Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0004345 glucose-6-phosphate dehydrogenase activity	IEA GO_REF:0000120	ACCEPT	Summary: This is the most specific and informative molecular-function annotation for Q88C32. UniProt identifies the protein as glucose-6-phosphate dehydrogenase, and the KT2440 isozyme study shows that the strain carries three distinct G6PDH enzymes with different cofactor preferences. Even if PP_5351 is not the dominant in vivo isozyme, the specific catalytic activity itself is still the correct function for this gene product. Reason: The annotation captures the exact catalytic activity of the protein. The evidence argues for a minor or condition-specific role, but not for removal of the G6PDH molecular function itself. Supporting Evidence: file:PSEPK/zwf/zwf-uniprot.txt RecName: Full=Glucose-6-phosphate 1-dehydrogenase ... EC=1.1.1.49 file:PSEPK/zwf/zwf-notes.md The key KT2440 isozyme paper shows that the strain carries three G6PDH isozymes with different cofactor specificities
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: This parent oxidoreductase term is technically compatible with a glucose-6-phosphate dehydrogenase, but it is much less informative than the specific catalytic term already present in the annotation set. Reason: GO:0004345 already captures the exact activity. Retaining this broader oxidoreductase term adds redundancy without improving biological precision.
GO:0050661 NADP binding	IEA GO_REF:0000120	ACCEPT	Summary: NADP binding is consistent with both the UniProt family annotation and the 2021 isozyme study, which concludes that the KT2440 G6PDH isozymes have distinct cofactor specificities. For PP_5351, this is an informative molecular-property annotation rather than a vague binding over-annotation. Reason: Cofactor specificity is central to how the different KT2440 G6PDH isozymes partition redox functions. For this paralog, NADP binding is specific and useful. Supporting Evidence: file:PSEPK/zwf/zwf-uniprot.txt DR GO; GO:0050661; F:NADP binding file:PSEPK/zwf/zwf-notes.md the strain carries three G6PDH isozymes with different cofactor specificities
GO:0006006 glucose metabolic process	IEA GO_REF:0000120	MARK AS OVER ANNOTATED	Summary: This broad process assignment is plausible by homology, but the best KT2440 evidence does not support PP_5351 as a major contributor to glucose catabolism. The main experimentally supported glucose-processing G6PDH activity in KT2440 is carried by zwfA, with zwfB also contributing more than this paralog. Reason: Assigning the generic glucose metabolic process to this specific paralog overstates the available evidence for its physiological importance. Supporting Evidence: file:PSEPK/zwf/zwf-notes.md the isoforms encoded by zwfA and zwfB carry most of the activity
GO:0006098 pentose-phosphate shunt	IEA GO_REF:0000120	MARK AS OVER ANNOTATED	Summary: G6PDH chemistry connects directly to the oxidative pentose-phosphate branch, but for PP_5351 the current KT2440 evidence supports only a minor or poorly expressed isozyme. The process term is therefore too strong as a gene-specific statement for this paralog. Reason: The process assignment is inferred from enzyme class rather than a clear paralog-specific role in vivo. Supporting Evidence: file:PSEPK/zwf/zwf-notes.md the isoforms encoded by zwfA and zwfB carry most of the activity
GO:0009051 pentose-phosphate shunt, oxidative branch	IEA GO_REF:0000118	MARK AS OVER ANNOTATED	Summary: This is an even more pathway-committed version of the same process inference. For PP_5351, the current evidence base is insufficient to treat this paralog as a core oxidative pentose-phosphate enzyme in vivo. Reason: The annotation likely reflects family-level pathway propagation rather than paralog-specific physiological evidence. Supporting Evidence: file:PSEPK/zwf/zwf-notes.md the isoforms encoded by zwfA and zwfB carry most of the activity
GO:0005829 cytosol	IEA GO_REF:0000118	ACCEPT	Summary: Cytosolic localization is consistent with the catalytic role of a soluble glucose-6-phosphate dehydrogenase acting on phosphorylated sugar intermediates, and UniProt also places the protein in the cytosol. Reason: This localization is compatible with both enzyme family expectations and the curated UniProt record, and there is no evidence for secretion or a membrane-confined role. Supporting Evidence: file:PSEPK/zwf/zwf-uniprot.txt DR GO; GO:0005829; C:cytosol

Core Functions

Cytosolic glucose-6-phosphate dehydrogenase isozyme with NADP-binding capacity. The available KT2440 evidence suggests that PP_5351/zwfC is a real G6PDH paralog but not the dominant carrier of glucose-6-phosphate dehydrogenase flux under standard tested conditions.

Molecular Function:

glucose-6-phosphate dehydrogenase activity

Cellular Locations:

cytosol

Supporting Evidence:

file:PSEPK/zwf/zwf-uniprot.txt
RecName: Full=Glucose-6-phosphate 1-dehydrogenase ... DR GO; GO:0005829; C:cytosol
file:PSEPK/zwf/zwf-notes.md
the isoforms encoded by zwfA and zwfB carry most of the activity

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

InterPro2GO supplies family/domain-based automated annotations for glucose-6-phosphate dehydrogenase that require curator review against the P. putida zwf paralog context.

GO_REF:0000118

TreeGrafter-generated GO annotations

TreeGrafter transfers GO terms from phylogenetic families; curator review checks whether the transferred term matches the PP_5351 zwf paralog.

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

The combined UniProt automated pipeline annotation provides IEA terms that must be checked for specificity and evidence fit.

PMID:12534463

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

KT2440 genome sequencing establishes the PP_5351/zwf locus in the strain background under review.

PMID:33727391

Cofactor Specificity of Glucose-6-Phosphate Dehydrogenase Isozymes in Pseudomonas putida Reveals a General Principle Underlying Glycolytic Strategies in Bacteria.

The KT2440 G6PDH isozyme study defines three zwf paralogs and their cofactor preferences; PP_5351 is a minor or condition-specific isozyme.

file:PSEPK/zwf/zwf-notes.md

Curator notes on zwf function

Curator notes synthesize UniProt and the G6PDH isozyme paper to distinguish PP_5351 from the dominant zwfA and zwfB paralogs.

file:PSEPK/zwf/zwf-deep-research-falcon.md

Falcon deep research on zwf function

Falcon report summarizes the zwfC/G6PDH-C family assignment and its likely condition-specific contribution.

file:PSEPK/zwf/zwf-uniprot.txt

UniProt record for zwf (Q88C32)

UniProt identifies Q88C32 as glucose-6-phosphate 1-dehydrogenase with EC 1.1.1.49 and NADP-binding GO annotations.

