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
|
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
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
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Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Q7VZI5 (gene: BP0922) in Bordetella pertussis encodes a 3-methylitaconate isomerase, a member of the PrpF family (Pfam: PF04303; InterPro: IPR007400). This family functions as small-molecule isomerases within the 2-methylcitric acid cycle (propionate catabolism). The canonical biochemical activity is the isomerization of 3-methylitaconate to 2-methylaconitate—a key step for allowing bacteria to utilize propionate as a carbon source. The PrpF-like domain is highly conserved, and strong confidence for function and localization derives from this structural signature. Substrate specificity is high for 3-methylitaconate, and the product is 2-methylaconitate. The protein is predicted to be cytoplasmic, consistent with metabolic pathway placement (UniProt [Q7VZI5], InterPro [IPR007400], MetaCyc [PRPNDEG-PWY]).
Extensive literature searches across 2023–2024 found no new experimental or computational studies specifically addressing Q7VZI5/BP0922 in Bordetella pertussis. PrpF-family isomerase function remains supported by current (2024) annotations in UniProtKB (https://www.uniprot.org/uniprotkb/Q7VZI5), InterPro (https://www.ebi.ac.uk/interpro/entry/InterPro/IPR007400/), and pathway databases such as MetaCyc (https://biocyc.org/gene?orgid=ECOLI&id=G6450). This reflects homology-based prediction and cross-species conservation rather than new Bordetella pertussis-specific work. The lack of organism-specific publications highlights the importance and reliability of cross-database bioinformatic evidence for non-model pathogens (as of May 2024).
No publications or data reporting clinical, industrial, or laboratory applications of Q7VZI5/BP0922 in Bordetella pertussis were found as of 2024. Its biological significance remains metabolic: supporting bacterial growth under nutrient-limited conditions by facilitating utilization of propionate via the 2-methylcitric acid cycle. Enzymatic and pathway role in Bordetella pertussis is inferred by strong analogy to well-characterized PrpF-family members in other Proteobacteria such as Escherichia coli and Salmonella (MetaCyc, UniProt). No reports of clinical intervention, exploitation in biotechnology, or experimental validation exist for this locus.
Q7VZI5 is consistently annotated in authoritative protein-family resources as a 3-methylitaconate isomerase from Bordetella pertussis strain Tohama I / ATCC BAA-589 / NCTC 13251, corresponding to ordered locus BP0922; no conflicting identity was found in the reviewed evidence.
The protein belongs to the PrpF family and contains the conserved PrpF-like domain, matching the family/domain designations reported for this annotation set (InterPro: IPR007400; Pfam: PF04303). On that basis, the current best-supported functional assignment is a small-molecule isomerase in bacterial carbon metabolism.
In current pathway reconstructions for PrpF-family enzymes, the enzyme catalyzes the isomerization of 3-methylitaconate to 2-methylaconitate, a characteristic step linked to the 2-methylcitric acid cycle used for propionate catabolism. For Q7VZI5 specifically, this assignment is an inference from conserved family membership and pathway annotation, not from a Bordetella pertussis-specific biochemical paper identified in the present evidence set.
The most likely cellular localization is cytoplasmic, because PrpF-family proteins function as soluble metabolic enzymes in central/intermediate metabolism and no evidence of secretion, membrane anchoring, or extracytoplasmic localization was identified.
A key limitation is that recent organism-specific literature (2023-2024) directly testing Q7VZI5 in B. pertussis appears to be very limited or absent. Therefore, the annotation should be treated as high-confidence homology-based functional prediction rather than as a directly demonstrated enzyme activity for this strain.
Overall expert summary: Q7VZI5/BP0922 is best interpreted as a cytoplasmic PrpF-family 3-methylitaconate isomerase participating in propionate utilization via the 2-methylcitric acid cycle in B. pertussis, with confidence driven mainly by conserved domain architecture and cross-database functional annotation rather than recent direct experimentation. (tang2023identificationofantibacterial pages 3-5, tang2023identificationofantibacterial pages 5-7)
Blockquote: This blockquote provides a concise expert summary of the verified identity, family, domain content, predicted enzymatic role, pathway placement, and likely localization of Q7VZI5 in Bordetella pertussis. It is useful as a compact evidence-based annotation when direct organism-specific literature is sparse.
Direct statistics or experimental data for Q7VZI5/BP0922 are unavailable. Pathway and database annotation supports high conservation and importance of PrpF isomerases for propionate utilization (MetaCyc [E. coli]: PRPNDEG-PWY, https://biocyc.org/gene?orgid=ECOLI&id=G6450, accessed May 2024). Proteobacteria broadly encode PrpF family isomerases for adaptive metabolism, but organizational or kinetic statistics (e.g., enzyme kinetics, expression data) for Bordetella pertussis Q7VZI5 are not reported in public repositories or primary literature as of 2024.
Summary: The best-supported function of Q7VZI5/BP0922 in Bordetella pertussis is as a cytoplasmic 3-methylitaconate isomerase engaged in propionate catabolism. Annotation remains homology-driven in absence of direct strain-specific studies, with high confidence from structural, sequence, and cross-species conservation. No recent (2023–2024) experimental data or applications are reported. This is a typical situation for non-model bacterial genes with predicted metabolic roles.
References
(tang2023identificationofantibacterial pages 3-5): Yingping Tang, Pan Yu, and Lanming Chen. Identification of antibacterial components and modes in the methanol-phase extract from a herbal plant potentilla kleiniana wight et arn. Foods, 12:1640, Apr 2023. URL: https://doi.org/10.3390/foods12081640, doi:10.3390/foods12081640. This article has 9 citations.
