Curator Guide: Enzymes and Reactions

From GO Wiki
Revision as of 20:02, 8 April 2011 by Girlwithglasses (talk | contribs) (Created page with "This guide is for editors adding molecular function terms to represent enzyme reactions. There are five websites that are particularly useful when adding reaction terms. These a...")

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

This guide is for editors adding molecular function terms to represent enzyme reactions.

There are five websites that are particularly useful when adding reaction terms. These are:

EC enzyme nomenclature IntEnz KEGG MetaCyc Rhea


Example 1: A simple



Example 2: farnesol kinase

From SourceForge:

 definition: farnesol + an NTP = farnesol-phosphate + an NDP
 EC: 2.7.1.-
 One example of a more specific case of this is: MetaCyc: RXN-11625
 
 PMID: 21395888, 10557276
 
 NARROW synonym: trans,trans-farnesol kinase
 NARROW synonym: 2-trans, 6-trans-farnesol kinase


Example 3: phosphomethylethanolamine N-methyltransferase activity

From SourceForge:

 Def: Catalysis of the reaction: phosphomethylethanolamine (PMEA) + AdoMet -> phosphodimethylethanolamine
 Ref: GOC:tb
 PMID 20650897

Step 1: Look up all three compounds mentioned in MetaCyc and KEGG.

Step 2: Check the reactions for these compounds.

  • KEGG: R06868 looks like a match:
 S-Adenosyl-L-methionine + N-Methylethanolamine phosphate <=>
 S-Adenosyl-L-homocysteine + Phosphodimethylethanolamine
 N-methylethanolamine phosphate + S-adenosyl-L-methionine <=>
 N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H+
  • Check that N-dimethylethanolamine phosphate (from the MetaCyc reaction) is also known as phosphodimethylethanolamine
    • phosphodimethylethanolamine is a synonym on the MetaCyc compound page; the KEGG compound ID C13482 matches that in the KEGG reaction
    • If in doubt, search for the compound in ChEBI and check the synonyms.
  • MetaCyc states that the reaction is one of three catalysed by EC:2.1.1.103, so go to IntEnz and look up 2.1.1.103. Although the comments mention subsequent reactions, the reaction list doesn't, so we will use the more generic EC:2.1.1.- as a reference.