Suggested Experiments

Experiment: Measure zwf, zwfA, and zwfB transcript levels and promoter activity across glucose, gluconate, ribose, oxidative stress, and redox-imbalancing conditions to identify contexts that induce PP_5351.

Type: promoter reporter and RNA-seq

Experiment: Compare WT, Δzwf, and combinatorial zwf paralog mutants by 13C flux analysis and intracellular NADPH/NADH measurements under oxidative and sugar-shift conditions to test whether PP_5351 has a backup redox-balancing role.

Type: fluxomics and redox phenotyping

Experiment: Purify the PP_5351 enzyme from KT2440 or recombinant expression and determine kinetic constants with NADP and NAD for glucose-6-phosphate to quantify how much catalytic capacity remains relative to ZwfA and ZwfB.

Type: enzymology

Deep Research

Falcon

(zwf-deep-research-falcon.md)

this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 21 citations 2026-03-21T13:59:23.501810

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.

Research report: functional annotation of zwf (PP_5351; UniProt Q88C32) in Pseudomonas putida KT2440

0) Target verification (mandatory disambiguation)

The UniProt accession Q88C32 corresponds to the P. putida KT2440 locus PP_5351, which is one of three glucose-6-phosphate dehydrogenase (G6PDH) paralogs in this strain (often referred to as zwfC / zwf-3 in the literature). In KT2440, the three G6PDH genes are zwfA (PP_1022), zwfB (PP_4042), and zwfC (PP_5351), and the connecting point between ED and (partial) EMP metabolism is the G6PDH reaction catalyzed by these isozymes. (volke2021cofactorspecificityof pages 2-4, nikel2015pseudomonasputidakt2440 pages 21-25)

Accordingly, this report is specifically about zwfC = PP_5351 = UniProt Q88C32, while also summarizing how this paralog relates to the better-studied zwfA/zwfB system that dominates glycolytic physiology in KT2440. (volke2021cofactorspecificityof pages 9-11, volke2021cofactorspecificityof pages 7-9)

1) Key concepts and definitions (current understanding)

1.1 Enzymatic function and reaction chemistry

Glucose-6-phosphate dehydrogenase (G6PDH; EC 1.1.1.49) catalyzes the first committed step of the oxidative pentose phosphate (PP) pathway and also supplies carbon into the Entner–Doudoroff (ED) pathway via 6-phosphogluconate. In P. putida KT2440, the zwf-1 product is described as required to convert glucose-6-phosphate (G6P) to 6-phosphogluconolactone with reduction of NAD(P)+ to NAD(P)H (reported in the context of zwf-1 as the major isozyme). (kim2008dualregulationof pages 4-6)

A standard biochemical description of the reaction is:
- D-glucose-6-phosphate + NAD(P)+ → 6-phospho-D-glucono-δ-lactone + NAD(P)H + H+

Because NAD(P)H (often predominantly NADPH) supports biosynthesis and oxidative-stress defense (e.g., via glutathione reduction), Zwf enzymes are central determinants of redox balance in KT2440. (volke2021cofactorspecificityof pages 1-2, i.2021reconfigurationofmetabolic pages 8-10)

1.2 Pathway context in P. putida: ED–EMP–PP “EDEMP cycle”

A key concept for KT2440 is that glucose catabolism is organized as an interconnected network (often called the EDEMP cycle) that merges the ED pathway with a gluconeogenic operation of (incomplete) EMP and PP pathway reactions to tune precursor supply and NADPH formation. (nikel2015pseudomonasputidakt2440 pages 1-2, volke2021cofactorspecificityof pages 2-4)

This network architecture is directly relevant to zwf paralogs because G6PDH activity sits at the connection between ED and EMP/PP routing, and can be rate- and redox-controlling. (volke2021cofactorspecificityof pages 2-4)

1.3 Isozyme multiplicity and cofactor specificity

Unlike the “default” assumption (from E. coli) that bacterial G6PDH is strictly NADP+-specific, KT2440 encodes three G6PDH isozymes with distinct cofactor preferences and kinetic behaviors, interpreted as an evolutionary/physiological strategy to balance NADPH vs NADH production depending on carbon source and redox state. (volke2021cofactorspecificityof pages 1-2, volke2021cofactorspecificityof pages 7-9)

2) Gene product-specific functional annotation: ZwfC (PP_5351; UniProt Q88C32)

2.1 Molecular function

ZwfC is a G6PDH-family enzyme (glucose-6-phosphate dehydrogenase isozyme C) that conserves canonical G6PDH sequence motifs for cofactor and substrate binding. (volke2021cofactorspecificityof pages 9-11, volke2021cofactorspecificityof pages 7-9)

Cofactor specificity and kinetics (isozyme-level): ZwfC/G6PDH-C is described as highly NADP+-specific, with a specificity coefficient ω reported to be ~5× higher than the canonical E. coli enzyme’s ω (~410), but with very low turnover (reported kcat < 1 s−1), consistent with low physiological contribution under tested conditions. (volke2021cofactorspecificityof pages 7-9)

2.2 Biological process and pathway role

Although ZwfC is a bona fide G6PDH, multiple lines of evidence indicate that in KT2440 it contributes little to bulk glucose catabolism in standard laboratory conditions:
- Transcription is very low: reporter constructs for the zwfC promoter/5′UTR showed almost no detectable expression across tested carbon sources. (volke2021cofactorspecificityof pages 9-11)
- Phenotype is minimal: deletion of zwfC alone produced no significant growth phenotype in the tested substrate panel (whereas zwfA loss severely affects growth on glucose). (volke2021cofactorspecificityof pages 7-9, volke2021cofactorspecificityof pages 2-4)

Thus, the most defensible functional statement from current evidence is that ZwfC encodes an NADP+-specific G6PDH isozyme with low expression and low catalytic turnover, likely acting as a condition-dependent or auxiliary redox enzyme rather than the primary entry point for glycolytic carbon in KT2440. (volke2021cofactorspecificityof pages 9-11, volke2021cofactorspecificityof pages 7-9)

2.3 Cellular localization

Direct subcellular localization measurements for ZwfC were not identified in the retrieved evidence. However, the pathway context and enzyme assays described for KT2440 focus on cytoplasmic sugar phosphorylation and intracellular flux through the ED/PP network connected by G6PDHs, consistent with Zwf isozymes functioning as intracellular (cytosolic) dehydrogenases acting on G6P. This should be treated as pathway-based inference rather than a direct localization experiment. (volke2021cofactorspecificityof pages 2-4, kim2008dualregulationof pages 4-6)

3) Regulation and control (KT2440-specific)

