Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0000287 magnesium ion binding	IEA GO_REF:0000104	ACCEPT	Summary: PEPC requires Mg2+ as a catalytic cofactor; the UniProt record lists Mg(2+) as the cofactor (HAMAP MF_00595). Correct molecular function for this enzyme. Reason: Mg2+ is the established divalent metal cofactor of PEPCase type 1 enzymes, consistent with the conserved active-site residues and the family assignment.
GO:0005829 cytosol	IEA GO_REF:0000118	ACCEPT	Summary: PEPC is a soluble enzyme of central carbon metabolism with no membrane or signal/transit-peptide features; cytosolic localization is the expected and consistent assignment. Reason: Consistent with the soluble enzyme class and TreeGrafter/PANTHER family inference; bacterial PEPC has no localization signals and acts in the cytoplasm.
GO:0006099 tricarboxylic acid cycle	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: PEPC is an anaplerotic enzyme that replenishes oxaloacetate feeding the TCA cycle, but it is not itself a reaction of the TCA cycle. The PEP->OAA carboxylation is an anaplerotic/CO2-fixation step at the PEP-pyruvate-OAA node, not a cyclic TCA reaction. This InterPro2GO inference over-states the role. Reason: PEPC supports TCA cycle function anaplerotically but does not participate in the cycle's reactions; the more precise process annotations (oxaloacetate metabolic process, carbon fixation) better capture the actual role.
GO:0006107 oxaloacetate metabolic process	IEA GO_REF:0000104	ACCEPT	Summary: PEPC directly produces oxaloacetate from PEP, so participation in the oxaloacetate metabolic process is well supported and captures the core anaplerotic role. Reason: The catalytic product is oxaloacetate; this is a direct and accurate process annotation for an anaplerotic PEPC.
GO:0008964 phosphoenolpyruvate carboxylase activity	IEA GO_REF:0000120	ACCEPT	Summary: This is the defining molecular function of the gene product (EC 4.1.1.31, RHEA:28370). Supported by the HAMAP rule, conserved active-site residues (His137, His542 region), and PEPCase type 1 family membership. Reason: Core catalytic activity of PEPC; carboxylation of PEP with bicarbonate to yield oxaloacetate and phosphate. Represents the primary function of the gene. Supporting Evidence: file:PSEPK/ppc/ppc-deep-research-falcon.md PEPC catalyzes PEP + HCO3- -> oxaloacetate + Pi, an essentially irreversible anaplerotic carboxylation at the PEP-pyruvate-oxaloacetate node (deep research; ppc-deep-research-falcon.md).
GO:0015977 carbon fixation	IEA GO_REF:0000120	ACCEPT	Summary: PEPC fixes inorganic carbon (bicarbonate) into an organic compound (oxaloacetate), the molecular event underlying anaplerotic CO2/bicarbonate assimilation. The UniProt keyword "Carbon dioxide fixation" applies. This is heterotrophic anaplerotic carbon fixation rather than autotrophic primary production, but the term is appropriate. Reason: The carboxylation reaction incorporates inorganic bicarbonate carbon into central metabolism, an accurate (if broad) description of the process.

Core Functions

Catalyzes the Mg2+-dependent, essentially irreversible carboxylation of phosphoenolpyruvate with bicarbonate to form oxaloacetate and inorganic phosphate, serving as an anaplerotic enzyme that replenishes the oxaloacetate pool of the TCA cycle and central biosynthesis at the PEP-pyruvate-oxaloacetate node.

Molecular Function:

phosphoenolpyruvate carboxylase activity

Directly Involved In:

oxaloacetate metabolic process carbon fixation

Supporting Evidence:

GO_REF:0000120
EC 4.1.1.31; RHEA:28370 oxaloacetate + phosphate = phosphoenolpyruvate + hydrogencarbonate; HAMAP MF_00595 PEPCase type 1.

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000104

Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features

GO_REF:0000118

TreeGrafter-generated GO annotations

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:12534463

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440.

PMID:33289792

The PEP-pyruvate-oxaloacetate node: variation at the heart of metabolism.

Suggested Experiments

Experiment: Determine kinetic parameters (Km for PEP and bicarbonate, kcat) and Mg2+ dependence of purified KT2440 Ppc, and test the effect of candidate effectors (acetyl-CoA, fructose-1,6-bisphosphate, aspartate, malate).

Experiment: Characterize a ppc deletion/overexpression strain for growth phenotypes and 13C-fluxomics of anaplerotic OAA supply on different carbon sources.

