Glk is the cytosolic glucokinase of Pseudomonas putida KT2440. It phosphorylates imported glucose to glucose-6-phosphate using ATP and feeds the phosphorylative branch of glucose assimilation into the Entner-Doudoroff-centered carbohydrate catabolic network. In KT2440, glk is part of the edd-glk operon and mutant and flux analyses indicate that the glucokinase branch is quantitatively important for growth on glucose even though P. putida can also oxidize glucose through periplasmic gluconate and 2-ketogluconate routes.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0004340
glucokinase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: This is the core molecular function of glk. UniProt assigns the protein as glucokinase (EC 2.7.1.2), and pathway work in KT2440 places Glk at the ATP-dependent phosphorylation step that converts cytoplasmic glucose to glucose-6-phosphate.
Reason: This term is specific, mechanistically correct, and central to the gene's function.
Supporting Evidence:
file:PSEPK/glk/glk-uniprot.txt
RecName: Full=Glucokinase
file:PSEPK/glk/glk-uniprot.txt
Reaction=D-glucose + ATP = D-glucose 6-phosphate + ADP + H(+);
file:PSEPK/glk/glk-notes.md
In KT2440, glucose imported into the cytoplasm is phosphorylated by glucokinase to glucose-6-phosphate before conversion to 6-phosphogluconate.
file:PSEPK/glk/glk-deep-research-falcon.md
The UniProt target **Q88P42** corresponds to **glk** in *Pseudomonas putida* KT2440 (ordered locus **PP_1011**) encoding the cytosolic enzyme **glucokinase (Glk)**, which phosphorylates imported glucose to **glucose‑6‑phosphate (G6P)** as the entry step of the phosphorylative branch of glucose catabolism.
|
|
GO:0005524
ATP binding
|
IEA
GO_REF:0000120 |
MARK AS OVER ANNOTATED |
Summary: ATP binding is mechanistically true for a kinase, but it is much less informative than the specific catalytic term glucokinase activity and is redundant for describing the core function of this enzyme.
Reason: The catalytic activity term already captures the biologically informative function.
Supporting Evidence:
file:PSEPK/glk/glk-uniprot.txt
/ligand="ATP"
file:PSEPK/glk/glk-notes.md
ATP binding and D-glucose binding are mechanistically true but substantially less informative than the specific catalytic term glucokinase activity.
|
|
GO:0005536
D-glucose binding
|
IEA
GO_REF:0000002 |
MARK AS OVER ANNOTATED |
Summary: Substrate recognition is implicit in glucokinase activity, so this term is not wrong but is less informative than the specific catalytic annotation.
Reason: This binding term adds little beyond the core enzymatic activity term.
Supporting Evidence:
file:PSEPK/glk/glk-notes.md
In KT2440, glucose imported into the cytoplasm is phosphorylated by glucokinase to glucose-6-phosphate before conversion to 6-phosphogluconate.
file:PSEPK/glk/glk-notes.md
ATP binding and D-glucose binding are mechanistically true but substantially less informative than the specific catalytic term glucokinase activity.
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000120 |
MODIFY |
Summary: Glk is a soluble intracellular enzyme and cytoplasmic localization is correct, but the more precise term in this context is cytosol.
Reason: Cytoplasm is broader than needed for a soluble bacterial enzyme.
Proposed replacements:
cytosol
Supporting Evidence:
file:PSEPK/glk/glk-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm
file:PSEPK/glk/glk-notes.md
For cellular component, cytosol is the more specific GO term for a soluble bacterial cytoplasmic enzyme, while cytoplasm is acceptable but broader.
|
|
GO:0005829
cytosol
|
IEA
GO_REF:0000118 |
ACCEPT |
Summary: This is the preferred cellular component term for a soluble cytoplasmic enzyme such as Glk and is more precise than the broader term cytoplasm.
Reason: Specific and biologically appropriate localization term.
Supporting Evidence:
file:PSEPK/glk/glk-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm
file:PSEPK/glk/glk-notes.md
For cellular component, cytosol is the more specific GO term for a soluble bacterial cytoplasmic enzyme, while cytoplasm is acceptable but broader.
|
|
GO:0006096
glycolytic process
|
IEA
GO_REF:0000120 |
MODIFY |
Summary: Glk participates in glucose catabolism to pyruvate, but in P. putida KT2440 that process is routed through the Entner-Doudoroff-centered network rather than a generic undifferentiated glycolysis term.
Reason: A more pathway-specific biological process term is available.
Proposed replacements:
glycolytic process via Entner-Doudoroff Pathway
Supporting Evidence:
file:PSEPK/glk/glk-notes.md
glk is physically linked to the Entner-Doudoroff pathway because edd and glk form one operon in KT2440.
file:PSEPK/glk/glk-notes.md
Because of this genomic organization, the glucokinase pathway is co-induced with Entner-Doudoroff genes and is expressed even during growth on gluconate or 2-ketogluconate.
file:PSEPK/glk/glk-deep-research-falcon.md
This physical linkage is consistent with functional coupling: the **glucokinase entry step (Glk)** and the subsequent ED processing step (Edd) are transcriptionally coordinated.
|
|
GO:0051156
glucose 6-phosphate metabolic process
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: This term accurately reflects the immediate pathway context of Glk, which generates glucose-6-phosphate from glucose and ATP.
Reason: Directly describes the metabolic process in which the enzymatic reaction participates.
Supporting Evidence:
file:PSEPK/glk/glk-uniprot.txt
Reaction=D-glucose + ATP = D-glucose 6-phosphate + ADP + H(+);
file:PSEPK/glk/glk-notes.md
In KT2440, glucose imported into the cytoplasm is phosphorylated by glucokinase to glucose-6-phosphate before conversion to 6-phosphogluconate.
|
Q: How does flux through the glucokinase branch versus the periplasmic gluconate and 2-ketogluconate branches change across different glucose concentrations and oxygen or redox conditions in KT2440?
Q: Does Glk have kinetic or regulatory specialization that distinguishes it from glucokinases in other pseudomonads that use different balances of oxidative and phosphorylative glucose uptake?
Q: How strongly does HexR-mediated control of the edd-glk operon constrain mixed-substrate utilization when glucose and gluconate are simultaneously available?
Experiment: Purify PP_1011 and measure steady-state kinetics for glucose and ATP, substrate specificity, and cofactor dependence under physiologically relevant ionic conditions.