3.1 HexR as a major transcriptional regulator of zwf in KT2440

For the major zwf gene (historically “zwf-1”), the transcription factor HexR acts as a repressor: zwf promoter activity in glucose or gluconate is reported to be 25–50-fold higher than in pyruvate/succinate, and HexR knockout yields constitutively high reporter signal across conditions. (kim2008dualregulationof pages 4-6)

Mechanistically, KDPG (2-keto-3-deoxy-6-phosphogluconate)—a key ED intermediate—acts as an inducer by blocking HexR binding to the zwf promoter region; this is supported by EMSA and by edd/eda mutants that modulate intracellular KDPG (edd cannot make KDPG; eda accumulates KDPG). (kim2008dualregulationof pages 6-7)

For zwfC (PP_5351) specifically, upstream sequence analysis reported a HexR binding motif, but functional reporter assays still detected almost no zwfC expression under the conditions tested, implying that (i) zwfC is under tighter/alternative regulation, (ii) it may require specific inducing conditions not present in the tested set, or (iii) it is effectively silent in many standard regimes. (volke2021cofactorspecificityof pages 9-11)

3.2 Oxidative-stress induction and physiological relevance

Oxidative stress strongly increases the cellular need for NADPH. In KT2440, network-level 13C flux analysis under sublethal H2O2 showed that periplasmic glucose processing is rerouted toward cytoplasmic oxidation and a cyclic PP operation, generating NADPH fluxes that exceed biosynthetic demands by ~50%. (i.2021reconfigurationofmetabolic pages 1-2)

Quantitatively, net NADPH generation under oxidative stress is reported to increase to 14.4 ± 0.3 mmol gCDW−1 h−1, producing ~50% NADPH surplus relative to biosynthetic requirements. (i.2021reconfigurationofmetabolic pages 8-10)

In vitro enzyme assays support this metabolic reconfiguration: under H2O2, specific activities of the two major NADPH-generating dehydrogenases in the PP-related network increased strongly, with Zwf activity increasing 4.7-fold (and GntZ 9.2-fold). (i.2021reconfigurationofmetabolic pages 8-10)

These results establish Zwf-linked metabolism as a key, rapidly tunable NADPH supply route under redox stress, even if the evidence does not isolate ZwfC’s specific contribution (given its low expression/activity). (i.2021reconfigurationofmetabolic pages 8-10, volke2021cofactorspecificityof pages 7-9)

Visual evidence: Figure panels summarizing the NADPH balance shift and enzyme activity changes under oxidative stress are available in the extracted images. (i.2021reconfigurationofmetabolic media b8b02296, i.2021reconfigurationofmetabolic media a2c989ad)

4) Quantitative cofactor specificity and redox outputs (KT2440)

4.1 Whole-cell-extract cofactor preference (combined Zwf activity)

Because KT2440 has multiple Zwf isozymes, measured cofactor preference can depend on assay conditions and reflects the combined activity of all contributing isozymes.

In KT2440 glucose-grown extracts:
- Under saturating assay conditions, total Zwf activity showed ~67.1% NADP+ and ~32.9% NAD+ usage.
- Under non-saturating (quasi in vivo) conditions, the same activity becomes strongly NADP+-biased: ~93.8% NADP+ vs ~6.2% NAD+.

This supports a model where in vivo Zwf function is tuned toward NADPH production. (nikel2015pseudomonasputidakt2440 pages 21-25)

4.2 Isozyme-level specialization (notably zwfC)

Isozyme-resolved biochemical modeling/kinetic comparisons indicate:
- G6PDH-A (zwfA) produces NADH and NADPH in roughly equal amounts under physiological settings (NADH/NADPH near 1).
- G6PDH-B (zwfB) tends to produce mostly NADH and has ~5-fold lower Km for G6P than G6PDH-A, implying stronger activity at low G6P.
- G6PDH-C (zwfC = PP_5351 = Q88C32) is highly NADP+-specific but has kcat < 1 s−1 and is poorly expressed.

Together, this supports an “isozyme portfolio” hypothesis: KT2440 maintains multiple Zwf enzymes to flexibly balance NADH/NADPH output across carbon sources and environmental stresses. (volke2021cofactorspecificityof pages 7-9)

5) Recent developments (prioritizing 2023–2024)

5.1 2024 systems-level engineering: derepressing glycolysis/PPP via hexR deletion

A 2024 Nature Communications study on engineering KT2440 derivatives for xylose utilization used deletion of hexR to derepress native glycolysis-associated functions, and explicitly pursued enhancing the pentose phosphate pathway by implanting additional transketolase/transaldolase activities. This positions the HexR–PPP/ED control structure (which includes zwf regulation in KT2440) as a practical engineering lever for expanding substrate scope and improving growth on non-native feedstocks. (Published 2024-03; https://doi.org/10.1038/s41467-024-46812-9) (dvorak2024syntheticallyprimedadaptationof pages 1-2)

Within their multilevel comparisons of evolved/engineered states, they report differential expression for ZwfA in pathway schematics (log2 fold changes shown), emphasizing the continued centrality of Zwf-mediated redox generation in rewired central metabolism—even when the target phenotype is new substrate assimilation (xylose → X5P → EDEMP cycle). (dvorak2024syntheticallyprimedadaptationof pages 9-10)

While this work does not single out zwfC, it is an authoritative recent example of real-world strain development where PPP/ED routing (and by implication Zwf gatekeeping) is explicitly engineered for lignocellulosic bioprocess goals. (dvorak2024syntheticallyprimedadaptationof pages 1-2)

5.2 2023 preprint to 2024 paper trajectory (xylose adaptation)

A 2023 bioRxiv preprint on adapting P. putida to xylose (later published in 2024) emphasizes the importance of redox/PPP capacity and highlights Zwf as a key NADPH-supplying enzyme in this host’s physiology and engineering. (2023-05; https://doi.org/10.1101/2023.05.19.541448) (volke2021cofactorspecificityof pages 4-6)

6) Current applications and real-world implementations

6.1 Bioprocess robustness and oxidative-stress tolerance

Mechanistic fluxomics under oxidative stress demonstrates that KT2440 increases NADPH-forming fluxes (including via Zwf and GntZ) to generate a substantial NADPH surplus that fuels glutathione-based detoxification, linking Zwf-network function to stress robustness—a core reason KT2440 is widely used for harsh industrial biotransformations and bioremediation contexts. (i.2021reconfigurationofmetabolic pages 1-2, i.2021reconfigurationofmetabolic pages 8-10)

6.2 Metabolic engineering logic: using Zwf/PPP control for redox-intensive production

The broader metabolic-engineering literature treats zwf as an archetypal NADPH-supply lever (PPP entry) and highlights that cofactor supply limitations (especially NADPH regeneration) are frequent bottlenecks in redox-intensive whole-cell catalysis. While not KT2440-specific, this provides a conceptual rationale for why P. putida’s high-NADPH EDEMP architecture (with Zwf gatekeeping) is attractive as a chassis. (volke2021cofactorspecificityof pages 1-2)