Deep Research

Falcon

(ppc-deep-research-falcon.md)

Functional annotation research report: **ppc** (PP_1505; UniProt Q88MR4) in *Pseudomonas putida* KT2440 Falcon Edison Scientific Literature 16 citations 2 artifacts 2026-06-11T22:00:45.788087

Edison artifact artifact-00 (text/markdown)

## Context ID: pqac-00000007 Table 5, which lists the expression profile of genes including ppc (PP1505) and their fold changes, is spread across pages 11 and 1 (image/png)

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.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

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.

Functional annotation research report: ppc (PP_1505; UniProt Q88MR4) in Pseudomonas putida KT2440

1. Target verification (gene/protein identity and disambiguation)

The UniProt target Q88MR4 is annotated as phosphoenolpyruvate carboxylase (PEPC/Ppc; EC 4.1.1.31) encoded by ppc and mapped to the ordered locus PP_1505 in Pseudomonas putida KT2440. This mapping is supported by KT2440 transcriptomics tables in a peer‑reviewed study, where ppc is explicitly listed as “Phosphoenolpyruvate carboxylase” with locus tag PP1505. (acuna2014productionofmedium pages 9-10, acuna2014productionofmedium pages 10-12)

Because the symbol ppc can refer to different genes in other organisms, only literature explicitly addressing phosphoenolpyruvate carboxylase (EC 4.1.1.31) and/or explicitly mapping to PP_1505 (or clearly to Ppc/PEPC at the PEP–OAA node) is used here. (koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-6, acuna2014productionofmedium pages 9-10)

2. Key concepts, definitions, and current understanding

2.1 Enzymatic function (reaction and biochemical role)

Phosphoenolpyruvate carboxylase (PEPC/Ppc; EC 4.1.1.31) catalyzes the carboxylation of phosphoenolpyruvate (PEP) using bicarbonate, producing oxaloacetate (OAA) and inorganic phosphate:

PEP + HCO3− ⇌ OAA + Pi

This reaction is described as highly exergonic (ΔrG′m reported) and effectively irreversible under physiological conditions, functioning as a major route of bicarbonate fixation into central carbon metabolism to generate OAA. (koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-6)

In bacterial central carbon metabolism, OAA is a key entry point into the TCA cycle and also a precursor for biosynthesis (e.g., aspartate family amino acids). Accordingly, PEPC/Ppc is widely treated as an anaplerotic enzyme replenishing OAA when TCA cycle intermediates are drained for biosynthesis. (yin2024recentadvancesin pages 2-4, yin2024recentadvancesin pages 1-2)

2.2 Position in metabolic network (PEP–pyruvate–oxaloacetate node)

Reviews of the PEP–pyruvate–oxaloacetate (PPO/POP) node emphasize that flux partitioning among PEP, pyruvate, and OAA is central to bacterial growth, energetics, and precursor supply. In this context, PEPC/Ppc provides a direct anaplerotic connection from PEP to OAA. (koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-6, yin2024recentadvancesin pages 1-2)

2.3 Regulation (bacterial PEPC allostery and physiological logic)

Bacterial PEPCs commonly exhibit multi-effector allostery. In the bacterial PEPC regulatory scheme summarized in a PPO-node review:

Activators: fructose‑1,6‑bisphosphate (F1,6BP) and acetyl‑CoA
Inhibitors: aspartate and malate

These effectors integrate glycolytic state (F1,6BP), acetyl‑CoA availability, and product/branchpoint signals (aspartate/malate) to tune anaplerotic OAA formation. (koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-7)

A 2024 review focused on engineering the POP node likewise summarizes that PEPC is activated by acetyl‑CoA and fructose‑1,6‑bisphosphate and inhibited by aspartate and malate in model bacteria (e.g., E. coli and C. glutamicum), underscoring conservation of this regulation logic across bacteria. (yin2024recentadvancesin pages 2-4)

Implication for KT2440 (inference): given that KT2440 PP_1505 is annotated as a canonical bacterial PEPC/Ppc and belongs to the bacterial/plant-type PEPC family, these regulatory principles are a strong prior for KT2440 Ppc function, even though KT2440-specific biochemical effector measurements were not retrieved in the accessible text set. (koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-7, acuna2014productionofmedium pages 9-10)

3. Pseudomonas putida KT2440-specific functional context

3.1 Evidence for KT2440 ppc (PP_1505) being engaged during metabolic rewiring

In a KT2440 metabolic engineering study aimed at improving medium-chain-length polyhydroxyalkanoate (mcl-PHA) production from glucose, transcriptome profiling identified that “induction of the phosphoenolpyruvate carboxylase gene ppc was detected”, and the locus is explicitly referenced as PP_1505 in the discussion of pyruvate metabolism changes. (acuna2014productionofmedium pages 7-9)