Type: Enzyme biochemistry
Experiment: Construct a clean glk deletion and complemented strain, then quantify growth and intracellular carbon flux on glucose, gluconate, and mixed carbon sources using isotopic tracer experiments.
Type: Genetic perturbation and flux analysis
Experiment: Use promoter reporters or RNA-seq in wild type and hexR backgrounds to quantify how glucose, gluconate, 2-ketogluconate, and KDPG-related perturbations regulate the edd-glk-gltR2-gltS operon.
Type: Operon regulation
This report is retrieval-only and is generated directly from Asta results.
search_papers_by_relevance with snippet_search.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
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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.
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The UniProt target Q88P42 corresponds to glk in Pseudomonas putida KT2440 (ordered locus PP_1011) encoding the cytosolic enzyme glucokinase (Glk), which phosphorylates imported glucose to glucose‑6‑phosphate (G6P) as the entry step of the phosphorylative branch of glucose catabolism. This identity is directly supported by KT2440-focused studies that name glk (PP_1011) as glucokinase and place it in the edd–glk operon/cluster and broader glucose-catabolism gene neighborhood. (castillo2007convergentperipheralpathways pages 5-6, castillo2008asetof pages 1-2, daddaoua2009regulationofglucose pages 1-2, nguyen2024investigatinganaerobicmetabolism pages 27-30)
Glucokinase (Glk) is a sugar kinase that catalyzes phosphorylation of D-glucose to D-glucose‑6‑phosphate, coupling this to cellular energy metabolism (ATP consumption). In KT2440, glucose that is transported into the cytosol via an ABC transporter is then phosphorylated by Glk to G6P, which is further converted toward 6‑phosphogluconate by glucose‑6‑phosphate dehydrogenase (Zwf) and 6‑phosphogluconolactonase (Pgl). (chen2024gnurrepressesthe pages 1-3, daddaoua2009regulationofglucose pages 1-2)
Functional reaction (as used in KT2440 glucose assimilation):
- D‑glucose + ATP → D‑glucose‑6‑phosphate + ADP (commonly annotated as EC 2.7.1.2; EC number is not explicitly stated in the retrieved excerpts, but the enzyme is explicitly called “glucokinase” and described as catalyzing glucose→G6P). (chen2024gnurrepressesthe pages 1-3, daddaoua2009regulationofglucose pages 1-2)
A defining feature of Pseudomonas glucose metabolism is the co-existence of multiple peripheral routes that converge at 6‑phosphogluconate. In KT2440, glucose may enter central metabolism via:
1) a cytosolic phosphorylative route: glucose import → Glk → G6P → Zwf/Pgl → 6‑phosphogluconate; and
2) periplasmic oxidative routes producing gluconate and 2‑ketogluconate that are subsequently imported and metabolized to 6‑phosphogluconate. (castillo2007convergentperipheralpathways pages 1-2, nikel2015pseudomonasputidakt2440 pages 1-2)
KT2440 does not run a canonical linear Embden–Meyerhof–Parnas (EMP) glycolysis due to missing 6‑phosphofructo‑1‑kinase activity; instead, glucose is processed through an integrated cyclic architecture often described as an EDEMP cycle, combining Entner–Doudoroff (ED) reactions with upper‑EMP/gluconeogenic steps and pentose‑phosphate (PP) reactions. In this framework, Glk supplies G6P that can feed these interconnected modules, and carbon can be recycled from triose phosphates back to hexose phosphates. (nikel2015pseudomonasputidakt2440 pages 1-2, nikel2015pseudomonasputidakt2440 media d74e2f18)
Multiple sources report that glk is co-transcribed with edd (encoding 6‑phosphogluconate dehydratase), i.e. an edd–glk operon. The operon/cluster extends to include gltR2/gltS (transport-associated regulation), and edd is divergently transcribed relative to gap‑1 in the region. (castillo2007convergentperipheralpathways pages 5-6, daddaoua2009regulationofglucose pages 1-2)
This physical linkage is consistent with functional coupling: the glucokinase entry step (Glk) and the subsequent ED processing step (Edd) are transcriptionally coordinated. (castillo2007convergentperipheralpathways pages 5-6, castillo2008asetof pages 1-2)
In KT2440, enzymatic assays from cell extracts showed that glucokinase activity is inducible by growth on glucose. Specifically, glucokinase (and gluconokinase) activities were low during growth on citrate but increased ~10‑fold during growth on glucose, supporting that Glk is expressed and catalytically active under glucose conditions (and not only inferred from sequence annotation). (castillo2007convergentperipheralpathways pages 5-6)
13C flux analysis and physiology in KT2440 indicate that glucose catabolism strongly favors periplasmic oxidation under tested conditions: approximately 90% of consumed glucose was reported to proceed through the oxidative route (via gluconate) into central metabolism as 6‑phosphogluconate, while the remaining fraction enters via other routes, including the cytosolic phosphorylation route that depends on Glk. (nikel2015pseudomonasputidakt2440 pages 1-2)
A complementary flux/physiology study reported a glucose uptake rate ~6 mmol·g⁻¹·h⁻¹, growth rate 0.58 h⁻¹, and biomass yield 0.44 g biomass per g carbon for the wild type under the studied condition set. (castillo2007convergentperipheralpathways pages 1-2)
A KT2440 glk mutant exhibited measurable impairments in carbon consumption and biomass yield in the referenced physiological analyses; one excerpted dataset reports total carbon consumption of ~5.44 mmol·g⁻¹·h⁻¹ and biomass yield of ~0.35 g biomass per g carbon consumed for the glk mutant. (castillo2007convergentperipheralpathways pages 5-6)
Separate work on catabolite repression and pathway integration explicitly used a glk mutant strain to interrogate growth and regulation on mixed substrates (glucose + toluene), further emphasizing that glk is a tractable genetic node with measurable phenotypic consequences. (castillo2007convergentperipheralpathways pages 6-8)
Glk functions in the cytoplasm, acting on glucose that has been transported into the cytosol. This is explicitly described as glucose being transported into the cytoplasm and “subsequently phosphorylated by glucokinase (Glk) to glucose‑6‑phosphate.” (chen2024gnurrepressesthe pages 1-3)
