Curator Guide: Enzymes and Reactions

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.

• KEGG contains Phosphodimethylethanolamine
• MetaCyc contains AdoMet

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

• MetaCyc: RXN-5642 looks like a match:

 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.