Quantitatively, the same work reports PP_1505/ppc expression values in central metabolism gene-expression tables (engineered strains vs parental backgrounds). In Table 5, ppc (PP1505) fold changes are reported as 0.0 (Δgcd‑pgl) and 1.4 (KT2440‑pgl). (acuna2014productionofmedium pages 10-12)

Visual evidence for these tabulated values is available in the cropped Table 5 images. (acuna2014productionofmedium media e91fc827, acuna2014productionofmedium media d4d2fe46)

3.2 Phenotypic/bioprocess context where ppc induction was observed

While ppc itself was not the engineered target in the mcl‑PHA study, the ppc induction occurred within strains engineered by pgl overexpression (and in some cases gcd deletion) and was discussed alongside rearrangements in pyruvate metabolism.

For two pgl-overexpressing strains, quantitative physiological outcomes were reported:

KT2440‑pgl: μmax = 0.33 h−1; biomass yield YX/S = 0.21 g/g; gluconate yield Ygluconate/S = 0.55 g/g; PHA yield YPHA/S = 0.05 g/g.
KT2440Δgcd‑pgl: μmax = 0.21 h−1; YX/S = 0.24 g/g; YPHA/S = 0.08 g/g.

In this context, ppc induction is best interpreted as part of a broader central metabolism response (likely affecting anaplerosis and pyruvate/PEP balance) accompanying the engineered perturbations that changed redox and carbon partitioning. (acuna2014productionofmedium pages 7-9)

3.3 Recent (2024) proteomics evidence implicating Ppc during adaptation/engineering

A 2024 Nature Communications study investigating “synthetically‑primed adaptation” of KT2440 to D‑xylose includes a central metabolism proteomics map where Ppc (phosphoenolpyruvate carboxylase) is annotated with a statistically significant log2 fold change of −1.01 (adjusted p ≤ 0.05), indicating decreased abundance in one of the reported comparisons. (dvorak2024syntheticallyprimedadaptationof pages 10-11)

This supports the view that Ppc abundance is condition-dependent in KT2440 during major metabolic rewiring (engineering + adaptive evolution), consistent with Ppc being an adjustable anaplerotic/POP-node lever rather than a constitutively fixed activity. (dvorak2024syntheticallyprimedadaptationof pages 10-11)

4. Recent developments and latest research (prioritizing 2023–2024)

4.1 2024: Central-node engineering framed for production of POP-node–derived products

A 2024 review on engineering the POP node for amino acid production summarizes that PEPC is a key enzymatic “handle” to route carbon from PEP toward OAA and downstream products; it highlights conserved allosteric regulation (activation by acetyl‑CoA/F1,6BP; inhibition by malate/aspartate) and frames PEPC as a frequent target in metabolic engineering strategies when OAA supply is limiting. (yin2024recentadvancesin pages 2-4, yin2024recentadvancesin pages 1-2)

4.2 2024: Proteomics-linked system-level analysis in KT2440

The 2024 KT2440 xylose adaptation study exemplifies a current trend: rather than focusing on single-enzyme characterization, it uses multi-level analysis (including proteomics) to interpret how central metabolism shifts under engineering and evolution. Within this systems context, Ppc abundance changes (log2FC −1.01) provide measurable evidence that anaplerotic routing via Ppc is remodeled under non-native substrate assimilation. (dvorak2024syntheticallyprimedadaptationof pages 10-11)

5. Current applications and real-world implementations

5.1 Biopolymer (mcl‑PHA) production in P. putida

The mcl‑PHA production study provides a direct bioprocess/industrial biotechnology setting in which KT2440’s ppc responds transcriptionally during strain engineering on glucose, and reports quantitative growth and product-yield metrics in engineered strains. This supports functional annotation of ppc as part of the tunable central carbon module that influences precursor supply/redox balance for polymer synthesis (even when not directly engineered). (acuna2014productionofmedium pages 7-9)

5.2 General metabolic engineering logic for the POP node

Across bacterial systems, PEPC is repeatedly highlighted as a key intervention point for improving yields of PEP/OAA/pyruvate-derived products and rebalancing precursor supply, because it directly controls OAA replenishment from PEP and therefore impacts the TCA cycle and biosynthetic precursor pools. (yin2024recentadvancesin pages 2-4, yin2024recentadvancesin pages 1-2)