7) Expert synthesis and interpretation (authoritative-source-backed)

ZwfC (PP_5351/Q88C32) is a confirmed G6PDH-family enzyme but is not the dominant glycolytic Zwf in KT2440. Evidence strongly supports very low zwfC transcription and minimal phenotype upon zwfC deletion, while showing that zwfA (and to a lesser extent zwfB) carries most G6PDH function in typical glycolytic regimes. (volke2021cofactorspecificityof pages 9-11, volke2021cofactorspecificityof pages 7-9, volke2021cofactorspecificityof pages 2-4)
KT2440’s multi-zwf design is best understood as a redox-balancing strategy rather than redundancy. Isozyme differences in cofactor preference and substrate affinity (e.g., zwfB low Km for G6P; zwfC extreme NADP+ specificity but low kcat) support a division of labor that can reshape NADH vs NADPH production as carbon entry points and redox conditions vary. (volke2021cofactorspecificityof pages 7-9, volke2021cofactorspecificityof pages 1-2)
Zwf-linked NADPH generation is a cornerstone of oxidative-stress tolerance and thus industrial robustness, but attributing this system-level phenotype specifically to zwfC is not currently justified by available evidence. Under oxidative stress, overall metabolic flux is rerouted to increase Zwf- and GntZ-linked NADPH formation, with net NADPH generation rising to 14.4 ± 0.3 mmol gCDW−1 h−1 and producing ~50% excess over biosynthetic demands; however, these analyses and enzyme activity measurements do not resolve zwfC’s individual contribution and likely reflect predominantly zwfA/zwfB activity. (i.2021reconfigurationofmetabolic pages 8-10, volke2021cofactorspecificityof pages 7-9)

8) High-value quantitative statistics for annotation (selected)

zwf-1 promoter induction by carbon source: glucose/gluconate induce ~25–50× higher reporter activity than pyruvate/succinate; HexR deletion leads to constitutively high activity. (Kim et al., 2008-12; https://doi.org/10.1099/mic.0.2008/020362-0) (kim2008dualregulationof pages 4-6)
Oxidative stress NADPH surplus: cyclic PPP operation yields NADPH formation exceeding biosynthetic demand by ~50%; net NADPH generation reported 14.4 ± 0.3 mmol gCDW−1 h−1 in H2O2-stressed cultures. (Nikel et al., 2021-01-11; https://doi.org/10.1038/s41396-020-00884-9) (i.2021reconfigurationofmetabolic pages 8-10)
Enzyme activity shifts under oxidative stress: Zwf activity +4.7×, GntZ activity +9.2× in vitro (cell-free extracts) under H2O2 vs control. (i.2021reconfigurationofmetabolic pages 8-10)
Total Zwf cofactor usage in extracts (glucose-grown): saturating assays ~67.1% NADP+ / 32.9% NAD+; quasi in vivo assays ~93.8% NADP+ / 6.2% NAD+. (Nikel et al., 2015-10; https://doi.org/10.1074/jbc.M115.687749) (nikel2015pseudomonasputidakt2440 pages 21-25)
zwfC-specific biochemistry: strongly NADP+-specific, with kcat < 1 s−1 and very low transcription, consistent with minor contribution in standard conditions. (Volke et al., 2021-03-16; https://doi.org/10.1128/mSystems.00014-21) (volke2021cofactorspecificityof pages 7-9, volke2021cofactorspecificityof pages 9-11)

9) Summary table (isoform map; includes target mapping)

The following table maps UniProt Q88C32 to the correct KT2440 zwf paralog and contrasts all zwf isozymes for practical annotation.

Isoform / target mapping	Locus tag / identifier	Role in metabolism and growth phenotype	Expression / regulation notes	Cofactor specificity / kinetic highlights
zwfA (G6PDH-A)	PP_1022	Major G6PDH for glycolytic conditions; provides the bulk of total G6PDH activity. Deletion causes a major glucose-growth defect (reported as ~84% lower specific growth rate than WT on glucose), and activity is almost lost in mutants lacking zwfA; also important for fructose/ribose entry into the EDEMP/PP network (volke2021cofactorspecificityof pages 4-6, volke2021cofactorspecificityof pages 9-11, volke2021cofactorspecificityof pages 2-4)	Part of the zwfA-pgl-eda operon. Strongly expressed on glucose/glycolytic substrates. Negatively regulated by HexR; deleting hexR caused a ~2.5-fold increase in a PzwfA reporter on fructose (volke2021cofactorspecificityof pages 9-11, volke2021cofactorspecificityof pages 2-4)	Produces roughly balanced NADH and NADPH under simulated physiological conditions (NADH/NADPH output near 1). In total-cell Zwf activity assays, G6PDH activity in KT2440 is strongly NADP+-biased under quasi in vivo conditions (~93.8% NADP+ versus ~6.2% NAD+), though this reflects combined isozyme activity rather than zwfA alone (volke2021cofactorspecificityof pages 7-9, nikel2015pseudomonasputidakt2440 pages 21-25)
zwfB (G6PDH-B)	PP_4042	Contributes substantially alongside zwfA, especially as a metabolic gatekeeper for carbon sources entering different network nodes; double/triple zwf mutants show strong defects, including no growth of ΔzwfAB on ribose and ~70% lower growth rate of ΔzwfABC on fructose (volke2021cofactorspecificityof pages 4-6, volke2021cofactorspecificityof pages 2-4)	Cotranscribed with gntZ; less emphasized than zwfA in HexR-controlled glycolytic induction, but retained as an active isozyme in central carbon metabolism (volke2021cofactorspecificityof pages 9-11, volke2021cofactorspecificityof pages 2-4)	Reported as dual-cofactor in P. putida KT2440 comparative analysis. Simulations indicate zwfB tends to generate mostly NADH; it has an approximately 5-fold lower Km for G6P than G6PDH-A, suggesting effectiveness at lower substrate concentrations (volke2021cofactorspecificityof pages 7-9, shah2022glucose6phosphatedehydrogenasezwfa pages 5-8)
zwfC (G6PDH-C)	PP_5351; UniProt Q88C32 target	This is the user’s target protein. Present in KT2440 but appears to make little contribution to growth under tested conditions; deletion of zwfC alone had no significant effect on growth patterns, and the enzyme likely has a minor physiological role under standard conditions (volke2021cofactorspecificityof pages 7-9, volke2021cofactorspecificityof pages 2-4)	Poorly transcribed across tested conditions; upstream region contains a duplicated/consensus HexR-binding motif and adjacent RpiR-family regulator gene (PP_5350), but reporter assays detected almost no PzwfC expression (volke2021cofactorspecificityof pages 9-11)	Highly NADP+-specific. Sequence conserves the canonical cofactor-binding motif and substrate-contact residues. The specificity coefficient (ω) is reported as about 5-fold higher than the canonical E. coli G6PDH value (~410), but turnover is very low (kcat < 1 s⁻¹), consistent with near-zero activity in vivo (volke2021cofactorspecificityof pages 7-9, volke2021cofactorspecificityof pages 9-11)
Total Zwf activity in KT2440 extracts	Combined activity of zwfA/zwfB/zwfC	Supports the oxidative PP / ED-linked EDEMP cycle that underpins glucose catabolism and redox balancing in P. putida KT2440 (nikel2015pseudomonasputidakt2440 pages 1-2, volke2021cofactorspecificityof pages 2-4)	Under oxidative stress, carbon flux is rerouted toward cytosolic oxidation and Zwf-linked NADPH formation; Zwf activity increased 4.7-fold in vitro, contributing to increased NADPH supply (i.2021reconfigurationofmetabolic pages 8-10)	Combined cofactor use in extracts grown on glucose: under saturating conditions ~67.1% NADP+ / 32.9% NAD+; under quasi in vivo conditions ~93.8% NADP+ / 6.2% NAD+ (nikel2015pseudomonasputidakt2440 pages 21-25)

