L-gulonolactone oxidase
Enable an agent to identify L-gulonolactone oxidase, assess whether a particular protein preparation is catalytically competent, and judge its suitability for a specified biochemical use.
Bundle → Layer → Finding → Questions Filled
6 bundles · 11 layers · 16 findings · 26 questions
Enzyme identity Establish which protein form is being represented and how strongly its catalytic assignment is supported.
Reaction assignment
Connect the registered thing to a supported enzyme classification.
EC assignment evidence
Record whether assignment to EC 1.1.3.8 follows direct catalytic characterization, curated annotation or sequence inference.
- What evidence supports assigning this protein to L-gulonolactone oxidase activity? definition
- Which accession, publication or assay record supports the assignment, and was its evidence inspected? provenance
Protein form
Identify the biological molecule rather than only its gene symbol.
Orthologue and construct
Attach observations to a specific organism, sequence and native or engineered protein form.
- Which organism, protein sequence and accession version define the material? provenance
- Does the record describe an intact protein, a modified construct or a genetic locus without demonstrated protein production? boundary
Catalytic transformation Represent the substrate, acceptor and products that establish the enzyme's biochemical function.
Substrate recognition
Resolve lactone identity and experimentally supported substrate range.
Lactone specificity
Record substrate stereochemistry and ring form, and distinguish tested alternative substrates from assumed equivalents.
- Was the tested substrate verified as L-gulono-1,4-lactone, and what was its purity? measurement
- Which related lactones were tested under comparable conditions, and how did their turnover differ? boundary
Oxygen and products
Separate enzymatic oxidation from subsequent product chemistry.
Reaction accounting
Track oxygen consumption, peroxide formation and the distinction between immediate oxidation product and final ascorbate endpoint.
- Which measurements establish oxygen-dependent lactone oxidation and peroxide production in this preparation? measurement
- Does the reported rate measure immediate oxidation, subsequent ascorbate appearance or a coupled reporter reaction? definition
Functional protein context Record the cofactor and physical environment associated with the measured protein.
Flavin state
Assess cofactor identity and occupancy independently of protein concentration.
FAD competence
Capture measured FAD content, evidence concerning its attachment and the relationship between cofactor state and activity.
- What measurements establish FAD identity, occupancy and attachment in this protein form? measurement
- If flavin occupancy is deficient, is there evidence that a specified reconstitution procedure restores activity? action
Membrane environment
Preserve the distinction between native localization and the physical form used experimentally.
Localization and solubilization
Record localization evidence and any membrane extraction, detergent exposure or reconstitution associated with the activity result.
- Is the reported membrane localization demonstrated for this organism or transferred from another protein? provenance
- How did solubilization or a change in lipid environment affect recovered L-gulonolactone oxidase activity? measurement
Activity and assay validity Determine whether an observed signal supports a quantitative claim about this enzyme.
Conditional kinetics
Keep kinetic measurements attached to the conditions that produced them.
Rate conditions
Record substrate concentration, dissolved oxygen, pH, temperature and the normalization basis for each rate.
- Under what substrate, oxygen, pH and temperature conditions was the initial rate measured? measurement
- Do the data justify a kinetic parameter estimate, or only an activity value at one condition? boundary
Signal attribution
Separate target-enzyme turnover from background and coupled-assay limitations.
Orthogonal assay controls
Require controls for substrate-independent signals, peroxide removal and product loss where they affect interpretation.
- What do no-substrate, no-enzyme and validated inactive-enzyme controls show? measurement
- Which independent product or oxygen measurement can confirm that the reporter signal tracks the target reaction? action
Preparation fitness Judge whether a particular enzyme preparation can support its intended biochemical use.
Composition and interference
Characterize the preparation components that affect turnover or its measurement.
Active material quality
Record target-protein content, degradation and components that could consume peroxide, oxidize ascorbate or interfere with detection.
- How much intact target protein is present, and how was its proportion measured? measurement
- Which contaminants or formulation components could change the measured peroxide or ascorbate signal? boundary
Handling and use
Translate preparation-specific stability evidence into a use decision.