This contrasts with the periplasmic oxidative route (glucose→gluconate/2‑ketogluconate) which is initiated outside the cytosol and later converges internally at phosphorylated intermediates. (nikel2015pseudomonasputidakt2440 pages 1-2)
Mechanistic regulatory work in Pseudomonas identifies HexR as a central transcriptional regulator controlling expression of promoters including those for ED/glucose catabolism (e.g., Pedd and Pzwf/Pgap). HexR binds target promoters with nanomolar-range affinity and is released by the ED intermediate KDPG (2‑keto‑3‑deoxy‑6‑phosphogluconate), linking metabolic state to gene expression. This regulatory logic couples expression of the edd–glk operon to ED pathway flux. (daddaoua2009regulationofglucose pages 1-2)
Consistently, systems-level analysis describing peripheral glucose control reports that HexR controls genes encoding glucokinase and glucose‑6‑phosphate dehydrogenase, integrating the Glk entry step with downstream conversion of G6P toward 6‑phosphogluconate. (castillo2008asetof pages 1-2)
Beyond HexR, the KT2440 glucose catabolic region is described as being under multiple transcriptional regulators, including transport-associated regulation (e.g., GltR/GltS) and regulators of gluconate/2‑ketogluconate utilization (e.g., PtxS, GnuR in related frameworks). (castillo2008asetof pages 1-2, daddaoua2009regulationofglucose pages 1-2)
Recent 2024 development (high priority): A KT2440 study used multi‑omics to define the GnuR regulon, showing that GnuR directly represses catabolic genes involved in the Entner–Doudoroff and peripheral glucose/gluconate metabolism pathways, and that expression of the glucose catabolism genes is induced by both glucose and gluconate. This work modernizes the regulatory map around glucose utilization while maintaining Glk’s core biochemical assignment as the glucose→G6P phosphorylation step. (Publication date: Nov 2024; URL: https://doi.org/10.1111/1751-7915.70059) (chen2024gnurrepressesthe pages 1-3)
The 2024 study on GnuR provides a KT2440-focused, contemporary update: it reports that glucose and gluconate induce expression of glucose catabolism genes and identifies direct repression targets of GnuR within ED/peripheral metabolism, improving the mechanistic basis for engineering glucose catabolism. (Nov 2024; https://doi.org/10.1111/1751-7915.70059) (chen2024gnurrepressesthe pages 1-3)
A 2024 study of anaerobic glucose uptake in a bioelectrochemical system explicitly frames energy accounting around “sugar phosphorylation in the upper part of metabolism (at the level of glucokinase…)” and tests uptake-route mutants to determine whether uptake stoichiometry limits electro-fermentation performance. In the studied setup, deletion of uptake routes affected sugar consumption/current output, but secreted acetate levels were not significantly altered among strains—suggesting other constraints (e.g., energy limitation or regulation) rather than the glucokinase stoichiometry per se. (Publication date: Nov 2024; URL: https://doi.org/10.1111/1751-7915.14375) (nguyen2024investigatinganaerobicmetabolism pages 27-30)
A 2024 metabolic engineering study in P. putida reported that modifying glucose metabolism and regulatory nodes can markedly improve medium-chain-length PHA titers (e.g., increases in titer reported for combined knockouts and regulatory modifications), reflecting ongoing real-world implementation of glucose catabolism rewiring in Pseudomonas production strains. (Publication date: Nov 2024; URL: https://doi.org/10.3390/cimb46110761) (chen2024gnurrepressesthe pages 1-3)
Note on limitations: Using the provided tool-accessible corpus, I could not retrieve 2023–2024 sources specifically focused on structural mechanism or family-wide biochemical kinetics for PF02685 bacterial glucokinases; therefore, mechanistic/structural claims beyond the demonstrated pathway role are not made here. (nikel2015pseudomonasputidakt2440 pages 1-2, chen2024gnurrepressesthe pages 1-3)
The edd–glk node is repeatedly leveraged as a defined genetic “handle” to rewire upper sugar metabolism. For example, refactoring/expanding sugar utilization (e.g., cellobiose/xylose modules) relies on intracellular glucose being phosphorylated and routed into central metabolism via the native upper network in KT2440 derivatives. (https://doi.org/10.1016/j.ymben.2018.05.019; 2018) (bujdos2021inženýrstvípseudomonasputida pages 40-43)
A synthetic biology strategy (“GlucoBricks”) reported measurable glucokinase specific activities in engineered strains and evaluated portability of glycolytic modules to Gram-negative hosts including Pseudomonas. While the excerpted kinetic data are reported for engineered E. coli backgrounds, this work frames Glk as the first committed step enabling engineered glycolytic flux. (https://doi.org/10.1021/acssynbio.6b00230; Feb 2017) (sanchezpascuala2017refactoringtheembden–meyerhof–parnas pages 4-6)
Under electro-fermentative conditions, selection/engineering of glucose uptake routes (including those requiring cytosolic phosphorylation via glucokinase) is being studied to improve carbon turnover and product formation; route mutants were used to evaluate whether the energetic/redox demands of uptake and phosphorylation are limiting. (https://doi.org/10.1111/1751-7915.14375; Nov 2024) (nguyen2024investigatinganaerobicmetabolism pages 27-30)
Unavailable in retrieved excerpts: explicit Glk kinetic constants (Km, kcat) and direct substrate-specificity panels for purified P. putida Glk were not accessible from the available text snippets. (nikel2015pseudomonasputidakt2440 pages 17-19)
The schematic depiction of the EDEMP cycle in KT2440 provides a concise visual explanation of how ED, PP and upper‑EMP reactions integrate in KT2440 glucose metabolism, contextualizing where the Glk-dependent G6P entry step can feed into the broader network. (nikel2015pseudomonasputidakt2440 media d74e2f18)
Gene: glk (PP_1011)
Protein: Glucokinase (Glk)
Cellular location: Cytosol; acts on cytosolic glucose after import. (chen2024gnurrepressesthe pages 1-3)