Table: This table maps the user’s UniProt target Q88C32 to zwfC/PP_5351 and contrasts all three Pseudomonas putida KT2440 zwf-encoded G6PDH isoforms by locus, physiological importance, regulation, and cofactor/kinetic properties. It is useful for distinguishing the specific target from the better-studied zwfA and zwfB paralogs.

10) Practical functional annotation statements (recommended)

Gene: zwfC (PP_5351; UniProt Q88C32)

Recommended molecular function: Glucose-6-phosphate dehydrogenase isozyme (G6PDH-C); oxidizes G6P to 6-phosphogluconolactone with reduction of NADP+ (high specificity) and supports NADPH generation capacity in the ED/PP-linked central carbon metabolism network. (kim2008dualregulationof pages 4-6, volke2021cofactorspecificityof pages 7-9)

Recommended pathway assignment: Oxidative PP / ED interface (EDEMP cycle connection point), but likely auxiliary under many laboratory conditions due to low expression and low turnover. (volke2021cofactorspecificityof pages 2-4, volke2021cofactorspecificityof pages 9-11, volke2021cofactorspecificityof pages 7-9)

Regulatory notes: Promoter region contains HexR motifs, yet zwfC reporter expression is near-zero under tested conditions; core HexR/KDPG regulation is clearly demonstrated for the major zwf promoter system in KT2440. (kim2008dualregulationof pages 6-7, volke2021cofactorspecificityof pages 9-11)

Phenotype notes: zwfC deletion alone: no significant growth effect across tested substrates; contrast with zwfA deletion showing strong growth impairment on glucose. (volke2021cofactorspecificityof pages 2-4, volke2021cofactorspecificityof pages 7-9)

Figures (evidence)

NADPH balance shift under oxidative stress and enzyme activity ratios including Zwf/GntZ: (i.2021reconfigurationofmetabolic media b8b02296, i.2021reconfigurationofmetabolic media a2c989ad)

