Difference between revisions of "Curator Guide: Enzymes and Reactions"

From GO Wiki
Jump to: navigation, search
(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...")
 
Line 3: Line 3:
 
There are five websites that are particularly useful when adding reaction terms. These are:
 
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]
+
*[http://www.chem.qmul.ac.uk/iubmb/enzyme/index.html EC enzyme nomenclature]
[http://www.ebi.ac.uk/intenz IntEnz]
+
*[http://www.ebi.ac.uk/intenz IntEnz]
[http://www.genome.jp/kegg KEGG]
+
*[http://www.genome.jp/kegg KEGG]
[http://www.metacyc.org MetaCyc]
+
*[http://www.metacyc.org MetaCyc]
[http://www.ebi.ac.uk/rhea Rhea]
+
*[http://www.ebi.ac.uk/rhea Rhea]
  
 +
For chemical names, one should consult [http://www.ebi.ac.uk/chebi ChEBI].
  
Example 1: A simple  
+
 
 +
==Example 1: A simple reaction==
  
  
Line 38: Line 40:
 
   Ref: GOC:tb
 
   Ref: GOC:tb
 
   PMID 20650897
 
   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 1: Look up all three compounds mentioned in MetaCyc and KEGG.
Line 61: Line 67:
  
 
*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.
 
*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.
 +
 +
 +
 +
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

Revision as of 08:36, 11 April 2011

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: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