Retained catalytic fitness
Base storage and reuse decisions on retained activity under documented conditions, including any effects of reaction-associated peroxide.
- What fraction of activity remains after the recorded storage period, freeze-thaw history or reaction exposure? measurement
- What activity threshold and peroxide-management conditions must this preparation satisfy for the intended use? action
Evidence and external alignment What the world already says about this thing, gathered so the model can be checked against it.
Reported evidence
Findings from the breadth pass, kept separate from the structural claims.
Check these first
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these check these first hold for the sense of L-gulonolactone oxidase this model covers, and on what evidence? provenance
Identifiers and schemes
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these identifiers and schemes hold for the sense of L-gulonolactone oxidase this model covers, and on what evidence? provenance
Standards and regulation
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these standards and regulation hold for the sense of L-gulonolactone oxidase this model covers, and on what evidence? provenance
Real-world use
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these real-world use hold for the sense of L-gulonolactone oxidase this model covers, and on what evidence? provenance
Failure modes and hazards
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these failure modes and hazards hold for the sense of L-gulonolactone oxidase this model covers, and on what evidence? provenance
Neighbouring kinds and how to tell them apart
Recalled without web access and unsourced; every item is a lead to verify.
- Which of these neighbouring kinds and how to tell them apart hold for the sense of L-gulonolactone oxidase this model covers, and on what evidence? provenance
Classifiers Filled
- Family
- Thing Registry
- Category
- Physical world and living systems
- Entry kind
- thing
- Plane
- PHY
- Domain
- PHY.MAT
What it is Filled
L-gulonolactone oxidase is a flavin-dependent enzyme (EC 1.1.3.8) that oxidizes L-gulono-1,4-lactone using molecular oxygen, producing hydrogen peroxide and an intermediate that spontaneously rearranges to L-ascorbate in the final step of vitamin C biosynthesis in animals possessing this pathway.
In scope
- Enzyme identity and evidence for assignment to EC 1.1.3.8
- Organism, protein sequence, native form and engineered variants
- Substrate recognition, oxygen-dependent catalysis and product formation
- Flavin cofactor state and preparation-specific membrane context
- Activity measurements, preparation quality and retained catalytic function
Out of scope
- GULO genes and pseudogenes as independently modelled genetic entities
- L-gulonolactone, ascorbate and hydrogen peroxide as chemical substances
- Complete vitamin C biosynthetic pathways and organismal nutritional requirements
- Other lactone oxidases and dehydrogenases as separate enzyme identities
- Commercial reagent formulations and therapeutic interventions as products or procedures
Why it exists Filled
Enable an agent to identify L-gulonolactone oxidase, assess whether a particular protein preparation is catalytically competent, and judge its suitability for a specified biochemical use.
Distinguishing features Filled
- Require evidence connecting the protein to EC 1.1.3.8 rather than relying on the abbreviation GULO alone; the accepted identity is documented by [IUBMB](https://iubmb.qmul.ac.uk/enzyme/EC1/1/3/8.html).
- Test L-gulono-1,4-lactone turnover with oxygen as acceptor and peroxide formation; ascorbate production alone is insufficient to establish this reaction identity. See [IUBMB reaction nomenclature](https://iubmb.qmul.ac.uk/enzyme/EC1/1/3/8.html).
- Distinguish the immediate oxidation product from ascorbate formed through subsequent spontaneous isomerization, as specified by [IUBMB](https://iubmb.qmul.ac.uk/enzyme/EC1/1/3/8.html).
- Resolve a protein accession and organism separately from its encoding gene: the [pig UniProt entry](https://www.uniprot.org/uniprotkb/Q8HXW0/entry) identifies protein Q8HXW0 and gene GULO as different records.
- Compare substrate and electron-acceptor dependence with candidate neighbouring lactone enzymes instead of identifying the enzyme from vitamin C pathway association alone.
What robots and AI may and may not do Filled
Must not
- Use the human gene loss to support claims that some groups of people are inferior.
