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:
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.
- 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.
- 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.
Resulting term:
phosphomethylethanolamine N-methyltransferase
name: S-adenosyl-L-methionine:methylethanolamine phosphate N-methyltransferase 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 KEGG:R06868 xref: EC:2.1.1.- xref: KEGG:R06868 xref: MetaCyc:RNX-5642 xref: RHEA:25322