6. Expert opinions and authoritative analysis (interpretation anchored in reviews)

Two convergent review-level perspectives underpin the most confident functional annotation statements for KT2440 PP_1505 Ppc:

Biochemistry-first view (PPO-node review): PEPC reaction stoichiometry, irreversibility, and conserved effector logic imply Ppc is a central anaplerotic gatekeeper that integrates carbon status (F1,6BP), acetyl‑CoA, and product signals (malate/aspartate). (koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-6, koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-7)
Engineering-first view (POP-node engineering review): PEPC is a recurring metabolic engineering target for improving OAA supply and POP-node flux partitioning, with regulation constraints (feedback/activation) being key considerations in strain design. (yin2024recentadvancesin pages 2-4, yin2024recentadvancesin pages 1-2)

For KT2440 specifically, these general principles are strengthened by direct condition-dependent transcription/protein-abundance evidence for PP_1505/ppc, consistent with the gene functioning at a regulated metabolic bottleneck rather than a peripheral pathway. (acuna2014productionofmedium pages 7-9, dvorak2024syntheticallyprimedadaptationof pages 10-11)

7. Quantitative summary (statistics/data)

A compact quantitative summary is provided in the table below.

Claim/Parameter	Value/Observation	Organism/Context	Source (first author year)	URL	Evidence citation id
Target identity	ppc / PP_1505 / UniProt Q88MR4 annotated as phosphoenolpyruvate carboxylase (PEPC/Ppc; EC 4.1.1.31)	Pseudomonas putida KT2440; transcriptomics tables list locus as PP1505 under pyruvate metabolism	Acuña 2014	https://doi.org/10.1186/1475-2859-13-88	(acuna2014productionofmedium pages 9-10, acuna2014productionofmedium pages 10-12)
Reaction stoichiometry	Phosphoenolpyruvate + HCO3- ⇌ oxaloacetate + Pi; described as an essentially irreversible bicarbonate-fixation reaction in vivo	Bacterial/plant-type PEPC general biochemistry	Koendjbiharie 2021	https://doi.org/10.1093/femsre/fuaa061	(koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-6)
Core function	Produces oxaloacetate (OAA) from PEP, supplying the PEP-pyruvate-oxaloacetate node	General bacterial central metabolism	Yin 2024	https://doi.org/10.3390/molecules29122893	(yin2024recentadvancesin pages 1-2)
Biological role	Anaplerotic enzyme that replenishes the TCA cycle by converting PEP to OAA	Bacteria including E. coli and Corynebacterium glutamicum; relevant inference for KT2440 Ppc family member	Yin 2024	https://doi.org/10.3390/molecules29122893	(yin2024recentadvancesin pages 2-4, yin2024recentadvancesin pages 1-2)
Typical bacterial activators	Fructose-1,6-bisphosphate and acetyl-CoA activate bacterial PEPC	General bacterial PEPC regulation	Koendjbiharie 2021	https://doi.org/10.1093/femsre/fuaa061	(koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-7)
Typical bacterial inhibitors	Aspartate and malate inhibit bacterial PEPC	General bacterial PEPC regulation	Koendjbiharie 2021	https://doi.org/10.1093/femsre/fuaa061	(yin2024recentadvancesin pages 2-4, koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-7)
KT2440 transcriptomic observation	ppc induction detected in engineered KT2440 with pgl overexpression; discussed as part of altered pyruvate metabolism	P. putida KT2440 engineering study on mcl-PHA production	Acuña 2014	https://doi.org/10.1186/1475-2859-13-88	(acuna2014productionofmedium pages 7-9)
KT2440 Table 4 value	ppc (PP1505) expression values reported as 0.5 and 0.4; table note indicates these entries were not bolded (not marked as differentiated expression in that table)	P. putida KT2440 engineered strains vs parental strains	Acuña 2014	https://doi.org/10.1186/1475-2859-13-88	(acuna2014productionofmedium pages 9-10)
KT2440 Table 5 values	ppc (PP1505) fold-change values reported as 0.0 for Δgcd-pgl and 1.4 for KT2440-pgl	P. putida KT2440 engineered strains vs parental strains	Acuña 2014	https://doi.org/10.1186/1475-2859-13-88	(acuna2014productionofmedium pages 10-12)
Localization inference	No organism-specific localization data were retrieved here; as a canonical bacterial PEPC in central carbon metabolism, Ppc is most consistently interpreted as a cytosolic enzyme rather than membrane or secreted	Inference from enzyme class and pathway role; direct KT2440 localization evidence not retrieved in cited contexts	Koendjbiharie 2021; Yin 2024	https://doi.org/10.1093/femsre/fuaa061 ; https://doi.org/10.3390/molecules29122893	(koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-6, yin2024recentadvancesin pages 1-2)

Table: This table compiles the key functional-annotation facts for Pseudomonas putida KT2440 ppc/PP_1505, including the PEPC reaction, anaplerotic role, canonical bacterial regulation, and KT2440-specific transcriptomic observations from Acuña et al. 2014.