Primary biochemical function: Phosphorylates glucose to glucose‑6‑phosphate to initiate the cytosolic phosphorylative glucose assimilation route in KT2440; downstream routing proceeds via Zwf/Pgl to 6‑phosphogluconate and ED/EDEMP-associated metabolism. (chen2024gnurrepressesthe pages 1-3, daddaoua2009regulationofglucose pages 1-2, nikel2015pseudomonasputidakt2440 pages 1-2)
Genomic/pathway context: Part of an edd–glk operon/cluster linked to ED entry, co-regulated with glucose transport and ED genes (including gltR2/gltS), embedded within the multi-route peripheral glucose utilization architecture of Pseudomonas. (castillo2007convergentperipheralpathways pages 5-6, daddaoua2009regulationofglucose pages 1-2)
Regulatory context (high confidence): Expression of edd/glk-linked functions is controlled by HexR, with effector KDPG modulating promoter binding; additional regulators (e.g., GnuR) shape global glucose/gluconate catabolism responses in KT2440. (daddaoua2009regulationofglucose pages 1-2, chen2024gnurrepressesthe pages 1-3)
| Claim / topic | Evidence-backed summary | Quantitative findings | Example application / implementation (year; DOI/URL) | Key sources (context IDs) |
|---|---|---|---|---|
| Gene/protein identity | glk in Pseudomonas putida KT2440 encodes the cytosolic glucokinase Glk; locus PP_1011; this matches UniProt Q88P42 and the glucose-phosphorylation branch of sugar catabolism. | PP_1011 explicitly linked to Glk in KT2440 pathway/genome context. | Used as a defined engineering target in KT2440 derivatives lacking glk to block glucose assimilation (2025; https://doi.org/10.1093/synbio/ysaf012). | (nguyen2024investigatinganaerobicmetabolism pages 27-30, escapa2013theroleof pages 37-41, chen2024gnurrepressesthe pages 1-3) |
| Enzymatic reaction | Glk catalyzes ATP-dependent phosphorylation of glucose → glucose-6-phosphate (G6P), feeding upper central metabolism; downstream G6P is oxidized by Zwf/Pgl toward 6-phosphogluconate. | Reaction is described qualitatively; no Glk-specific Km/kcat retrieved in the available evidence. | Central step in glucose entry retained or rewired in KT2440 metabolic engineering for mixed-sugar use (2018; https://doi.org/10.1016/j.ymben.2018.05.019). | (chen2024gnurrepressesthe pages 1-3, daddaoua2009regulationofglucose pages 1-2, nikel2015pseudomonasputidakt2440 pages 1-2) |
| Pathway role in KT2440 | In KT2440, glucose can enter metabolism either by direct cytosolic phosphorylation via Glk or by periplasmic oxidation to gluconate/2-ketogluconate before convergence at 6-phosphogluconate; Glk is part of the phosphorylative branch. | Approx. 90% of consumed glucose was reported to proceed through the periplasmic oxidative route, implying a minority enters via direct phosphorylation under tested conditions. | Important for quantitative physiology and flux-guided redesign of KT2440 glucose metabolism (2015; https://doi.org/10.1074/jbc.M115.687749). | (nikel2015pseudomonasputidakt2440 pages 1-2, castillo2007convergentperipheralpathways pages 1-2) |
| Operon / genomic context | glk is physically and transcriptionally linked with edd (6-phosphogluconate dehydratase), i.e. an edd-glk operon/cluster; broader local context includes gltR2/gltS and nearby glucose-uptake genes. | glk and edd were reported to overlap and be transcriptionally coupled. | This native organization motivated “GlucoBrick”/upper-glycolysis refactoring efforts in Gram-negative hosts including P. putida (2017; https://doi.org/10.1021/acssynbio.6b00230). | (castillo2007convergentperipheralpathways pages 5-6, castillo2008asetof pages 1-2, daddaoua2009regulationofglucose pages 1-2) |
| Regulation by HexR | HexR controls expression of glucose-catabolic genes including the edd-glk branch and the zwf/pgl/eda branch; induction links glucose sensing to ED-pathway entry. | HexR binds target promoters with nanomolar-range affinity and is released by the ED intermediate KDPG. | Regulatory understanding is used for pathway rewiring and control of carbon flux in KT2440 chassis engineering (2024; https://doi.org/10.3390/cimb46110761). | (castillo2008asetof pages 1-2, daddaoua2009regulationofglucose pages 1-2) |
| Regulation by GnuR / peripheral glucose control | Recent multi-omics work shows GnuR directly represses genes of peripheral glucose/gluconate catabolism and ED-pathway functions in KT2440; Glk participates in the induced glucose-response program. | Expression of catabolic/TF genes was significantly induced by glucose and gluconate; exact fold change not stated in retrieved excerpt. | Provides a modern regulatory framework for improving glucose utilization in KT2440 (2024; https://doi.org/10.1111/1751-7915.70059). | (chen2024gnurrepressesthe pages 1-3) |
| Additional regulatory systems | Glucose-catabolic gene expression around glk/edd is integrated with other regulators including GltR/GltS (transport-associated regulation) and PtxS / the kgu branch for 2-ketogluconate metabolism. | No Glk-specific kinetic constants provided, but regulatory coupling to transporter/peripheral oxidation branches is well supported. | Relevant for engineering strains that favor specific uptake routes under aerobic or electro-fermentative conditions (2024; https://doi.org/10.1111/1751-7915.14375). | (castillo2007convergentperipheralpathways pages 6-8, castillo2008asetof pages 1-2, daddaoua2009regulationofglucose pages 1-2) |
| Enzyme induction / activity evidence | Glucokinase activity in KT2440 cell extracts is inducible by glucose, supporting Glk as an active enzyme rather than a purely inferred annotation. | ~10-fold increase in glucokinase and gluconokinase activities in glucose-grown cells versus citrate-grown cells. | Biochemical activity evidence underpins strain-design choices when redirecting sugar catabolism (2007; https://doi.org/10.1128/JB.00203-07). | (castillo2007convergentperipheralpathways pages 5-6) |
