Curator Guide: Enzymes and Reactions

From GO Wiki
Revision as of 12:12, 11 April 2011 by Girlwithglasses (talk | contribs)

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:

For chemical names, one should consult ChEBI.

Example 1: A simple reaction

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

Searching for the enzyme name brings up no results in EC, MetaCyc and KEGG, so let's look up the reaction instead.

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:, so go to IntEnz and look up 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.
  • Get the ChEBI names for the substances and generate a balanced equation. Check to see if the reaction is in Rhea. I looked at the automatic xrefs for N-methylethanolamine phosphate in ChEBI and clicked on the Rhea xrefs. RHEA:25322 is a match! Checking the xrefs for the Rhea reaction, they match the reactions in KEGG and MetaCyc that we found earlier.

  • Term name: a quick Google search reveals that 'phosphomethylethanolamine N-methyltransferase' appears to be the most common name for this term.
  • Synonyms: added the KEGG name for the reaction as an exact synonym with the scope set as 'systematic synonym'; also added a synonym using the ChEBI name for the chemical instead of phosphomethylethanolamine.
  • Term parentage: this term can go under N-methyltransferase activity.
name: phosphomethylethanolamine N-methyltransferase activity
definition: Catalysis of the reaction: N-methylethanolamine phosphate + S-adenosyl-L-methionine = N,N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+). [RHEA:25322, KEGG:R06868, MetaCyc:RXN-5642]
synonym: "N-methylethanolamine phosphate N-methyltransferase activity" EXACT
synonym: "S-adenosyl-L-methionine:methylethanolamine phosphate N-methyltransferase activity" EXACT systematic_synonym [KEGG:R06868]
xref: EC:2.1.1.-
xref: KEGG:R06868
xref: MetaCyc:RXN-5642
xref: RHEA:25322