References

(volke2021cofactorspecificityof pages 2-4): Daniel Christoph Volke, Karel Olavarría, and Pablo Iván Nikel. Cofactor specificity of glucose-6-phosphate dehydrogenase isozymes in pseudomonas putida reveals a general principle underlying glycolytic strategies in bacteria. Apr 2021. URL: https://doi.org/10.1128/msystems.00014-21, doi:10.1128/msystems.00014-21. This article has 40 citations and is from a peer-reviewed journal.
(nikel2015pseudomonasputidakt2440 pages 21-25): Pablo I. Nikel, Max Chavarría, Tobias Fuhrer, Uwe Sauer, and Víctor de Lorenzo. Pseudomonas putida kt2440 strain metabolizes glucose through a cycle formed by enzymes of the entner-doudoroff, embden-meyerhof-parnas, and pentose phosphate pathways. Journal of Biological Chemistry, 290:25920-25932, Oct 2015. URL: https://doi.org/10.1074/jbc.m115.687749, doi:10.1074/jbc.m115.687749. This article has 427 citations and is from a domain leading peer-reviewed journal.
(volke2021cofactorspecificityof pages 9-11): Daniel Christoph Volke, Karel Olavarría, and Pablo Iván Nikel. Cofactor specificity of glucose-6-phosphate dehydrogenase isozymes in pseudomonas putida reveals a general principle underlying glycolytic strategies in bacteria. Apr 2021. URL: https://doi.org/10.1128/msystems.00014-21, doi:10.1128/msystems.00014-21. This article has 40 citations and is from a peer-reviewed journal.
(volke2021cofactorspecificityof pages 7-9): Daniel Christoph Volke, Karel Olavarría, and Pablo Iván Nikel. Cofactor specificity of glucose-6-phosphate dehydrogenase isozymes in pseudomonas putida reveals a general principle underlying glycolytic strategies in bacteria. Apr 2021. URL: https://doi.org/10.1128/msystems.00014-21, doi:10.1128/msystems.00014-21. This article has 40 citations and is from a peer-reviewed journal.
(kim2008dualregulationof pages 4-6): Juhyun Kim, Che Ok Jeon, and Woojun Park. Dual regulation of zwf-1 by both 2-keto-3-deoxy-6-phosphogluconate and oxidative stress in pseudomonas putida. Microbiology, 154 Pt 12:3905-16, Dec 2008. URL: https://doi.org/10.1099/mic.0.2008/020362-0, doi:10.1099/mic.0.2008/020362-0. This article has 75 citations and is from a peer-reviewed journal.
(volke2021cofactorspecificityof pages 1-2): Daniel Christoph Volke, Karel Olavarría, and Pablo Iván Nikel. Cofactor specificity of glucose-6-phosphate dehydrogenase isozymes in pseudomonas putida reveals a general principle underlying glycolytic strategies in bacteria. Apr 2021. URL: https://doi.org/10.1128/msystems.00014-21, doi:10.1128/msystems.00014-21. This article has 40 citations and is from a peer-reviewed journal.
(i.2021reconfigurationofmetabolic pages 8-10): Pablo I. Nikel, Tobias Fuhrer, Max Chavarria, Alberto Sanchez-Pascuala, Uwe Sauer, and Victor de Lorenzo. Reconfiguration of metabolic fluxes in pseudomonas putida as a response to sub-lethal oxidative stress. The ISME Journal, 15:1751-1766, Jan 2021. URL: https://doi.org/10.1038/s41396-020-00884-9, doi:10.1038/s41396-020-00884-9. This article has 152 citations.
(nikel2015pseudomonasputidakt2440 pages 1-2): Pablo I. Nikel, Max Chavarría, Tobias Fuhrer, Uwe Sauer, and Víctor de Lorenzo. Pseudomonas putida kt2440 strain metabolizes glucose through a cycle formed by enzymes of the entner-doudoroff, embden-meyerhof-parnas, and pentose phosphate pathways. Journal of Biological Chemistry, 290:25920-25932, Oct 2015. URL: https://doi.org/10.1074/jbc.m115.687749, doi:10.1074/jbc.m115.687749. This article has 427 citations and is from a domain leading peer-reviewed journal.
(kim2008dualregulationof pages 6-7): Juhyun Kim, Che Ok Jeon, and Woojun Park. Dual regulation of zwf-1 by both 2-keto-3-deoxy-6-phosphogluconate and oxidative stress in pseudomonas putida. Microbiology, 154 Pt 12:3905-16, Dec 2008. URL: https://doi.org/10.1099/mic.0.2008/020362-0, doi:10.1099/mic.0.2008/020362-0. This article has 75 citations and is from a peer-reviewed journal.
(i.2021reconfigurationofmetabolic pages 1-2): Pablo I. Nikel, Tobias Fuhrer, Max Chavarria, Alberto Sanchez-Pascuala, Uwe Sauer, and Victor de Lorenzo. Reconfiguration of metabolic fluxes in pseudomonas putida as a response to sub-lethal oxidative stress. The ISME Journal, 15:1751-1766, Jan 2021. URL: https://doi.org/10.1038/s41396-020-00884-9, doi:10.1038/s41396-020-00884-9. This article has 152 citations.
(i.2021reconfigurationofmetabolic media b8b02296): Pablo I. Nikel, Tobias Fuhrer, Max Chavarria, Alberto Sanchez-Pascuala, Uwe Sauer, and Victor de Lorenzo. Reconfiguration of metabolic fluxes in pseudomonas putida as a response to sub-lethal oxidative stress. The ISME Journal, 15:1751-1766, Jan 2021. URL: https://doi.org/10.1038/s41396-020-00884-9, doi:10.1038/s41396-020-00884-9. This article has 152 citations.
(i.2021reconfigurationofmetabolic media a2c989ad): Pablo I. Nikel, Tobias Fuhrer, Max Chavarria, Alberto Sanchez-Pascuala, Uwe Sauer, and Victor de Lorenzo. Reconfiguration of metabolic fluxes in pseudomonas putida as a response to sub-lethal oxidative stress. The ISME Journal, 15:1751-1766, Jan 2021. URL: https://doi.org/10.1038/s41396-020-00884-9, doi:10.1038/s41396-020-00884-9. This article has 152 citations.
(dvorak2024syntheticallyprimedadaptationof pages 1-2): 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 33 citations and is from a highest quality peer-reviewed journal.
(dvorak2024syntheticallyprimedadaptationof pages 9-10): 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 33 citations and is from a highest quality peer-reviewed journal.
(volke2021cofactorspecificityof pages 4-6): Daniel Christoph Volke, Karel Olavarría, and Pablo Iván Nikel. Cofactor specificity of glucose-6-phosphate dehydrogenase isozymes in pseudomonas putida reveals a general principle underlying glycolytic strategies in bacteria. Apr 2021. URL: https://doi.org/10.1128/msystems.00014-21, doi:10.1128/msystems.00014-21. This article has 40 citations and is from a peer-reviewed journal.
(shah2022glucose6phosphatedehydrogenasezwfa pages 5-8): Bhavik A. Shah, Sravanti T. Kasarlawar, and Prashant S. Phale. Glucose-6-phosphate dehydrogenase, zwfa, a dual cofactor-specific isozyme is predominantly involved in the glucose metabolism of pseudomonas bharatica csv86 ^t. Dec 2022. URL: https://doi.org/10.1128/spectrum.03818-22, doi:10.1128/spectrum.03818-22. This article has 7 citations and is from a domain leading peer-reviewed journal.

Citations

kim2008dualregulationof pages 4-6
volke2021cofactorspecificityof pages 2-4
volke2021cofactorspecificityof pages 7-9
volke2021cofactorspecificityof pages 9-11
kim2008dualregulationof pages 6-7
dvorak2024syntheticallyprimedadaptationof pages 1-2
dvorak2024syntheticallyprimedadaptationof pages 9-10
volke2021cofactorspecificityof pages 4-6
volke2021cofactorspecificityof pages 1-2
https://doi.org/10.1038/s41467-024-46812-9
https://doi.org/10.1101/2023.05.19.541448
https://doi.org/10.1099/mic.0.2008/020362-0
https://doi.org/10.1038/s41396-020-00884-9
https://doi.org/10.1074/jbc.M115.687749
https://doi.org/10.1128/mSystems.00014-21
https://doi.org/10.1128/msystems.00014-21,
https://doi.org/10.1074/jbc.m115.687749,
https://doi.org/10.1099/mic.0.2008/020362-0,
https://doi.org/10.1038/s41396-020-00884-9,
https://doi.org/10.1038/s41467-024-46812-9,
https://doi.org/10.1128/spectrum.03818-22,

📚 Additional Documentation

Notes

(zwf-notes.md)