| Mutant phenotype | Disrupting the glucokinase branch impairs efficient glucose assimilation; foundational studies concluded the glucokinase pathway is functionally important and in some tested genetic backgrounds essential for growth on glucose. | Example values reported for a glk mutant: total carbon consumption about 5.44 mmol g⁻¹ h⁻¹ and biomass yield about 0.35 g biomass/g carbon consumed. | Δglk strains are deliberately used as chassis components to eliminate glucose growth in synthetic consortia or substrate-partitioning designs (2025; https://doi.org/10.1093/synbio/ysaf012). | (castillo2007convergentperipheralpathways pages 5-6, castillo2007convergentperipheralpathways pages 1-2) |
| Flux architecture / EDEMP cycle | Glk supplies G6P to the unusual EDEMP cycle of KT2440, where ED, upper EMP/gluconeogenic reactions, and PP-pathway enzymes are integrated to support NADPH generation and flexible carbon redistribution. | About 10% of triose phosphates were estimated to recycle back to hexose phosphates in the EDEMP architecture. | Core concept for systems biology, modeling, and redox-aware chassis engineering in KT2440 (2015; https://doi.org/10.1074/jbc.M115.687749). | (nikel2015pseudomonasputidakt2440 pages 1-2, nikel2015pseudomonasputidakt2440 media d74e2f18, nikel2015pseudomonasputidakt2440 media d533aa4f) |
| Engineering for sugar co-utilization | Native glk (PP_1011) is exploited in refactoring upper sugar metabolism so intracellular glucose released from cellobiose or imported sugars can be funneled into central metabolism. | Engineering studies identify PP_1011 as the native glucokinase node supporting growth on glucose-containing mixtures. | Co-utilization of cellobiose, xylose, and glucose in engineered KT2440/EM42 (2018; https://doi.org/10.1016/j.ymben.2018.05.019). | (bujdos2021inženýrstvípseudomonasputida pages 40-43, sanchezpascuala2017refactoringtheembden–meyerhof–parnas pages 4-6) |
| Engineering for product formation | Manipulating glucose catabolic routing upstream/downstream of Glk improves production phenotypes such as medium-chain-length PHA in P. putida. | One 2024 study reported 33.7% higher mcl-PHA titer in a ΔgcdΔgltA mutant and up to 117.5% increase in an additional regulatory mutant background, illustrating the leverage of glucose-routing interventions around the Glk branch. | Glucose-pathway modification for enhanced PHA synthesis (2024; https://doi.org/10.3390/cimb46110761). | (chen2024gnurrepressesthe pages 1-3) |
| Bioelectrochemical / anaerobic relevance | Under electro-fermentative conditions, the Glk-dependent phosphorylation route remains part of the energetic accounting for glucose use, and route-specific mutants helped test whether uptake stoichiometry limits anaerobic turnover. | Deletion of individual sugar-uptake routes altered sugar consumption/current output, but secreted acetate concentrations were not significantly different among strains in the reported setup. | Anaerobic glucose uptake in a bioelectrochemical system (2024; https://doi.org/10.1111/1751-7915.14375). | (nguyen2024investigatinganaerobicmetabolism pages 27-30) |
Table: This table summarizes evidence-backed functional annotation for Pseudomonas putida KT2440 glucokinase Glk (PP_1011; UniProt Q88P42), including reaction, pathway role, regulation, quantitative findings, and representative engineering applications. It is useful as a compact reference for assigning function and pathway context to the gene.
References
(castillo2007convergentperipheralpathways pages 5-6): Teresa del Castillo, Juan L. Ramos, José J. Rodríguez-Herva, Tobias Fuhrer, Uwe Sauer, and Estrella Duque. Convergent peripheral pathways catalyze initial glucose catabolism inpseudomonas putida: genomic and flux analysis. Jul 2007. URL: https://doi.org/10.1128/jb.00203-07, doi:10.1128/jb.00203-07. This article has 310 citations and is from a peer-reviewed journal.
(castillo2008asetof pages 1-2): Teresa del Castillo, Estrella Duque, and Juan L. Ramos. A set of activators and repressors control peripheral glucose pathways in pseudomonas putida to yield a common central intermediate. Journal of Bacteriology, 190:2331-2339, Apr 2008. URL: https://doi.org/10.1128/jb.01726-07, doi:10.1128/jb.01726-07. This article has 128 citations and is from a peer-reviewed journal.
(daddaoua2009regulationofglucose pages 1-2): A. Daddaoua, T. Krell, and J. Ramos. Regulation of glucose metabolism in pseudomonas. The Journal of Biological Chemistry, 284:21360-21368, Jun 2009. URL: https://doi.org/10.1074/jbc.m109.014555, doi:10.1074/jbc.m109.014555. This article has 106 citations.
(nguyen2024investigatinganaerobicmetabolism pages 27-30): HAV Nguyen. Investigating anaerobic metabolism of pseudomonas putida using bioelectrochemical cultivation. Unknown journal, 2024.
(chen2024gnurrepressesthe pages 1-3): Wenbo Chen, Rao Ma, Yong Feng, Yunzhu Xiao, Agnieszka Sekowska, Antoine Danchin, and Conghui You. Gnur represses the expression of glucose and gluconate catabolism in pseudomonas putida kt2440. Microbial Biotechnology, Nov 2024. URL: https://doi.org/10.1111/1751-7915.70059, doi:10.1111/1751-7915.70059. This article has 2 citations and is from a peer-reviewed journal.
(castillo2007convergentperipheralpathways pages 1-2): Teresa del Castillo, Juan L. Ramos, José J. Rodríguez-Herva, Tobias Fuhrer, Uwe Sauer, and Estrella Duque. Convergent peripheral pathways catalyze initial glucose catabolism inpseudomonas putida: genomic and flux analysis. Jul 2007. URL: https://doi.org/10.1128/jb.00203-07, doi:10.1128/jb.00203-07. This article has 310 citations and is from a peer-reviewed journal.
(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.
(nikel2015pseudomonasputidakt2440 media d74e2f18): 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.
(castillo2007convergentperipheralpathways pages 6-8): Teresa del Castillo, Juan L. Ramos, José J. Rodríguez-Herva, Tobias Fuhrer, Uwe Sauer, and Estrella Duque. Convergent peripheral pathways catalyze initial glucose catabolism inpseudomonas putida: genomic and flux analysis. Jul 2007. URL: https://doi.org/10.1128/jb.00203-07, doi:10.1128/jb.00203-07. This article has 310 citations and is from a peer-reviewed journal.
(bujdos2021inženýrstvípseudomonasputida pages 40-43): D Bujdoš. Inženýrství pseudomonas putida pro ko-utilizaci a zužitkování celobiózy s glukózou. Unknown journal, 2021.