Key primary quantitative points (KT2440):

ppc (PP1505) transcript fold-changes reported as 0.0 (Δgcd‑pgl) and 1.4 (KT2440‑pgl) in Table 5; see Table 5 image crops. (acuna2014productionofmedium pages 10-12, acuna2014productionofmedium media e91fc827, acuna2014productionofmedium media d4d2fe46)
Ppc protein abundance change in 2024 proteomics map: log2FC = −1.01 (adjusted p ≤ 0.05). (dvorak2024syntheticallyprimedadaptationof pages 10-11)
Engineered strain phenotypes in the setting where ppc induction was reported include μmax and yields (e.g., KT2440‑pgl μmax 0.33 h−1; YPHA/S 0.05 g/g; KT2440Δgcd‑pgl μmax 0.21 h−1; YPHA/S 0.08 g/g). (acuna2014productionofmedium pages 7-9)

8. Subcellular localization

Direct KT2440 experimental localization data were not retrieved in the accessible corpus. However, given that Ppc/PEPC catalyzes a soluble central carbon reaction (PEP carboxylation to OAA) and is discussed as part of cytosolic metabolic network models and node reviews, the most consistent interpretation is that KT2440 Ppc is a cytosolic enzyme participating in central metabolism rather than a membrane or secreted protein (inference consistent with enzyme class and pathway location). (koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-6, yin2024recentadvancesin pages 1-2)

9. Evidence gaps and recommended next steps (for deeper annotation)

Despite strong support for core function and regulation logic from authoritative reviews, the following KT2440-specific details were not obtained from the current retrieved full texts and therefore should be treated as not yet evidenced for this specific protein:

KT2440-specific enzyme kinetics (Km, kcat), metal requirements, and detailed substrate specificity.
Direct experimental verification of KT2440 Ppc allosteric effectors (acetyl‑CoA/F1,6BP/aspartate/malate) rather than inference from bacterial consensus.
ppc knockout/overexpression phenotypes in KT2440 explicitly tied to growth on specific substrates or to fluxomics results.

Recommended next retrieval targets would include (i) KT2440-specific biochemical characterization papers of PEPC/Ppc (if available), and (ii) KT2440 genome-scale model/fluxomics studies that explicitly quantify the Ppc anaplerotic flux or examine ppc deletion.

Key references (with URLs and publication dates)

Koendjbiharie JG et al. “The PEP-pyruvate-oxaloacetate node: variation at the heart of metabolism” (FEMS Microbiology Reviews), Dec 2021. https://doi.org/10.1093/femsre/fuaa061 (koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-6, koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-7)
Yin L et al. “Recent Advances in Metabolic Engineering for the Biosynthesis of Phosphoenol Pyruvate–Oxaloacetate–Pyruvate-Derived Amino Acids” (Molecules), Jun 2024. https://doi.org/10.3390/molecules29122893 (yin2024recentadvancesin pages 2-4, yin2024recentadvancesin pages 1-2)
Borrero-de Acuña JM et al. “Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida” (Microbial Cell Factories), Jun 2014. https://doi.org/10.1186/1475-2859-13-88 (acuna2014productionofmedium pages 9-10, acuna2014productionofmedium pages 10-12, acuna2014productionofmedium pages 7-9)
Dvořák P et al. “Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose” (Nature Communications), Mar 2024. https://doi.org/10.1038/s41467-024-46812-9 (dvorak2024syntheticallyprimedadaptationof pages 10-11)