- Promote vitamin C megadoses as treatments based on this enzyme without evidence.
- Help modify animals or people genetically outside lawful, ethically approved research.
Only with a human decision
- Animal research involving the enzyme or its gene.
May
- Describe L-gulonolactone oxidase and why humans and some animals cannot make vitamin C.
- Annotate the enzyme and its gene using recognized databases.
Moral aspects Filled
- Animals that lack it, such as guinea pigs, depend on keepers to provide vitamin C.
- Evolutionary findings can be twisted to support false health claims.
Who is affected
- Animals in care
- Patients exposed to false claims
- Researchers
Owners Filled
Steward
Nobody owns the enzyme; curated enzyme databases maintain records of it.
Master systems
- Enzyme nomenclature and protein databases
Links to other meta-models Filled
parent
- Q106925555 - registry parent class
- Q4713306 - registry parent class
What else AI and robots need to interact with it Filled
Identity and identifiers required Filled
- Vercy registry: vr.tr.l-gulonolactone-oxidase
- Wikidata: Q2282493 (https://www.wikidata.org/wiki/Q2282493)
Direct properties required Filled
- Catalytic identity: EC 1.1.3.8; experimentally supported, sequence-inferred or unresolved assignment
- Biological and sequence identity: Organism and strain identifiers; protein accession and version; sequence; variant or construct
- Preparation form: Native membrane fraction, detergent-solubilized protein, purified recombinant protein or other documented form
- FAD occupancy: mol FAD/mol protein, with method and uncertainty
- Specific activity: µmol defined substrate consumed or product formed/min/mg protein, under stated assay conditions
- Apparent substrate kinetics: Apparent Km in mM; Vmax in µmol/min/mg; temperature, pH and oxygen conditions required
- Oxygen availability: Dissolved O2 in µM or documented oxygenation conditions
- Catalytic competence: Demonstrated active, below detection under stated conditions, inactive by validated test or untested
- Retained activity: % of initial activity after specified storage or handling exposure
Recognition required Filled
- Not visible; detected by enzyme assays or genetic analysis.
Capabilities and actions required Filled
- Resolve an enzyme name to a supported protein identity and related gene record.
- Select a preparation whose organism, construct and physical form match the intended experiment.
- Design a substrate- and oxygen-controlled assay with independent confirmation of product identity.
- Compare catalytic performance across preparations using compatible assay conditions.
- Investigate low activity through cofactor, oxygen, membrane-context and preparation-quality checks.
- Accept, recharacterize or reject a preparation against explicit activity and stability criteria.
Hazards and failure modes required Filled
- Lack of the active enzyme means scurvy if diet lacks vitamin C.
Standards and interfaces required Filled
- The enzyme classification maintained by the International Union of Biochemistry and Molecular Biology assigns L-gulonolactone oxidase to EC 1.1.3.8.
Context of use required Filled
- This enzyme participates in the final stage of vitamin C biosynthesis in animals that retain a functional pathway.
- Biochemical research uses it to investigate flavin-dependent oxidation, ascorbate synthesis and differences between species.
- Assessment of an enzyme preparation considers its biological source, catalytic activity and compatibility with the intended assay.
Sources Filled
- Wikidata item Q2282493: L-gulonolactone oxidase - identity and sense of the item
- Wikipedia: L-gulonolactone oxidase - general description of the item
Open questions
- Does the registry intend all proteins assigned EC 1.1.3.8 or a particular biological enzyme form, and does an existing Vercy model already cover that identity?
- Which orthologues have directly demonstrated substrate specificity, FAD attachment and membrane localization rather than inferred annotations?
- Which primary studies provide comparable kinetic and stability measurements with explicit oxygen and preparation conditions?
- What assay controls are necessary to quantify this enzyme reliably in each intended crude, microsomal or purified preparation?
- Which preparation-specific handling limits and peroxide exposures preserve sufficient activity for the intended applications?
Machine files
Provenance
thing registry research (pass 2) · unreviewed
Built from: models/things/publications/thing-q2282493/spec.json