(sanchezpascuala2017refactoringtheembden–meyerhof–parnas pages 4-6): Alberto Sánchez-Pascuala, Víctor de Lorenzo, and Pablo I. Nikel. Refactoring the embden–meyerhof–parnas pathway as a whole of portable glucobricks for implantation of glycolytic modules in gram-negative bacteria. Feb 2017. URL: https://doi.org/10.1021/acssynbio.6b00230, doi:10.1021/acssynbio.6b00230. This article has 74 citations and is from a domain leading peer-reviewed journal.
(nikel2015pseudomonasputidakt2440 pages 17-19): 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.
(escapa2013theroleof pages 37-41): I. F. Escapa, C. del Cerro, J. L. García, and M. A. Prieto. The role of glpr repressor in pseudomonas putida kt2440 growth and pha production from glycerol. Environmental microbiology, 15 1:93-110, May 2013. URL: https://doi.org/10.1111/j.1462-2920.2012.02790.x, doi:10.1111/j.1462-2920.2012.02790.x. This article has 131 citations and is from a domain leading peer-reviewed journal.
(nikel2015pseudomonasputidakt2440 media d533aa4f): 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.
glk in Pseudomonas putida KT2440 corresponds to UniProt Q88P42 and locus PP_1011, and UniProt annotates the protein as glucokinase (EC 2.7.1.2) in the bacterial glucokinase family with cytoplasmic localization. [file:PSEPK/glk/glk-uniprot.txt "RecName: Full=Glucokinase"; "EC=2.7.1.2"; "SUBCELLULAR LOCATION: Cytoplasm"; "Belongs to the bacterial glucokinase family."]In KT2440, glucose imported into the cytoplasm is phosphorylated by glucokinase to glucose-6-phosphate before conversion to 6-phosphogluconate. [PMID:17483213 Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis, "Glucose is transported to the cytoplasm in a process mediated by an ABC uptake system encoded by open reading frames PP1015 to PP1018 and is then phosphorylated by glucokinase (encoded by the glk gene) and converted by glucose-6-phosphate dehydrogenase (encoded by the zwf genes) to 6-phosphogluconate."]
P. putida catabolizes glucose through three simultaneous routes that converge at 6-phosphogluconate, and the glucokinase branch is quantitatively important within that network. [PMID:17483213 Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis, "glucose catabolism in Pseudomonas putida occurs through the simultaneous operation of three pathways that converge at the level of 6-phosphogluconate"; "although all three functioned simultaneously, the glucokinase pathway and the 2-ketogluconate loop were quantitatively more important than the direct phosphorylation of gluconate."]
The 2007 mutant and flux study concluded that the glucokinase pathway is required for growth on glucose in KT2440. [PMID:17483213 Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis, "It can therefore be concluded that the glucokinase pathway is a sine qua non condition for P. putida to grow with glucose."]
glk is physically linked to the Entner-Doudoroff pathway because edd and glk form one operon in KT2440. [PMID:19506074 Regulation of Glucose Metabolism in Pseudomonas: The Phosphorylative Branch and Entner-Doudoroff Enzymes Are Regulated by a Repressor Containing a Sugar Isomerase Domain, "The edd and glk genes form another operon that encodes, respectively, 6-phosphogluconate dehydratase (the first enzyme of the Entner-Doudoroff pathway) and glucokinase (an enzyme of the glucose phosphorylative pathway)."]
Because of this genomic organization, the glucokinase pathway is co-induced with Entner-Doudoroff genes and is expressed even during growth on gluconate or 2-ketogluconate. [PMID:19506074 Regulation of Glucose Metabolism in Pseudomonas: The Phosphorylative Branch and Entner-Doudoroff Enzymes Are Regulated by a Repressor Containing a Sugar Isomerase Domain, "the glucokinase pathway genes are co-transcribed with Entner-Doudoroff pathway enzymes"; "the glucokinase pathway is induced when bacteria are exposed to gluconate and 2-ketogluconate."]
HexR controls the relevant promoters through sensing KDPG rather than glucose or glucose-6-phosphate, placing glk in a broader glucose-responsive Entner-Doudoroff regulatory module. [PMID:19506074 Regulation of Glucose Metabolism in Pseudomonas: The Phosphorylative Branch and Entner-Doudoroff Enzymes Are Regulated by a Repressor Containing a Sugar Isomerase Domain, "Binding of the Entner-Doudoroff pathway intermediate 2-keto-3-deoxy-6-phosphogluconate to HexR released the repressor from its target operators, whereas other chemicals such as glucose, glucose 6-phosphate, and 6-phosphogluconate did not induce complex dissociation."]
The strongest core annotation for glk is glucokinase activity coupled to glucose catabolism through the Entner-Doudoroff-centered network.
ATP binding and D-glucose binding are mechanistically true but substantially less informative than the specific catalytic term glucokinase activity.
For cellular component, cytosol is the more specific GO term for a soluble bacterial cytoplasmic enzyme, while cytoplasm is acceptable but broader.
id: Q88P42
gene_symbol: glk
product_type: PROTEIN
status: COMPLETE
aliases:
- PP_1011
- Glucokinase
- Glucose kinase
taxon:
id: NCBITaxon:160488
label: Pseudomonas putida KT2440
description: Glk is the cytosolic glucokinase of Pseudomonas putida KT2440. It
phosphorylates imported glucose to glucose-6-phosphate using ATP and feeds the
phosphorylative branch of glucose assimilation into the Entner-Doudoroff-centered
carbohydrate catabolic network. In KT2440, glk is part of the edd-glk operon and
mutant and flux analyses indicate that the glucokinase branch is quantitatively
important for growth on glucose even though P. putida can also oxidize glucose
through periplasmic gluconate and 2-ketogluconate routes.
existing_annotations:
- term:
id: GO:0004340
label: glucokinase activity
qualifier: enables
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: This is the core molecular function of glk. UniProt assigns the protein
as glucokinase (EC 2.7.1.2), and pathway work in KT2440 places Glk at the
ATP-dependent phosphorylation step that converts cytoplasmic glucose to glucose-6-phosphate.
action: ACCEPT
reason: This term is specific, mechanistically correct, and central to the gene's
function.
supported_by:
- reference_id: file:PSEPK/glk/glk-uniprot.txt
supporting_text: 'RecName: Full=Glucokinase'
- reference_id: file:PSEPK/glk/glk-uniprot.txt
supporting_text: 'Reaction=D-glucose + ATP = D-glucose 6-phosphate + ADP + H(+);'
- reference_id: file:PSEPK/glk/glk-notes.md
supporting_text: In KT2440, glucose imported into the cytoplasm is phosphorylated
by glucokinase to glucose-6-phosphate before conversion to 6-phosphogluconate.
