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Research draft

lyase

vr.tr.lyase · PHY.MAT

Let an agent explain lyases and their classification, relay subclasses and examples from enzyme databases, describe roles in metabolism and biotechnology, and distinguish lyases from other enzyme classes.

Thing Registry Physical world and living systems

Research draft, second pass

A second pass drafted this model: the structure a model of this thing needs, and what is known about it in the world. The line under this one says how the second half was obtained - researched against sources, or recalled without web access, in which case nothing here was read anywhere and every claim is a lead to verify. Unreviewed either way.

written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify

Researched by: Claude

Purpose and description

Let an agent explain lyases and their classification, relay subclasses and examples from enzyme databases, describe roles in metabolism and biotechnology, and distinguish lyases from other enzyme classes.

A class of enzymes that catalyse the breaking of chemical bonds by means other than hydrolysis or oxidation, forming a double bond or ring, or the reverse addition of groups to double bonds, classified as EC 4 and including decarboxylases, aldolases, dehydratases such as dihydroxy-acid dehydratase, desulfhydrases such as D-cysteine desulfhydrase, methionine gamma-lyase, holocytochrome-c synthase and many others; lyases are central to metabolism and are used in biocatalysis.

What it is for: Catalysing non-hydrolytic bond cleavage and addition.

It can be explain the class and subclasses; relay examples and nomenclature; describe metabolic and industrial roles; distinguish from other classes.

Distinguishing features

Non-hydrolytic cleavage

Double bond or ring formation

Seven subclasses

Reversible addition

What it looks like

Not visible; proteins shown as structural models.

How it is recognised

EC 4 enzymes

Carbon-carbon, carbon-oxygen, carbon-nitrogen and carbon-sulfur lyases

Hydrolases use water; oxidoreductases transfer electrons; ligases join with ATP

Related models

is a kind of - in registry terms

enzyme

is classified as - in the Enzyme Commission system

EC 4

is contrasted with - EC 3

hydrolase

acts in - such as glycolysis

metabolic pathway

In practice

Families and kinds

carbon-carbon lyases such as decarboxylases and aldolases

carbon-oxygen lyases such as dehydratases

carbon-nitrogen lyases

carbon-sulfur lyases such as desulfhydrases and methionine gamma-lyase

carbon-halide and phosphorus-oxygen lyases

other lyases such as holocytochrome-c synthase

Identifiers

EC number 4.-.-.-

Gene Ontology GO:0016829 lyase activity

Standards and regulation

IUBMB enzyme nomenclature

Regulation of enzymes used in food and pharmaceuticals

Failure modes and hazards

Misclassifying enzymes

Outdated nomenclature

Confusing lyases with synthases in naming

Also called

Dihydroxy-acid/6-phosphogluconate dehydrataseHolocytochrome-c synthasePeptidylamidoglycolate lyase1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenBD-cysteine desulphhydrase, bacterialL-methionine gamma-lyaseCystathionine beta-lyase, eukaryoticCystathionine beta-lyase, bacterialAminodeoxychorismate lyase, class IV3-dehydroquinate synthasecarbon-sulfur lyasephosphorus-oxygen lyasecarbon-halide lyasecarbon-nitrogen lyaseDrimenol cyclaseRibonuclease T2Bacillus subtilis ribonucleaseRibonuclease U2Enterobacter ribonucleaseTRNA-intron endonucleaseMesaconyl-CoA hydrataseIsoprene synthaseIndole-3-glycerol-phosphate lyaseMandelonitrile lyase4-(2-carboxyphenyl)-2-oxobut-3-enoate aldolaseD-threonine aldolase3-hexulose-6-phosphate synthaseBenzoyl-CoA-dihydrodiol lyaseTrans-o-hydroxybenzylidenepyruvate hydratase-aldolaseAliphatic (R)-hydroxynitrile lyase(S)-hydroxynitrile lyaseLow-specificity L-threonine aldolase6-carboxytetrahydropterin synthaseN-acetylneuraminate lyaseNaphthoate synthase3-hydroxy-D-aspartate aldolase(6-4)DNA photolyasePhosphomethylpyrimidine synthaseCyclic pyranopterin monophosphate synthase2-iminoacetate synthase

+428

Where this came from

wikidata · CC0 1.0

Source repository Registry entry point

Drafted structure

Bundle to layer to finding to question, as the second pass will find it: 4 bundles · 8 layers · 8 findings · 16 questions.

Understand What lyases are.

Science.

Definition

Definition and subclasses.

Definition

Definition.

  1. What is a lyase, and what subclasses exist? definition
  2. Is the enzyme a lyase or another class? boundary

Mechanism

Mechanisms.

Mechanism

Mechanism.

  1. How do lyases catalyse elimination and addition reactions? definition
  2. Which entry fits the specific enzyme? action
Biology Metabolic roles.

Science.

Metabolism

Metabolism.

Metabolism

Metabolism.

  1. What roles do lyases play in glycolysis, amino acid metabolism and other pathways? provenance
  2. Which entry fits the specific pathway? action

Disease

Disease.

Disease

Disease.

  1. Which lyase deficiencies cause disease, in general terms? provenance
  2. Is the user asking about a personal diagnosis, which needs a clinician? boundary
Apply Applications.

Application.

Biocatalysis

Biocatalysis.

Biocatalysis

Biocatalysis.

  1. How are lyases used in industrial biocatalysis and synthesis? provenance
  2. Which references are standard? provenance

Therapy

Therapeutic and diagnostic uses.

Therapy

Therapy.

  1. How are lyases such as methionine gamma-lyase studied for therapy, with findings attributed? provenance
  2. Which sources are cited? provenance
Context Nomenclature and history.

Context.

Nomenclature

Nomenclature.

Nomenclature

Nomenclature.

  1. How does the EC system classify lyases, and why are some named synthases? provenance
  2. Which entry fits enzyme nomenclature? action

History

History.

History

History.

  1. How were lyases discovered and classified? provenance
  2. Which entry fits the history of enzymology? action

What the second pass must settle

  • Should each subclass be a separate entry?
  • How should enzyme databases be linked?
  • The registry entry has merged aliases naming specific enzymes; should they be split off?
Draft as JSON