Curator Guide: Enzymes and Reactions: Difference between revisions

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This guide is for editors adding molecular function terms to represent enzyme reactions.
#REDIRECT: [[Database_cross_references]]


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


*[http://www.chem.qmul.ac.uk/iubmb/enzyme/index.html EC enzyme nomenclature]
[[Category:GO Editors]]
*[http://www.ebi.ac.uk/intenz IntEnz]
*[http://www.genome.jp/kegg KEGG]
*[http://www.metacyc.org MetaCyc]
*[http://www.ebi.ac.uk/rhea Rhea]
 
For chemical names, one should consult [http://www.ebi.ac.uk/chebi 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 [http://www.genome.jp/dbget-bin/www_bget?cpd:C13482 Phosphodimethylethanolamine]
*MetaCyc contains [http://biocyc.org/META/NEW-IMAGE?type=COMPOUND&object=S-ADENOSYLMETHIONINE AdoMet]
 
Step 2: Check the reactions for these compounds.
 
*KEGG: [http://www.genome.jp/dbget-bin/www_bget?rn:R06868 R06868] looks like a match:
 
  S-Adenosyl-L-methionine + N-Methylethanolamine phosphate <=>
  S-Adenosyl-L-homocysteine + Phosphodimethylethanolamine
 
*MetaCyc: [http://biocyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-5642 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 [http://www.genome.jp/dbget-bin/www_bget?cpd:C13482 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 [http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=2.1.1.103 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 [http://www.ebi.ac.uk/chebi/displayAutoXrefs.do?chebiId=CHEBI:57781 automatic xrefs for N-methylethanolamine phosphate in ChEBI] and clicked on the Rhea xrefs. [http://www.ebi.ac.uk/rhea/reaction.xhtml?id=RHEA:25322 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

Latest revision as of 12:09, 9 February 2021