zwf notes

UniProt Q88C32 is the zwf gene product in Pseudomonas putida KT2440, with ordered locus PP_5351, annotated as glucose-6-phosphate 1-dehydrogenase / G6PD (EC 1.1.1.49). [file:PSEPK/zwf/zwf-uniprot.txt, "RecName: Full=Glucose-6-phosphate 1-dehydrogenase"; "GN Name=zwf"; "OrderedLocusNames=PP_5351"; "EC=1.1.1.49"]
UniProt classifies the protein in the glucose-6-phosphate dehydrogenase family and maps GO terms for glucose-6-phosphate dehydrogenase activity, NADP binding, glucose metabolic process, pentose-phosphate shunt, oxidative pentose-phosphate branch, and cytosol. [file:PSEPK/zwf/zwf-uniprot.txt, "Belongs to the glucose-6-phosphate dehydrogenase family"; "DR GO; GO:0004345; F:glucose-6-phosphate dehydrogenase activity"; "DR GO; GO:0050661; F:NADP binding"; "DR GO; GO:0006006; P:glucose metabolic process"; "DR GO; GO:0006098; P:pentose-phosphate shunt"; "DR GO; GO:0009051; P:pentose-phosphate shunt, oxidative branch"; "DR GO; GO:0005829; C:cytosol"]
The key KT2440 isozyme paper shows that the strain carries three G6PDH isozymes with different cofactor specificities, and that zwfA plus zwfB carry most of the measurable activity. This supports treating the PP_5351 isozyme as a bona fide G6PDH but not the dominant in vivo source of flux under the tested conditions. [PMID:33727391 Cofactor Specificity of Glucose-6-Phosphate Dehydrogenase Isozymes in Pseudomonas putida Reveals a General Principle Underlying Glycolytic Strategies in Bacteria, "We show that the three G6PDHs of strain KT2440 have different cofactor specificities and that the isoforms encoded by zwfA and zwfB carry most of the activity"]
Working curation interpretation: retain the specific molecular function terms for G6PDH activity and NADP binding, but downgrade the broad biological-process annotations because the available KT2440 evidence argues that this isozyme is not a major contributor to glucose or oxidative pentose-phosphate flux in standard growth conditions. [PMID:33727391 Cofactor Specificity of Glucose-6-Phosphate Dehydrogenase Isozymes in Pseudomonas putida Reveals a General Principle Underlying Glycolytic Strategies in Bacteria, "the isoforms encoded by zwfA and zwfB carry most of the activity"]
The 2002 genome paper is useful only as genome-context support for KT2440, not as functional evidence for this specific isozyme. [PMID:12534463 Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440, "Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems"]

📄 View Raw YAML

id: Q88C32
gene_symbol: zwf
product_type: PROTEIN
aliases:
- PP_5351
- zwfC
- G6PDH-C
status: DRAFT
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
    / KT2440)
description: Glucose-6-phosphate 1-dehydrogenase isozyme of Pseudomonas putida KT2440
  (ordered locus PP_5351), corresponding to the minor zwfC/G6PDH-C paralog. Sequence
  and family annotations support canonical glucose-6-phosphate dehydrogenase chemistry
  with NADP binding, but the best KT2440 experimental synthesis indicates that zwfA
  and zwfB carry most of the detectable G6PDH activity under the tested conditions.
  Accordingly, this gene is best curated as a bona fide cytosolic G6PDH isozyme with
  limited or condition-specific physiological contribution compared with the other
  two paralogs.
existing_annotations:
- term:
    id: GO:0004345
    label: glucose-6-phosphate dehydrogenase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: This is the most specific and informative molecular-function annotation
      for Q88C32. UniProt identifies the protein as glucose-6-phosphate dehydrogenase,
      and the KT2440 isozyme study shows that the strain carries three distinct G6PDH
      enzymes with different cofactor preferences. Even if PP_5351 is not the dominant
      in vivo isozyme, the specific catalytic activity itself is still the correct
      function for this gene product.
    action: ACCEPT
    reason: The annotation captures the exact catalytic activity of the protein. The
      evidence argues for a minor or condition-specific role, but not for removal
      of the G6PDH molecular function itself.
    supported_by:
    - reference_id: file:PSEPK/zwf/zwf-uniprot.txt
      supporting_text: 'RecName: Full=Glucose-6-phosphate 1-dehydrogenase ... EC=1.1.1.49'
    - reference_id: file:PSEPK/zwf/zwf-notes.md
      supporting_text: The key KT2440 isozyme paper shows that the strain carries
        three G6PDH isozymes with different cofactor specificities
- term:
    id: GO:0016614
    label: oxidoreductase activity, acting on CH-OH group of donors
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: This parent oxidoreductase term is technically compatible with a glucose-6-phosphate
      dehydrogenase, but it is much less informative than the specific catalytic term
      already present in the annotation set.
    action: MARK_AS_OVER_ANNOTATED
    reason: GO:0004345 already captures the exact activity. Retaining this broader
      oxidoreductase term adds redundancy without improving biological precision.
- term:
    id: GO:0050661
    label: NADP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: NADP binding is consistent with both the UniProt family annotation and
      the 2021 isozyme study, which concludes that the KT2440 G6PDH isozymes have
      distinct cofactor specificities. For PP_5351, this is an informative molecular-property
      annotation rather than a vague binding over-annotation.
    action: ACCEPT
    reason: Cofactor specificity is central to how the different KT2440 G6PDH isozymes
      partition redox functions. For this paralog, NADP binding is specific and useful.
    supported_by:
    - reference_id: file:PSEPK/zwf/zwf-uniprot.txt
      supporting_text: DR   GO; GO:0050661; F:NADP binding
    - reference_id: file:PSEPK/zwf/zwf-notes.md
      supporting_text: the strain carries three G6PDH isozymes with different cofactor
        specificities
- term:
    id: GO:0006006
    label: glucose metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: This broad process assignment is plausible by homology, but the best
      KT2440 evidence does not support PP_5351 as a major contributor to glucose catabolism.
      The main experimentally supported glucose-processing G6PDH activity in KT2440
      is carried by zwfA, with zwfB also contributing more than this paralog.
    action: MARK_AS_OVER_ANNOTATED
    reason: Assigning the generic glucose metabolic process to this specific paralog
      overstates the available evidence for its physiological importance.
    supported_by:
    - reference_id: file:PSEPK/zwf/zwf-notes.md
      supporting_text: the isoforms encoded by zwfA and zwfB carry most of the activity
- term:
    id: GO:0006098
    label: pentose-phosphate shunt
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: G6PDH chemistry connects directly to the oxidative pentose-phosphate
      branch, but for PP_5351 the current KT2440 evidence supports only a minor or
      poorly expressed isozyme. The process term is therefore too strong as a gene-specific
      statement for this paralog.
    action: MARK_AS_OVER_ANNOTATED
    reason: The process assignment is inferred from enzyme class rather than a clear
      paralog-specific role in vivo.
    supported_by:
    - reference_id: file:PSEPK/zwf/zwf-notes.md
      supporting_text: the isoforms encoded by zwfA and zwfB carry most of the activity
- term:
    id: GO:0009051
    label: pentose-phosphate shunt, oxidative branch
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  review:
    summary: This is an even more pathway-committed version of the same process inference.
      For PP_5351, the current evidence base is insufficient to treat this paralog
      as a core oxidative pentose-phosphate enzyme in vivo.
    action: MARK_AS_OVER_ANNOTATED
    reason: The annotation likely reflects family-level pathway propagation rather
      than paralog-specific physiological evidence.
    supported_by:
    - reference_id: file:PSEPK/zwf/zwf-notes.md
      supporting_text: the isoforms encoded by zwfA and zwfB carry most of the activity
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  review:
    summary: Cytosolic localization is consistent with the catalytic role of a soluble
      glucose-6-phosphate dehydrogenase acting on phosphorylated sugar intermediates,
      and UniProt also places the protein in the cytosol.
    action: ACCEPT
    reason: This localization is compatible with both enzyme family expectations and
      the curated UniProt record, and there is no evidence for secretion or a membrane-confined
      role.
    supported_by:
    - reference_id: file:PSEPK/zwf/zwf-uniprot.txt
      supporting_text: DR   GO; GO:0005829; C:cytosol
core_functions:
- description: Cytosolic glucose-6-phosphate dehydrogenase isozyme with NADP-binding
    capacity. The available KT2440 evidence suggests that PP_5351/zwfC is a real G6PDH
    paralog but not the dominant carrier of glucose-6-phosphate dehydrogenase flux
    under standard tested conditions.
  molecular_function:
    id: GO:0004345
    label: glucose-6-phosphate dehydrogenase activity
  locations:
  - id: GO:0005829
    label: cytosol
  supported_by:
  - reference_id: file:PSEPK/zwf/zwf-uniprot.txt
    supporting_text: 'RecName: Full=Glucose-6-phosphate 1-dehydrogenase ... DR   GO;
      GO:0005829; C:cytosol'
  - reference_id: file:PSEPK/zwf/zwf-notes.md
    supporting_text: the isoforms encoded by zwfA and zwfB carry most of the activity
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings:
  - statement: InterPro2GO supplies family/domain-based automated annotations for
      glucose-6-phosphate dehydrogenase that require curator review against the P.
      putida zwf paralog context.
- id: GO_REF:0000118
  title: TreeGrafter-generated GO annotations
  findings:
  - statement: TreeGrafter transfers GO terms from phylogenetic families; curator
      review checks whether the transferred term matches the PP_5351 zwf paralog.
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings:
  - statement: The combined UniProt automated pipeline annotation provides IEA terms
      that must be checked for specificity and evidence fit.
- id: PMID:12534463
  title: Complete genome sequence and comparative analysis of the metabolically versatile
    Pseudomonas putida KT2440.
  findings:
  - statement: KT2440 genome sequencing establishes the PP_5351/zwf locus in the strain
      background under review.
- id: PMID:33727391
  title: Cofactor Specificity of Glucose-6-Phosphate Dehydrogenase Isozymes in Pseudomonas
    putida Reveals a General Principle Underlying Glycolytic Strategies in Bacteria.
  findings:
  - statement: The KT2440 G6PDH isozyme study defines three zwf paralogs and their
      cofactor preferences; PP_5351 is a minor or condition-specific isozyme.
- id: file:PSEPK/zwf/zwf-notes.md
  title: Curator notes on zwf function
  findings:
  - statement: Curator notes synthesize UniProt and the G6PDH isozyme paper to distinguish
      PP_5351 from the dominant zwfA and zwfB paralogs.
- id: file:PSEPK/zwf/zwf-deep-research-falcon.md
  title: Falcon deep research on zwf function
  findings:
  - statement: Falcon report summarizes the zwfC/G6PDH-C family assignment and its
      likely condition-specific contribution.
- id: file:PSEPK/zwf/zwf-uniprot.txt
  title: UniProt record for zwf (Q88C32)
  findings:
  - statement: UniProt identifies Q88C32 as glucose-6-phosphate 1-dehydrogenase with
      EC 1.1.1.49 and NADP-binding GO annotations.
suggested_questions:
- question: Under which stress or nutrient conditions is PP_5351/zwfC actually expressed
    strongly enough to carry meaningful flux?
  experts:
  - Pablo Iván Nikel
  - Daniel Christoph Volke
- question: Does zwfC specialize in redox balancing under conditions where zwfA and
    zwfB are insufficient, or is it becoming dispensable in KT2440?
  experts:
  - Pablo Iván Nikel
  - Daniel Christoph Volke
suggested_experiments:
- description: Measure zwf, zwfA, and zwfB transcript levels and promoter activity
    across glucose, gluconate, ribose, oxidative stress, and redox-imbalancing conditions
    to identify contexts that induce PP_5351.
  experiment_type: promoter reporter and RNA-seq
- description: Compare WT, Δzwf, and combinatorial zwf paralog mutants by 13C flux
    analysis and intracellular NADPH/NADH measurements under oxidative and sugar-shift
    conditions to test whether PP_5351 has a backup redox-balancing role.
  experiment_type: fluxomics and redox phenotyping
- description: Purify the PP_5351 enzyme from KT2440 or recombinant expression and
    determine kinetic constants with NADP and NAD for glucose-6-phosphate to quantify
    how much catalytic capacity remains relative to ZwfA and ZwfB.
  experiment_type: enzymology