- reference_id: file:PSEPK/glk/glk-deep-research-falcon.md
supporting_text: The UniProt target **Q88P42** corresponds to **glk** in *Pseudomonas
putida* KT2440 (ordered locus **PP_1011**) encoding the cytosolic enzyme
**glucokinase (Glk)**, which phosphorylates imported glucose to **glucose‑6‑phosphate
(G6P)** as the entry step of the phosphorylative branch of glucose catabolism.
- term:
id: GO:0005524
label: ATP binding
qualifier: enables
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: ATP binding is mechanistically true for a kinase, but it is much less
informative than the specific catalytic term glucokinase activity and is redundant
for describing the core function of this enzyme.
action: MARK_AS_OVER_ANNOTATED
reason: The catalytic activity term already captures the biologically informative
function.
supported_by:
- reference_id: file:PSEPK/glk/glk-uniprot.txt
supporting_text: /ligand="ATP"
- reference_id: file:PSEPK/glk/glk-notes.md
supporting_text: ATP binding and D-glucose binding are mechanistically true
but substantially less informative than the specific catalytic term glucokinase
activity.
- term:
id: GO:0005536
label: D-glucose binding
qualifier: enables
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: Substrate recognition is implicit in glucokinase activity, so this term
is not wrong but is less informative than the specific catalytic annotation.
action: MARK_AS_OVER_ANNOTATED
reason: This binding term adds little beyond the core enzymatic activity term.
supported_by:
- reference_id: file:PSEPK/glk/glk-notes.md
supporting_text: In KT2440, glucose imported into the cytoplasm is phosphorylated
by glucokinase to glucose-6-phosphate before conversion to 6-phosphogluconate.
- reference_id: file:PSEPK/glk/glk-notes.md
supporting_text: ATP binding and D-glucose binding are mechanistically true
but substantially less informative than the specific catalytic term glucokinase
activity.
- term:
id: GO:0005737
label: cytoplasm
qualifier: located_in
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: Glk is a soluble intracellular enzyme and cytoplasmic localization is
correct, but the more precise term in this context is cytosol.
action: MODIFY
reason: Cytoplasm is broader than needed for a soluble bacterial enzyme.
proposed_replacement_terms:
- id: GO:0005829
label: cytosol
supported_by:
- reference_id: file:PSEPK/glk/glk-uniprot.txt
supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm'
- reference_id: file:PSEPK/glk/glk-notes.md
supporting_text: For cellular component, cytosol is the more specific GO term
for a soluble bacterial cytoplasmic enzyme, while cytoplasm is acceptable
but broader.
- term:
id: GO:0005829
label: cytosol
qualifier: located_in
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: This is the preferred cellular component term for a soluble cytoplasmic
enzyme such as Glk and is more precise than the broader term cytoplasm.
action: ACCEPT
reason: Specific and biologically appropriate localization term.
supported_by:
- reference_id: file:PSEPK/glk/glk-uniprot.txt
supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm'
- reference_id: file:PSEPK/glk/glk-notes.md
supporting_text: For cellular component, cytosol is the more specific GO term
for a soluble bacterial cytoplasmic enzyme, while cytoplasm is acceptable
but broader.
- term:
id: GO:0006096
label: glycolytic process
qualifier: involved_in
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: Glk participates in glucose catabolism to pyruvate, but in P. putida
KT2440 that process is routed through the Entner-Doudoroff-centered network
rather than a generic undifferentiated glycolysis term.
action: MODIFY
reason: A more pathway-specific biological process term is available.
proposed_replacement_terms:
- id: GO:0061688
label: glycolytic process via Entner-Doudoroff Pathway
supported_by:
- reference_id: file:PSEPK/glk/glk-notes.md
supporting_text: glk is physically linked to the Entner-Doudoroff pathway because
edd and glk form one operon in KT2440.
- reference_id: file:PSEPK/glk/glk-notes.md
supporting_text: Because of this genomic organization, the glucokinase pathway
is co-induced with Entner-Doudoroff genes and is expressed even during growth
on gluconate or 2-ketogluconate.
- reference_id: file:PSEPK/glk/glk-deep-research-falcon.md
supporting_text: 'This physical linkage is consistent with functional coupling:
the **glucokinase entry step (Glk)** and the subsequent ED processing step
(Edd) are transcriptionally coordinated.'
- term:
id: GO:0051156
label: glucose 6-phosphate metabolic process
qualifier: involved_in
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: This term accurately reflects the immediate pathway context of Glk, which
generates glucose-6-phosphate from glucose and ATP.
action: ACCEPT
reason: Directly describes the metabolic process in which the enzymatic reaction
participates.
supported_by:
- reference_id: file:PSEPK/glk/glk-uniprot.txt
supporting_text: 'Reaction=D-glucose + ATP = D-glucose 6-phosphate + ADP + H(+);'
- reference_id: file:PSEPK/glk/glk-notes.md
supporting_text: In KT2440, glucose imported into the cytoplasm is phosphorylated
by glucokinase to glucose-6-phosphate before conversion to 6-phosphogluconate.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms.
findings:
- statement: InterPro-based annotation captures the conserved glucokinase family
assignment and related substrate-level inferences.
- id: GO_REF:0000118
title: TreeGrafter-generated GO annotations
findings:
- statement: TreeGrafter provides a phylogeny-based cellular component inference
for this conserved bacterial glucokinase family.
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods.
findings:
- statement: Automated UniProt and rule-based methods recover the core glucokinase
activity and broad glucose catabolic process assignments for glk.
- id: PMID:17483213
title: "Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas
putida: genomic and flux analysis."
findings:
- statement: Glucose catabolism in P. putida occurs through three simultaneous pathways
converging at 6-phosphogluconate.
supporting_text: glucose catabolism in Pseudomonas putida occurs through the
simultaneous operation of three pathways that converge at the level of 6-phosphogluconate
- statement: Glucose imported into the cytoplasm is phosphorylated by glucokinase
to glucose-6-phosphate.
supporting_text: Glucose is transported to the cytoplasm in a process mediated
by an ABC uptake system encoded by open reading frames PP1015 to PP1018 and
is then phosphorylated by glucokinase (encoded by the glk gene) and converted
by glucose-6-phosphate dehydrogenase (encoded by the zwf genes) to 6-phosphogluconate.
