methylcitrate and 2-methylaconitate intermediates, to pyruvate and succinate. The protein contains the conserved PrpF-like domain (InterPro IPR007400, Pfam PF04303) and adopts a diaminopimelate epimerase-like fold (SUPFAM SSF54506). No direct biochemical characterization exists for this specific protein; functional assignment is based on conserved domain architecture, family membership, and cross-species pathway reconstruction. The protein is predicted to be a soluble cytoplasmic enzyme.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0050100 methylitaconate delta-isomerase activity | ISS file:BORPE/Q7VZI5/Q7VZI5-deep-research-falcon.md | NEW | Summary: Q7VZI5 belongs to the PrpF family (Pfam PF04303, InterPro IPR007400) which is characterized as methylitaconate delta-isomerases. The protein name assigned by ProtNLM is 3-methylitaconate isomerase. This specific molecular function term captures the predicted catalytic activity more precisely than the broad IEA-derived GO:0016853 (isomerase activity). Reason: No curated annotation exists for this molecular function. The PrpF family assignment and domain architecture strongly support this specific isomerase activity. Should be annotated with ISS evidence based on sequence similarity to characterized PrpF enzymes. Supporting Evidence: file:BORPE/Q7VZI5/Q7VZI5-uniprot.txt RecName: Full=3-methylitaconate isomerase file:BORPE/Q7VZI5/Q7VZI5-uniprot.txt Belongs to the PrpF family |
| GO:0019543 propionate catabolic process | ISS file:BORPE/Q7VZI5/Q7VZI5-deep-research-falcon.md | NEW | Summary: PrpF-family isomerases function within the 2-methylcitric acid cycle, which is the primary bacterial pathway for propionate catabolism. Propionyl-CoA is converted through methylcitrate and methylaconitate intermediates to pyruvate and succinate, with PrpF catalyzing the isomerization step. Reason: The 2-methylcitric acid cycle is the established pathway context for PrpF enzymes. No specific GO term exists for the methylcitric acid cycle, so propionate catabolic process is the most appropriate biological process term. Supporting Evidence: file:BORPE/Q7VZI5/Q7VZI5-deep-research-falcon.md the 2-methylcitric acid cycle used for propionate catabolism |
| GO:0005737 cytoplasm | ISS file:BORPE/Q7VZI5/Q7VZI5-deep-research-falcon.md | NEW | Summary: PrpF-family proteins are soluble metabolic enzymes that function in the cytoplasm. No signal peptide, transmembrane domain, or extracytoplasmic localization signal has been identified for Q7VZI5. Reason: Cytoplasmic localization is consistent with the soluble nature of PrpF-family isomerases and the cytoplasmic location of the 2-methylcitric acid cycle. Supporting Evidence: file:BORPE/Q7VZI5/Q7VZI5-deep-research-falcon.md PrpF-family proteins function as soluble metabolic enzymes in central/intermediate metabolism and no evidence of secretion, membrane anchoring, or extracytoplasmic localization was identified |
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Download this section (compressed HTML)Q: Is the 2-methylcitric acid cycle active in Bordetella pertussis, and does BP0922 contribute to propionate-dependent growth?
Q: Does BP0922 catalyze the same reaction as characterized PrpF enzymes in E. coli and Salmonella, or has its substrate specificity diverged?
Experiment: Construct a delta-BP0922 mutant in B. pertussis Tohama I and compare growth on propionate versus glucose or other carbon sources. Complement with wild-type BP0922 to confirm the phenotype is gene-specific.
Hypothesis: BP0922 encodes a functional methylitaconate isomerase that is required for propionate utilization in B. pertussis.
Type: microbial growth assay
Experiment: Express and purify Q7VZI5 from E. coli, then assay isomerase activity using 2-methylaconitate or 3-methylitaconate as substrate, monitoring product formation by HPLC or spectrophotometry.
Hypothesis: Recombinant Q7VZI5 protein catalyzes the isomerization of methylitaconate isomers in vitro.
Type: in vitro enzyme kinetics
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
View prediction review YAML · Q7VZI5-protnlm-predictions-review.yaml · Review status: COMPLETE
ProtNLM2 made no predictions (GO or subcellular location) for PrpF family protein. The model returned only a protein name.
Source documents: genes/BORPE/Q7VZI5/Q7VZI5-uniprot.txt · genes/BORPE/Q7VZI5/Q7VZI5-goa.tsv
No GO/EC predictions in the reviewed source.
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