zwf

Gene Description

Existing Annotations Review

Core Functions

Cytosolic glucose-6-phosphate dehydrogenase isozyme with NADP-binding capacity. The available KT2440 evidence suggests that PP_5351/zwfC is a real G6PDH paralog but not the dominant carrier of glucose-6-phosphate dehydrogenase flux under standard tested conditions.

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Research report: functional annotation of zwf (PP_5351; UniProt Q88C32) in Pseudomonas putida KT2440

0) Target verification (mandatory disambiguation)

1) Key concepts and definitions (current understanding)

1.1 Enzymatic function and reaction chemistry

1.2 Pathway context in P. putida: ED–EMP–PP “EDEMP cycle”

1.3 Isozyme multiplicity and cofactor specificity

2) Gene product-specific functional annotation: ZwfC (PP_5351; UniProt Q88C32)

2.1 Molecular function

2.2 Biological process and pathway role

2.3 Cellular localization

3) Regulation and control (KT2440-specific)

3.1 HexR as a major transcriptional regulator of zwf in KT2440

3.2 Oxidative-stress induction and physiological relevance

4) Quantitative cofactor specificity and redox outputs (KT2440)

4.1 Whole-cell-extract cofactor preference (combined Zwf activity)

4.2 Isozyme-level specialization (notably zwfC)

5) Recent developments (prioritizing 2023–2024)

5.1 2024 systems-level engineering: derepressing glycolysis/PPP via hexR deletion

5.2 2023 preprint to 2024 paper trajectory (xylose adaptation)

6) Current applications and real-world implementations

6.1 Bioprocess robustness and oxidative-stress tolerance

6.2 Metabolic engineering logic: using Zwf/PPP control for redox-intensive production

7) Expert synthesis and interpretation (authoritative-source-backed)

8) High-value quantitative statistics for annotation (selected)

9) Summary table (isoform map; includes target mapping)

10) Practical functional annotation statements (recommended)

Figures (evidence)

Citations

📚 Additional Documentation

Notes

zwf notes

📄 View Raw YAML