References

(acuna2014productionofmedium pages 9-10): José Manuel Borrero-de Acuña, Agata Bielecka, Susanne Häussler, Max Schobert, Martina Jahn, Christoph Wittmann, Dieter Jahn, and Ignacio Poblete-Castro. Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized pseudomonas putida. Microbial Cell Factories, 13:88-88, Jun 2014. URL: https://doi.org/10.1186/1475-2859-13-88, doi:10.1186/1475-2859-13-88. This article has 150 citations and is from a peer-reviewed journal.
(acuna2014productionofmedium pages 10-12): José Manuel Borrero-de Acuña, Agata Bielecka, Susanne Häussler, Max Schobert, Martina Jahn, Christoph Wittmann, Dieter Jahn, and Ignacio Poblete-Castro. Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized pseudomonas putida. Microbial Cell Factories, 13:88-88, Jun 2014. URL: https://doi.org/10.1186/1475-2859-13-88, doi:10.1186/1475-2859-13-88. This article has 150 citations and is from a peer-reviewed journal.
(koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-6): Jeroen G Koendjbiharie, Richard van Kranenburg, and Servé W M Kengen. The pep-pyruvate-oxaloacetate node: variation at the heart of metabolism. FEMS Microbiology Reviews, Dec 2021. URL: https://doi.org/10.1093/femsre/fuaa061, doi:10.1093/femsre/fuaa061. This article has 79 citations and is from a domain leading peer-reviewed journal.
(yin2024recentadvancesin pages 2-4): Lianghong Yin, Yanan Zhou, Nana Ding, and Yu Fang. Recent advances in metabolic engineering for the biosynthesis of phosphoenol pyruvate–oxaloacetate–pyruvate-derived amino acids. Molecules, 29:2893, Jun 2024. URL: https://doi.org/10.3390/molecules29122893, doi:10.3390/molecules29122893. This article has 14 citations.
(yin2024recentadvancesin pages 1-2): Lianghong Yin, Yanan Zhou, Nana Ding, and Yu Fang. Recent advances in metabolic engineering for the biosynthesis of phosphoenol pyruvate–oxaloacetate–pyruvate-derived amino acids. Molecules, 29:2893, Jun 2024. URL: https://doi.org/10.3390/molecules29122893, doi:10.3390/molecules29122893. This article has 14 citations.
(koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-7): Jeroen G Koendjbiharie, Richard van Kranenburg, and Servé W M Kengen. The pep-pyruvate-oxaloacetate node: variation at the heart of metabolism. FEMS Microbiology Reviews, Dec 2021. URL: https://doi.org/10.1093/femsre/fuaa061, doi:10.1093/femsre/fuaa061. This article has 79 citations and is from a domain leading peer-reviewed journal.
(acuna2014productionofmedium pages 7-9): José Manuel Borrero-de Acuña, Agata Bielecka, Susanne Häussler, Max Schobert, Martina Jahn, Christoph Wittmann, Dieter Jahn, and Ignacio Poblete-Castro. Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized pseudomonas putida. Microbial Cell Factories, 13:88-88, Jun 2014. URL: https://doi.org/10.1186/1475-2859-13-88, doi:10.1186/1475-2859-13-88. This article has 150 citations and is from a peer-reviewed journal.
(acuna2014productionofmedium media e91fc827): José Manuel Borrero-de Acuña, Agata Bielecka, Susanne Häussler, Max Schobert, Martina Jahn, Christoph Wittmann, Dieter Jahn, and Ignacio Poblete-Castro. Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized pseudomonas putida. Microbial Cell Factories, 13:88-88, Jun 2014. URL: https://doi.org/10.1186/1475-2859-13-88, doi:10.1186/1475-2859-13-88. This article has 150 citations and is from a peer-reviewed journal.
(acuna2014productionofmedium media d4d2fe46): José Manuel Borrero-de Acuña, Agata Bielecka, Susanne Häussler, Max Schobert, Martina Jahn, Christoph Wittmann, Dieter Jahn, and Ignacio Poblete-Castro. Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized pseudomonas putida. Microbial Cell Factories, 13:88-88, Jun 2014. URL: https://doi.org/10.1186/1475-2859-13-88, doi:10.1186/1475-2859-13-88. This article has 150 citations and is from a peer-reviewed journal.
(dvorak2024syntheticallyprimedadaptationof pages 10-11): Pavel Dvořák, Barbora Burýšková, Barbora Popelářová, Birgitta Elisabeth Ebert, Tibor Botka, Dalimil Bujdoš, Alberto Sánchez-Pascuala, Hannah Schöttler, Heiko Hayen, Víctor de Lorenzo, Lars M. Blank, and Martin Benešík. Synthetically-primed adaptation of pseudomonas putida to a non-native substrate d-xylose. Nature Communications, Mar 2024. URL: https://doi.org/10.1038/s41467-024-46812-9, doi:10.1038/s41467-024-46812-9. This article has 37 citations and is from a highest quality peer-reviewed journal.

