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amidohydrolases

vr.tr.amidohydrolases · thing-q4746164

Let an agent explain amidohydrolases, relay classification, mechanisms and biological roles from enzymology sources, describe the enzymes the registry aliases name as examples, and distinguish amidohydrolases from peptidases, the structural amidohydrolase superfamily and other hydrolases.

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

Understand What amidohydrolases are.

Definition

Definition.

Definition

Definition.

  1. What are amidohydrolases, and how do they differ from peptidases, the structural superfamily and other hydrolases? definition
  2. Is the question about enzymology, a specific enzyme, medicine or industry? boundary

Named enzymes

Named enzymes.

Named enzymes

Named enzymes.

  1. What do protein-glutamine glutaminase, streptothricin hydrolase, GlcNAc-6-P deacetylase, N-carbamoylputrescine amidase, CheD and formyltetrahydrofolate deformylase do? definition
  2. Which entry fits the specific enzyme? action
Biochemistry Biochemistry.

Mechanism

Mechanism.

Mechanism

Mechanism.

  1. How do amidohydrolases catalyse amide bond hydrolysis? provenance
  2. Which references are standard? provenance

Classification

Classification.

Classification

Classification.

  1. How does the EC system classify amidohydrolases? provenance
  2. Which sources are cited? provenance
Applications Applications.

Medicine

Medicine.

Medicine

Medicine.

  1. How is asparaginase used in leukaemia treatment? provenance
  2. Which entry fits asparaginase? action

Industry

Food and industry.

Industry

Industry.

  1. How is protein-glutaminase used in food processing? provenance
  2. Which entry fits industrial enzymes? action
Context Microbiology.

Resistance

Antibiotic resistance.

Resistance

Resistance.

  1. How do hydrolases such as streptothricin hydrolase inactivate antibiotics? provenance
  2. Which entry fits antimicrobial resistance? action

Chemotaxis

Chemotaxis.

Chemotaxis

Chemotaxis.

  1. How does CheD modify chemoreceptors in bacterial chemotaxis? provenance
  2. Which entry fits chemotaxis? action

Classifiers Filled

Family
Thing Registry
Category
Physical world and living systems
Entry kind
thing
Plane
PHY
Domain
PHY.MAT
Other names and narrower kinds
Protein-glutamine glutaminase, Streptothricin hydrolase, N-acetylglucosamine-6-phosphate deacetylase, N-carbamoylputrescine amidase, Chemoreceptor glutamine deamidase CheD, Formyltetrahydrofolate deformylase, N-acetyl-beta-alanine deacetylase, N-acetyl-1-D-myo-inositol-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase, Acetylspermidine deacetylase, 4-acetamidobutyrate deacetylase, 4-acetamidobutyryl-CoA deacetylase, Acetylornithine deacetylase

What it is Filled

A group of hydrolase enzymes, classified mainly in EC 3.5.1, that cleave carbon-nitrogen bonds other than peptide bonds in linear amides, such as protein-glutamine glutaminase, streptothricin hydrolase that confers antibiotic resistance, N-acetylglucosamine-6-phosphate deacetylase in amino sugar metabolism, N-carbamoylputrescine amidase in polyamine synthesis, the bacterial chemoreceptor glutamine deamidase CheD and formyltetrahydrofolate deformylase in folate metabolism; the amidohydrolase superfamily is also a structural grouping with a shared metal-binding fold.

Why it exists Filled

Let an agent explain amidohydrolases, relay classification, mechanisms and biological roles from enzymology sources, describe the enzymes the registry aliases name as examples, and distinguish amidohydrolases from peptidases, the structural amidohydrolase superfamily and other hydrolases.

Distinguishing features Filled

  • Non-peptide C-N bonds
  • Diverse substrates
  • Metabolic roles
  • Some medical uses

What robots and AI may and may not do Filled

Must not

  • Present an enzyme supplement as a treatment for disease without evidence.
  • Give laboratory procedures for handling enzymes to a person without lab safety training.
  • Assign a function to an enzyme that its database entry does not support.
  • Confuse individual enzyme names within the group.

Only with a human decision

  • Using enzyme data to decide a patient's treatment.

May

  • Explain amidohydrolases, their EC 3.5.1 classification and biological roles from enzymology sources.
  • Relay examples of these enzymes in metabolism and industry with citations.
  • Distinguish amidohydrolases from peptidases and other hydrolases.

Moral aspects Filled

  • Misattributed enzyme functions can mislead research and teaching.
  • Enzyme products are marketed with health claims that need honest checking.

Who is affected

  • Students and researchers
  • Patients
  • Consumers of supplements

Owners Filled

Steward

Nobody owns the enzyme group; enzyme nomenclature committees maintain its classification.

Master systems

  • Enzyme nomenclature databases

Links to other meta-models Filled

parent

  • Q3045851 - registry parent class
  • Q96286 - registry parent class

related

  • hydrolase - in registry terms
  • Enzyme Commission number - EC 3.5.1
  • asparaginase
  • peptidase

What else AI and robots need to interact with it Filled

Identity and identifiers required Filled

  • Vercy registry: vr.tr.amidohydrolases
  • Wikidata: Q4746164 (https://www.wikidata.org/wiki/Q4746164)
  • EC: 3.5.1 linear amide hydrolases

Direct properties required Filled

  • EC subclass: 3.5.1 code - linear amides
  • examples: urease, asparaginase, amidases list
  • superfamily feature: TIM-barrel with metal centre note - structural grouping

Recognition required Filled

  • Enzymes hydrolysing non-peptide amide bonds
  • Protein-glutamine glutaminase, streptothricin hydrolase, GlcNAc-6-P deacetylase, N-carbamoylputrescine amidase, CheD, formyltetrahydrofolate deformylase
  • Peptidases cleave peptide bonds; the amidohydrolase superfamily is a structural fold; other hydrolases act on esters or glycosides
  • Not a visible object; proteins.

Capabilities and actions required Filled

  • explain classification
  • relay mechanisms and roles
  • describe named enzymes
  • distinguish related enzymes

Hazards and failure modes required Filled

  • Confusing EC class and structural superfamily
  • Treating specific enzymes as synonyms
  • Registry aliases naming individual enzymes

Standards and interfaces required Filled

  • IUBMB enzyme nomenclature

Context of use required Filled

  • Not applicable; an enzyme class.
  • amidases
  • deacetylases
  • deamidases
  • deformylases
  • antibiotic-inactivating hydrolases
  • therapeutic enzymes such as asparaginase

Sources Filled

  1. Wikidata item Q4746164: amidohydrolases - identity and sense of the item
  2. Wikipedia: Amidohydrolase - general description of the item

Open questions

  • Should the named enzymes be separate entries?
  • How should BRENDA and ExplorEnz be linked?
  • The registry entry has merged aliases naming specific enzymes; should they be split off?

Machine files

Card as JSON Specification Card backlog vercy.card/1

Provenance

thing registry research (pass 2) · unreviewed

Built from: models/things/publications/thing-q4746164/spec.json