Published
alcohol oxidoreductase
vr.tr.alcohol-oxidoreductase · thing-q4713306
Let an agent handle alcohol oxidoreductases by EC class, reaction, cofactor, biological role and data sources.
Thing Registry Physical world and living systems PHY.MAT
Bundle → Layer → Finding → QuestionsClassifiersWhat it isWhy it existsDistinguishing featuresWhat robots and AI may and may not doMoral aspectsOwnersLinks to other meta-modelsIdentity and identifiersDirect propertiesRecognitionCapabilities and actionsHazards and failure modesStandards and interfacesContext of useSources
Bundle → Layer → Finding → Questions Filled
4 bundles · 8 layers · 8 findings · 16 questions
Classification EC numbers.
EC
Number.
EC
EC number.
- What is the full EC number of this enzyme? provenance
- Which acceptor subclass is it in? definition
Names
Systematic names.
Names
Names.
- What are its systematic and accepted names? provenance
- Has it been reclassified? provenance
Reaction Chemistry.
Substrate
Donor.
Substrate
Substrates.
- Which alcohol substrate does it oxidise, and what is the product? definition
- What is its substrate specificity? measurement
Cofactor
Acceptor.
Cofactor
Cofactor.
- Which cofactor or acceptor does it use? definition
- What are its kinetic parameters? measurement
Biology Role.
Pathway
Metabolism.
Pathway
Pathways.
- Which metabolic pathway does it participate in? provenance
- In which organisms? provenance
Health
Deficiency.
Health
Health links.
- Is a deficiency of this enzyme linked to a condition, according to medical sources? provenance
- Is the user asking about their own health? boundary
Data Databases.
Databases
BRENDA and UniProt.
Databases
Databases.
- Which database entries describe this enzyme? provenance
- Is a structure available in the PDB? provenance
Applications
Biotech.
Applications
Applications.
- How is the enzyme used in diagnostics or biocatalysis? provenance
- Which products use it? provenance
Classifiers Filled
- Family
- Thing Registry
- Category
- Physical world and living systems
- Entry kind
- thing
- Plane
- PHY
- Domain
- PHY.MAT
- Other names and narrower kinds
- Sulfopropanediol 3-dehydrogenase, Sulfoacetaldehyde reductase, Uracil dehydrogenase, 2-Deoxy-scyllo-inosamine dehydrogenase (SAM-dependent), PQQ-dependent membrane bound dehydrogenase, glucose-6-phosphate dehydrogenase, Bile-acid 7alpha-dehydroxylase, Testosterone 17-beta-dehydrogenase 3, oxidoreductase, acting on the CH-OH group of donors, NAD or NADP as acceptor, oxidoreductase, acting on the CH-OH group of donors, oxygen as acceptor, oxidoreductase, acting on the CH-OH group of donors, cytochrome as acceptor, oxidoreductase, acting on the CH-OH group of donors, quinone or similar compound as acceptor
What it is Filled
A group of oxidoreductase enzymes that act on the CH-OH group of donors, classified under EC 1.1, including alcohol dehydrogenase, lactate dehydrogenase and glucose-6-phosphate dehydrogenase, usually using NAD+ or NADP+ as acceptor.
Why it exists Filled
Let an agent handle alcohol oxidoreductases by EC class, reaction, cofactor, biological role and data sources.
Distinguishing features Filled
- Oxidise alcohol groups
- Mostly use NAD(P)+
- Very large class
- Central to metabolism
What robots and AI may and may not do Filled
Must not
- Confuse EC subclasses or assign wrong EC numbers.
- Interpret a person's enzyme test results as a diagnosis.
Only with a human decision
- Medical decisions based on enzyme tests.
May
- Report enzymes in this group with their EC numbers from enzyme nomenclature databases.
- Explain their reactions and roles in metabolism.
Moral aspects Filled
- Accurate classification underpins research and diagnostics.
Who is affected
- Researchers and students
- Patients undergoing tests
Owners Filled
Steward
Nobody owns the group; enzyme nomenclature is kept by the scientific community.
Master systems
- Enzyme nomenclature lists
Links to other meta-models Filled
parent
- Q407479 - registry parent class
related
- oxidoreductase - category
- alcohol dehydrogenase - example
- NAD+ - cofactor
- EC number - scheme
What else AI and robots need to interact with it Filled
Identity and identifiers required Filled
- Vercy registry: vr.tr.alcohol-oxidoreductase
- Wikidata: Q4713306 (https://www.wikidata.org/wiki/Q4713306)
- EC number: 1.1 enzyme subclass
Direct properties required Filled
- Molecular mass: kDa - Determine mass from the specific enzyme sequence or mass spectrometry, distinguishing individual subunits from assembled complexes.
- Isoelectric point: pH units - Measure the pH at which the specified enzyme has zero net charge using isoelectric focusing.
- Hydrodynamic radius: nm - Measure the effective solution radius using a suitable diffusion-based method while recording buffer conditions and aggregation state.
Recognition required Filled
- EC numbers beginning 1.1
- Dehydrogenases using NAD+ or NADP+
- Oxidases acting on other groups belong elsewhere
- Proteins, not visible; described by structures and reactions.
Capabilities and actions required Filled
- classify an enzyme by EC number
- describe the reaction and cofactor
- find enzyme data in databases
- relate enzymes to metabolism and disease in general terms
Hazards and failure modes required Filled
- Confusing EC subclasses
- Over-interpreting diagnostic enzyme tests
Standards and interfaces required Filled
- IUBMB enzyme nomenclature
Context of use required Filled
- Metabolism, biochemistry, diagnostics and biotechnology.
- EC 1.1.1 with NAD+ or NADP+ as acceptor
- EC 1.1.2 with a cytochrome as acceptor
- EC 1.1.3 with oxygen as acceptor
- EC 1.1.5 with a quinone as acceptor
- other acceptors
Sources Filled
- Wikidata item Q4713306: alcohol oxidoreductase - identity and sense of the item
- Wikipedia: Alcohol oxidoreductase - general description of the item
Open questions
- Should each enzyme be a separate entry?
- How should BRENDA and UniProt be linked?
- How should EC reclassification be tracked?
Machine files
Provenance
thing registry research (pass 2) · unreviewed
Built from: models/things/publications/thing-q4713306/spec.json