- statement: The glucokinase pathway and 2-ketogluconate loop are quantitatively
more important than direct gluconate phosphorylation.
supporting_text: although all three functioned simultaneously, the glucokinase
pathway and the 2-ketogluconate loop were quantitatively more important than
the direct phosphorylation of gluconate.
- statement: The glucokinase pathway is required for growth on glucose in KT2440.
supporting_text: It can therefore be concluded that the glucokinase pathway is
a sine qua non condition for P. putida to grow with glucose.
- id: PMID:19506074
title: "Regulation of Glucose Metabolism in Pseudomonas: The Phosphorylative
Branch and Entner-Doudoroff Enzymes Are Regulated by a Repressor Containing
a Sugar Isomerase Domain."
findings:
- statement: The glucose phosphorylative pathway and Entner-Doudoroff pathway
are organized into operons that include an edd-glk-gltR2-gltS operon.
supporting_text: In Pseudomonas putida, genes for the glucose phosphorylative
pathway and the Entner-Doudoroff pathway are organized in two operons; one
made up of the zwf, pgl, and eda genes and another consisting of the edd,
glk, gltR2, and gltS genes.
- statement: Expression from P(zwf), P(edd), and P(gap) is modulated by HexR
in response to glucose availability.
supporting_text: Expression from P(zwf), P(edd), and P(gap) is modulated by
HexR in response to the availability of glucose in the medium.
- statement: Binding of KDPG to HexR releases the repressor, whereas glucose,
glucose 6-phosphate, and 6-phosphogluconate do not.
supporting_text: Binding of the Entner-Doudoroff pathway intermediate 2-keto-3-deoxy-6-phosphogluconate
to HexR released the repressor from its target operators, whereas other chemicals
such as glucose, glucose 6-phosphate, and 6-phosphogluconate did not induce
complex dissociation.
- id: file:PSEPK/glk/glk-uniprot.txt
title: UniProt entry Q88P42
findings:
- statement: glk corresponds to PP_1011 in Pseudomonas putida KT2440.
- statement: UniProt annotates the protein as glucokinase EC 2.7.1.2.
- statement: The catalytic reaction is D-glucose plus ATP to D-glucose 6-phosphate
plus ADP and H+.
- statement: UniProt places the protein in the cytoplasm and in the bacterial glucokinase
family.
- id: file:PSEPK/glk/glk-notes.md
title: Curator notes for glk in Pseudomonas putida KT2440
findings:
- statement: The core role of glk is ATP-dependent phosphorylation of glucose to
glucose-6-phosphate.
- statement: glk is physically and transcriptionally linked to the Entner-Doudoroff
pathway.
- statement: Generic binding terms are less informative than glucokinase activity
for this enzyme.
- id: file:PSEPK/glk/glk-deep-research-falcon.md
title: Deep research report for glk generated with Falcon
findings:
- statement: Q88P42 corresponds to glk/PP_1011 and encodes the cytosolic glucokinase
of Pseudomonas putida KT2440.
- statement: Falcon research links glk to the phosphorylative branch of glucose
catabolism and the edd-glk operon.
- statement: Falcon research summarizes inducible glucokinase activity and mutant
phenotypes supporting pathway relevance in KT2440.
core_functions:
- description: Glk is a soluble cytosolic glucokinase that uses ATP to phosphorylate
imported glucose to glucose-6-phosphate, thereby feeding the phosphorylative
arm of glucose assimilation into the Entner-Doudoroff-centered glycolytic network
of Pseudomonas putida KT2440.
molecular_function:
id: GO:0004340
label: glucokinase activity
directly_involved_in:
- id: GO:0051156
label: glucose 6-phosphate metabolic process
- id: GO:0061688
label: glycolytic process via Entner-Doudoroff Pathway
locations:
- id: GO:0005829
label: cytosol
supported_by:
- reference_id: file:PSEPK/glk/glk-uniprot.txt
supporting_text: 'Reaction=D-glucose + ATP = D-glucose 6-phosphate + ADP + H(+);'
- reference_id: file:PSEPK/glk/glk-notes.md
supporting_text: In KT2440, glucose imported into the cytoplasm is phosphorylated
by glucokinase to glucose-6-phosphate before conversion to 6-phosphogluconate.
- reference_id: file:PSEPK/glk/glk-notes.md
supporting_text: glk is physically linked to the Entner-Doudoroff pathway because
edd and glk form one operon in KT2440.
- reference_id: file:PSEPK/glk/glk-deep-research-falcon.md
supporting_text: The UniProt target **Q88P42** corresponds to **glk** in *Pseudomonas
putida* KT2440 (ordered locus **PP_1011**) encoding the cytosolic enzyme **glucokinase
(Glk)**, which phosphorylates imported glucose to **glucose‑6‑phosphate (G6P)**
as the entry step of the phosphorylative branch of glucose catabolism.
proposed_new_terms: []
suggested_questions:
- question: How does flux through the glucokinase branch versus the periplasmic
gluconate and 2-ketogluconate branches change across different glucose concentrations
and oxygen or redox conditions in KT2440?
- question: Does Glk have kinetic or regulatory specialization that distinguishes
it from glucokinases in other pseudomonads that use different balances of oxidative
and phosphorylative glucose uptake?
- question: How strongly does HexR-mediated control of the edd-glk operon constrain
mixed-substrate utilization when glucose and gluconate are simultaneously available?
suggested_experiments:
- experiment_type: Enzyme biochemistry
description: Purify PP_1011 and measure steady-state kinetics for glucose and ATP,
substrate specificity, and cofactor dependence under physiologically relevant
ionic conditions.
- experiment_type: Genetic perturbation and flux analysis
description: Construct a clean glk deletion and complemented strain, then quantify
growth and intracellular carbon flux on glucose, gluconate, and mixed carbon
sources using isotopic tracer experiments.
- experiment_type: Operon regulation
description: Use promoter reporters or RNA-seq in wild type and hexR backgrounds
to quantify how glucose, gluconate, 2-ketogluconate, and KDPG-related perturbations
regulate the edd-glk-gltR2-gltS operon.