Artifacts

Edison artifact artifact-00

Citations

koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-6
koendjbiharie2021thepeppyruvateoxaloacetatenode pages 6-7
yin2024recentadvancesin pages 2-4
acuna2014productionofmedium pages 7-9
acuna2014productionofmedium pages 10-12
dvorak2024syntheticallyprimedadaptationof pages 10-11
yin2024recentadvancesin pages 1-2
acuna2014productionofmedium pages 9-10
https://doi.org/10.1186/1475-2859-13-88
https://doi.org/10.1093/femsre/fuaa061
https://doi.org/10.3390/molecules29122893
https://doi.org/10.1038/s41467-024-46812-9
https://doi.org/10.1186/1475-2859-13-88,
https://doi.org/10.1093/femsre/fuaa061,
https://doi.org/10.3390/molecules29122893,
https://doi.org/10.1038/s41467-024-46812-9,

📄 View Raw YAML

id: Q88MR4
gene_symbol: ppc
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
description: Phosphoenolpyruvate carboxylase (PEPC/PEPCase; EC 4.1.1.31), a soluble cytosolic enzyme of the PEPCase type 1 family. It catalyzes the essentially irreversible, Mg2+-dependent carboxylation of phosphoenolpyruvate (PEP) using bicarbonate (hydrogencarbonate) to form oxaloacetate (OAA) and inorganic phosphate. In bacterial central carbon metabolism PEPC functions as an anaplerotic enzyme that replenishes oxaloacetate at the PEP-pyruvate-oxaloacetate node, supplying the tricarboxylic acid cycle and biosynthetic precursor pools (e.g., the aspartate family of amino acids) when TCA intermediates are withdrawn. Bacterial PEPCs are typically homotetramers subject to allosteric regulation, commonly activated by acetyl-CoA and fructose-1,6-bisphosphate and inhibited by aspartate and malate, allowing anaplerotic OAA formation to be tuned to glycolytic and biosynthetic demand.
existing_annotations:
- term:
    id: GO:0000287
    label: magnesium ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  qualifier: enables
  review:
    summary: PEPC requires Mg2+ as a catalytic cofactor; the UniProt record lists Mg(2+) as the cofactor (HAMAP MF_00595). Correct molecular function for this enzyme.
    action: ACCEPT
    reason: Mg2+ is the established divalent metal cofactor of PEPCase type 1 enzymes, consistent with the conserved active-site residues and the family assignment.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  qualifier: located_in
  review:
    summary: PEPC is a soluble enzyme of central carbon metabolism with no membrane or signal/transit-peptide features; cytosolic localization is the expected and consistent assignment.
    action: ACCEPT
    reason: Consistent with the soluble enzyme class and TreeGrafter/PANTHER family inference; bacterial PEPC has no localization signals and acts in the cytoplasm.
- term:
    id: GO:0006099
    label: tricarboxylic acid cycle
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: PEPC is an anaplerotic enzyme that replenishes oxaloacetate feeding the TCA cycle, but it is not itself a reaction of the TCA cycle. The PEP->OAA carboxylation is an anaplerotic/CO2-fixation step at the PEP-pyruvate-OAA node, not a cyclic TCA reaction. This InterPro2GO inference over-states the role.
    action: MARK_AS_OVER_ANNOTATED
    reason: PEPC supports TCA cycle function anaplerotically but does not participate in the cycle's reactions; the more precise process annotations (oxaloacetate metabolic process, carbon fixation) better capture the actual role.
- term:
    id: GO:0006107
    label: oxaloacetate metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  qualifier: involved_in
  review:
    summary: PEPC directly produces oxaloacetate from PEP, so participation in the oxaloacetate metabolic process is well supported and captures the core anaplerotic role.
    action: ACCEPT
    reason: The catalytic product is oxaloacetate; this is a direct and accurate process annotation for an anaplerotic PEPC.
- term:
    id: GO:0008964
    label: phosphoenolpyruvate carboxylase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: This is the defining molecular function of the gene product (EC 4.1.1.31, RHEA:28370). Supported by the HAMAP rule, conserved active-site residues (His137, His542 region), and PEPCase type 1 family membership.
    action: ACCEPT
    reason: Core catalytic activity of PEPC; carboxylation of PEP with bicarbonate to yield oxaloacetate and phosphate. Represents the primary function of the gene.
    supported_by:
    - reference_id: file:PSEPK/ppc/ppc-deep-research-falcon.md
      supporting_text: PEPC catalyzes PEP + HCO3- -> oxaloacetate + Pi, an essentially irreversible anaplerotic carboxylation at the PEP-pyruvate-oxaloacetate node (deep research; ppc-deep-research-falcon.md).
- term:
    id: GO:0015977
    label: carbon fixation
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: PEPC fixes inorganic carbon (bicarbonate) into an organic compound (oxaloacetate), the molecular event underlying anaplerotic CO2/bicarbonate assimilation. The UniProt keyword "Carbon dioxide fixation" applies. This is heterotrophic anaplerotic carbon fixation rather than autotrophic primary production, but the term is appropriate.
    action: ACCEPT
    reason: The carboxylation reaction incorporates inorganic bicarbonate carbon into central metabolism, an accurate (if broad) description of the process.
core_functions:
- description: Catalyzes the Mg2+-dependent, essentially irreversible carboxylation of phosphoenolpyruvate with bicarbonate to form oxaloacetate and inorganic phosphate, serving as an anaplerotic enzyme that replenishes the oxaloacetate pool of the TCA cycle and central biosynthesis at the PEP-pyruvate-oxaloacetate node.
  molecular_function:
    id: GO:0008964
    label: phosphoenolpyruvate carboxylase activity
  supported_by:
  - reference_id: GO_REF:0000120
    supporting_text: EC 4.1.1.31; RHEA:28370 oxaloacetate + phosphate = phosphoenolpyruvate + hydrogencarbonate; HAMAP MF_00595 PEPCase type 1.
  directly_involved_in:
  - id: GO:0006107
    label: oxaloacetate metabolic process
  - id: GO:0015977
    label: carbon fixation
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000104
  title: Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
  findings: []
- id: GO_REF:0000118
  title: TreeGrafter-generated GO annotations
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:12534463
  title: Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Genome sequence/annotation paper for KT2440 that defines locus PP_1505 (ppc). Verified via the UniProt record cross-reference (PubMed 12534463).
- id: PMID:33289792
  title: "The PEP-pyruvate-oxaloacetate node: variation at the heart of metabolism."
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Authoritative review (Koendjbiharie et al., FEMS Microbiol Rev 2021, DOI 10.1093/femsre/fuaa061) cited for PEPC reaction stoichiometry, irreversibility, and conserved bacterial allosteric regulation. The previously listed PMID:34849727 was a wrong/hallucinated identifier (resolves to an unrelated paediatric cardiology paper); corrected to PMID:33289792, verified via DOI-to-PMID lookup and PubMed (title and abstract match the PPO-node review). The paraphrased supporting_text was re-anchored to the deep-research file since it is a report paraphrase, not a verbatim abstract quote.
suggested_questions:
- question: Has the allosteric regulation of P. putida KT2440 Ppc (e.g., activation by acetyl-CoA/fructose-1,6-bisphosphate, inhibition by aspartate/malate) been measured directly, or is it inferred from E. coli/C. glutamicum homologs?
suggested_experiments:
- description: Determine kinetic parameters (Km for PEP and bicarbonate, kcat) and Mg2+ dependence of purified KT2440 Ppc, and test the effect of candidate effectors (acetyl-CoA, fructose-1,6-bisphosphate, aspartate, malate).
- description: Characterize a ppc deletion/overexpression strain for growth phenotypes and 13C-fluxomics of anaplerotic OAA supply on different carbon sources.

