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]. RHEA is particularly useful because it gives EC reactions using ChEBI chemicals.
 
 
==Example 1: ent-cassa-12,15-diene synthase==
 
Add a term for EC 4.2.3.28, ent-cassa-12,15-diene synthase
 
*Check the reaction does not exist in GO by search on the name (in this case, I searched for terms with 'mycothiol' in the name) and the EC number.
 
*Look up the reaction in EC (using IntEnz), MetaCyc and KEGG.
 
*IntEnz: [http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=4.2.3.28 4.2.3.28]
*MetaCyc: [http://biocyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-4881 RXN-4881]
*KEGG: [http://www.genome.jp/dbget-bin/www_bget?ec:4.2.3.28 EC:4.2.3.28] is connected to one reaction, [http://www.genome.jp/dbget-bin/www_bget?rn:R09119 R09119]
 
Somewhat miraculously, all three sites show the reaction as
 
  ent-copalyl diphosphate = ent-cassa-12,15-diene + diphosphate
 
Check against the [http://www.ebi.ac.uk/rhea/reaction.xhtml?id=25535 RHEA reaction, RHEA:25535], linked from IntEnz so that we can be sure we're using the correct nomenclature.
 
Check for names for this enzyme. KEGG and EC both give us "ent-copalyl-diphosphate diphosphate-lyase (ent-cassa-12,15-diene-forming)", which is the systematic name, according to EC. We also have the names of two gene products, but I will leave them off as it isn't clear what they mean.
 
  name: ent-cassa-12,15-diene synthase activity
  def: "Catalysis of the reaction: ent-copalyl diphosphate = ent-cassa-12,15-diene + diphosphate." [EC:4.2.3.28, RHEA:25535]
  synonym: "ent-copalyl-diphosphate diphosphate-lyase (ent-cassa-12,15-diene-forming)" EXACT systematic_synonym
  xref: EC:4.2.3.28
  xref: KEGG:R09119
  xref: MetaCyc:RXN-4881
  xref: RHEA:25535
 
==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
  PMID 10557276
 
  NARROW synonym: trans,trans-farnesol kinase
  NARROW synonym: 2-trans, 6-trans-farnesol kinase
 
*Look up the MetaCyc reaction. It's
 
2-trans,-6-trans-farnesol + CTP = 2-trans,-6-trans-farnesyl monophosphate + CDP + H+
 
*Search GO, EC, KEGG and RHEA for farnesol. No results for reactions of a similar form.
*Checking the literature references, it is not clear whether the farnesol reactions are limited to the 2-trans,6-trans isomer, so we'll refer to 'farnesol' in the reaction.
*ChEBI searches for farnesol phosphates turn up a blank; however, "farnesyl phosphate" is a parent term for "farnesyl diphosphate" so we should use the name "farnesyl monophosphate" instead of "farnesol phosphate" to refer to the reaction product.
*Parentage: MetaCyc gives an EC ref of 2.7.1.- for RXN-11625; this corresponds to GO:0016773. We can have a look at the ChEBI hierarchy for "farnesyl phosphate" to get some hints as to whether there may be any generic terms under GO:0016773, but there don't seem to be any.
*Reaction equation: NTP and NDP are referred to in ChEBI as nucleoside triphosphate and nucleoside diphosphate.
name: farnesol kinase activity
definition: Catalysis of the reaction: farnesol + nucleoside triphosphate = farnesyl monophosphate + nucleoside diphosphate. [MetaCyc:RXN-11625]
synonym: "trans,trans-farnesol kinase activity" NARROW
xrefs: EC:2.7.1.-
 
*Add the MetaCyc reaction cited as a child of this new term. I gave it the name "2-trans,-6-trans-farnesol kinase activity" to reflect the specific substrate.
 
 
==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 GO, EC, MetaCyc and KEGG, so let's look up the reaction instead.
 
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]
 
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