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Research draft

ligases

vr.tr.ligases · PHY.MAT

Let an agent explain what ligases are and how they are classified, relay nomenclature and database identifiers, describe their roles in biology and biotechnology, and route detailed mechanism or clinical questions to the right resources.

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 what ligases are and how they are classified, relay nomenclature and database identifiers, describe their roles in biology and biotechnology, and route detailed mechanism or clinical questions to the right resources.

A class of enzymes that catalyse the joining of two molecules with the formation of a new chemical bond, usually powered by the hydrolysis of ATP or a similar nucleotide, classified as EC 6 and including DNA and RNA ligases, aminoacyl-tRNA synthetases and carboxylases; ligases are essential to DNA replication and repair, protein synthesis and metabolism, and DNA ligase is a basic tool of molecular biology.

What it is for: Not for anything; a class of biological catalysts.

It can be explain the class and subclasses; look up an enzyme by EC number; describe roles in replication, repair and metabolism; explain use in biotechnology.

Distinguishing features

Bond formation coupled to nucleotide hydrolysis

EC class 6

Subclasses by bond type

Central to nucleic acid biology

What it looks like

Not visible; proteins characterised by activity and structure.

Physical character

EC subclasses: 7 subclasses - EC 6.1 to 6.7 by bond formed

How it is recognised

EC number beginning with 6

Joins molecules using ATP energy

Lyases split bonds and hydrolases cleave with water

Related models

is a kind of - a class of enzymes

enzyme

includes - a major member

DNA ligase

is contrasted with - a neighbouring EC class

lyase

is used in - DNA ligase as a tool

molecular cloning

In practice

Families and kinds

DNA ligases

RNA ligases

aminoacyl-tRNA synthetases

carboxylases such as acetyl-CoA carboxylase

ubiquitin ligases

other ligases forming carbon-carbon, carbon-nitrogen and other bonds

Identifiers

EC number 6.x.x.x Enzyme Commission classification

UniProt accession alphanumeric for individual enzymes

Standards and regulation

IUBMB enzyme nomenclature

Biosafety rules for laboratory use

Regulation of enzyme products in diagnostics

Failure modes and hazards

Confusing the class with a specific enzyme

Ligation failures in laboratory protocols

Misclassifying ligases and lyases

Also called

Tubulin-tyrosine ligaseLipoate-protein ligaseDNA ligaseRNA-3'-phosphate cyclaseRNA ligase (ATP)Acetyl-CoA biotin carboxyl carriertRNA-specific 2-thiouridylaseNicotinate phosphoribosyltransferaseLipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurTarginine-tRNA ligaseglutamine-tRNA synthetaseligase, forming carbon-nitrogen bondsproton-transporting ATP synthase, rotational mechanismligase, forming carbon-oxygen bondsOxalate--CoA ligase Pcs60-likeMalonate-CoA ligasePyrrolysine-tRNAPyl ligaseO-phospho-L-serine-tRNA ligaseD-alanine-(R)-lactate ligaseCholate-CoA ligaseACP-SH:acetate ligase3-hydroxypropionyl-CoA synthase3-hydroxybenzoate-CoA ligase(2,2,3-trimethyl-5-oxocyclopent-3-enyl)acetyl-CoA synthase(butirosin acyl-carrier protein)-L-glutamate ligaseAdenosylcobinamide-phosphate synthaseL-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligaseUDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diamino-pimelate ligaseCyanophycin synthase (L-aspartate-adding)Cyanophycin synthase (L-arginine-adding)Coenzyme F420-0:L-glutamate ligaseCoenzyme gamma-F420-2:alpha-L-glutamate ligaseTetrahydrosarcinapterin synthaseCoenzyme F420-1:gamma-L-glutamate ligaseD-alanine-D-serine ligase4-phosphopantoate-beta-alanine ligaseUDP-N-acetylmuramoyl-L-alanyl-D-glutamate-D-lysine ligaseN2-citryl-N6-acetyl-N6-hydroxylysine synthaseGlutamate-methylamine ligaseTRNAIle-lysidine synthase

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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.

Classify What ligases are.

Classification.

Definition

Class definition.

Definition

Definition.

  1. What reaction defines a ligase, and how does EC 6 divide into subclasses? definition
  2. Is the question about the class or about one named enzyme? boundary

Nomenclature

Names and numbers.

Nomenclature

Nomenclature.

  1. How are ligases named and numbered, and where is the nomenclature published? provenance
  2. Which database record identifies the enzyme? action
Biology Roles in cells.

Function.

Nucleic acids

DNA and RNA ligases.

Nucleic

Nucleic.

  1. What roles do DNA and RNA ligases play in replication, repair and processing? provenance
  2. Which entry fits DNA repair? action

Metabolism

Synthetases and carboxylases.

Metabolism

Metabolism.

  1. What roles do aminoacyl-tRNA synthetases and carboxylases play? provenance
  2. Which references are standard? provenance
Use Biotechnology and medicine.

Applications.

Tools

Laboratory tools.

Tools

Tools.

  1. How is DNA ligase used in cloning and sequencing, in general terms? provenance
  2. Which entry fits molecular cloning? action

Medicine

Medical relevance.

Medicine

Medicine.

  1. Which ligases are drug targets or disease-related, in general terms? provenance
  2. Is the user asking about their own condition, which needs a clinician? boundary
Learn Mechanism and teaching.

Study.

Mechanism

Mechanism.

Mechanism

Mechanism.

  1. How do ligases couple bond formation to nucleotide hydrolysis? provenance
  2. Which entry fits enzyme mechanisms? action

Teach

Teaching.

Teach

Teaching.

  1. How is enzyme classification taught, and what misconceptions arise? action
  2. Which entry fits enzyme kinetics? action

What the second pass must settle

  • Should DNA ligase be a separate entry?
  • How should EC and UniProt records be linked?
  • The registry entry has merged aliases naming specific enzymes; should they be split off?
Draft as JSON