ppc

Gene Description

Existing Annotations Review

Core Functions

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Functional annotation research report: ppc (PP_1505; UniProt Q88MR4) in Pseudomonas putida KT2440

1. Target verification (gene/protein identity and disambiguation)

2. Key concepts, definitions, and current understanding

2.1 Enzymatic function (reaction and biochemical role)

2.2 Position in metabolic network (PEP–pyruvate–oxaloacetate node)

2.3 Regulation (bacterial PEPC allostery and physiological logic)

3. Pseudomonas putida KT2440-specific functional context

3.1 Evidence for KT2440 ppc (PP_1505) being engaged during metabolic rewiring

3.2 Phenotypic/bioprocess context where ppc induction was observed

3.3 Recent (2024) proteomics evidence implicating Ppc during adaptation/engineering

4. Recent developments and latest research (prioritizing 2023–2024)

4.1 2024: Central-node engineering framed for production of POP-node–derived products

4.2 2024: Proteomics-linked system-level analysis in KT2440

5. Current applications and real-world implementations

5.1 Biopolymer (mcl‑PHA) production in P. putida

5.2 General metabolic engineering logic for the POP node

6. Expert opinions and authoritative analysis (interpretation anchored in reviews)

7. Quantitative summary (statistics/data)

8. Subcellular localization

9. Evidence gaps and recommended next steps (for deeper annotation)

Key references (with URLs and publication dates)

Artifacts

Citations

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