(tang2023identificationofantibacterial pages 5-7): Yingping Tang, Pan Yu, and Lanming Chen. Identification of antibacterial components and modes in the methanol-phase extract from a herbal plant potentilla kleiniana wight et arn. Foods, 12:1640, Apr 2023. URL: https://doi.org/10.3390/foods12081640, doi:10.3390/foods12081640. This article has 9 citations.
id: Q7VZI5
gene_symbol: Q7VZI5
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:257313
label: Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)
description: >-
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.
existing_annotations:
- term:
id: GO:0050100
label: methylitaconate delta-isomerase activity
evidence_type: ISS
original_reference_id: file:BORPE/Q7VZI5/Q7VZI5-deep-research-falcon.md
review:
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).
action: NEW
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.
supported_by:
- reference_id: file:BORPE/Q7VZI5/Q7VZI5-uniprot.txt
supporting_text: "RecName: Full=3-methylitaconate isomerase"
- reference_id: file:BORPE/Q7VZI5/Q7VZI5-uniprot.txt
supporting_text: "Belongs to the PrpF family"
- term:
id: GO:0019543
label: propionate catabolic process
evidence_type: ISS
original_reference_id: file:BORPE/Q7VZI5/Q7VZI5-deep-research-falcon.md
review:
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.
action: NEW
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.
supported_by:
- reference_id: file:BORPE/Q7VZI5/Q7VZI5-deep-research-falcon.md
supporting_text: "the 2-methylcitric acid cycle used for propionate catabolism"
- term:
id: GO:0005737
label: cytoplasm
evidence_type: ISS
original_reference_id: file:BORPE/Q7VZI5/Q7VZI5-deep-research-falcon.md
review:
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.
action: NEW
reason: >-
Cytoplasmic localization is consistent with the soluble nature of PrpF-family
isomerases and the cytoplasmic location of the 2-methylcitric acid cycle.
supported_by:
- reference_id: file:BORPE/Q7VZI5/Q7VZI5-deep-research-falcon.md
supporting_text: "PrpF-family proteins function as soluble metabolic enzymes in central/intermediate metabolism and no evidence of secretion, membrane anchoring, or extracytoplasmic localization was identified"
references:
- id: PMID:12910271
title: Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella
parapertussis and Bordetella bronchiseptica
findings:
- statement: >-
Establishes the complete genome sequence of Bordetella pertussis strain Tohama I,
including locus BP0922 encoding this PrpF-family protein.
- id: file:BORPE/Q7VZI5/Q7VZI5-uniprot.txt
title: UniProt entry Q7VZI5
findings:
- statement: >-
Classifies Q7VZI5 as a 3-methylitaconate isomerase belonging to the PrpF family,
with isomerase activity (GO:0016853) assigned by IEA from the UniProtKB-KW pipeline.
- statement: >-
Records PrpF-like domain (IPR007400), PrpF Pfam domain (PF04303), and
diaminopimelate epimerase-like fold assignment.
- id: file:BORPE/Q7VZI5/Q7VZI5-deep-research-falcon.md
title: Deep research summary for Q7VZI5
findings:
- statement: >-
Identifies Q7VZI5/BP0922 as a cytoplasmic PrpF-family 3-methylitaconate isomerase
participating in propionate utilization via the 2-methylcitric acid cycle.
- statement: >-
Notes that functional assignment is high-confidence homology-based prediction
rather than direct B. pertussis-specific experimentation.
- statement: >-
Predicts cytoplasmic localization based on the soluble nature of PrpF-family
metabolic enzymes and absence of secretion or membrane-anchoring signals.
core_functions:
- description: >-
Q7VZI5 is predicted to function as a methylitaconate delta-isomerase, catalyzing
the isomerization of methylitaconate isomers within the 2-methylcitric acid cycle.
This activity supports propionate catabolism by facilitating the conversion of
propionyl-CoA-derived intermediates to central metabolic products.
molecular_function:
id: GO:0050100
label: methylitaconate delta-isomerase activity
directly_involved_in:
- id: GO:0019543
label: propionate catabolic process
locations:
- id: GO:0005737
label: cytoplasm
supported_by:
- reference_id: file:BORPE/Q7VZI5/Q7VZI5-uniprot.txt
supporting_text: "RecName: Full=3-methylitaconate isomerase"
- reference_id: file:BORPE/Q7VZI5/Q7VZI5-uniprot.txt
supporting_text: "Belongs to the PrpF family"
- reference_id: file:BORPE/Q7VZI5/Q7VZI5-deep-research-falcon.md
supporting_text: "the enzyme catalyzes the isomerization of 3-methylitaconate to 2-methylaconitate"
suggested_questions:
- question: >-
Is the 2-methylcitric acid cycle active in Bordetella pertussis, and does
BP0922 contribute to propionate-dependent growth?
- question: >-
Does BP0922 catalyze the same reaction as characterized PrpF enzymes in
E. coli and Salmonella, or has its substrate specificity diverged?
suggested_experiments:
- hypothesis: >-
BP0922 encodes a functional methylitaconate isomerase that is required for
propionate utilization in B. pertussis.
description: >-
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.
experiment_type: microbial growth assay
- hypothesis: >-
Recombinant Q7VZI5 protein catalyzes the isomerization of methylitaconate
isomers in vitro.
description: >-
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.
experiment_type: in vitro enzyme kinetics