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

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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.
==General Rules and Things of Note==
===Enzyme Commission===
The Enzyme Commission names and categorises enzymes, i.e. physical entities, whereas GO is interested in the various reactions that the enzyme performs. In the same way that a gene product may participate in a number of different processes, it may catalyse a number of different reactions; the ontology should contain each reaction, and the job of the annotator is to mark which reactions a certain gene product catalyses. A single enzyme may perform a number of different reactions, and it is also possible for several different EC enzymes to perform the same reaction.
This means that there is not a 1:1 correspondence between EC numbers and GO reaction terms.
There are a number of websites that mirror the EC data; my favourite is IntEnz as it shows the reactions from RHEA, so you are saved the trouble of having to find out what the ChEBI names for the reaction participants are.
At present, MetaCyc reactions are associated with one EC number, so if two different EC enzymes catalyse the same reaction, there will be two MetaCyc reactions, one for each EC number.
KEGG makes reactions independent of the EC number; you can look up an EC number and see the reactions that the enzyme performs (e.g. [http://www.genome.jp/dbget-bin/www_bget?ec: EC:]), or you can look up a reaction and see which EC enzymes perform that reaction (e.g. [http://www.genome.jp/dbget-bin/www_bget?rn:R01036 R01036]). Nifty!
Reactome currently provide mappings of their terms to GO terms, so they do the work for us!
===Precise vs. Imprecise EC Numbers===
GO has terms that represent the categories used by EC. These have EC xrefs of the form EC:n, EC:n.n and EC:n.n.n (where n is a number).
For reactions where the enzyme has not yet been added to EC, but it can be put into one of the EC categories, the xref should be of the form EC:n.n.n.-, i.e. ending with a dash.
According to the Enzyme Commission, NAD(P) means that the reaction occurs with NAD '''and''' with NADP; e.g.
  alditol + NAD(P)+ = aldose + NAD(P)H + H+
means that the enzyme performs
  alditol + NAD+ = aldose + NADH + H+
  alditol + NADP+ = aldose + NADPH + H+
==Example 1: epi-cedrol synthase==
Add a term for EC, epi-cedrol synthase
*Check the reaction does not exist in GO by searching on the name, EC number and the reactants. I searched for 'epicedrol' and 'epi-cedrol'.
*Look up the reaction in EC (using IntEnz), MetaCyc and KEGG.
*IntEnz: [http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=]
2-trans,6-trans-farnesyl diphosphate + H2O <=> epi-cedrol + diphosphate
*MetaCyc: [http://biocyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-10004 RXN-10004]
(2E,6E)-farnesyl diphosphate + H2O <=> 8-epi-cedrol + diphosphate
*KEGG: [http://www.genome.jp/dbget-bin/www_bget?ec: EC:] is connected to one reaction, [http://www.genome.jp/dbget-bin/www_bget?rn:R09140 R09140]
trans,trans-Farnesyl diphosphate + H2O <=> 8-epi-Cedrol + Diphosphate
Check against the [http://www.ebi.ac.uk/rhea/reaction.xhtml?id=26118 RHEA reaction, RHEA:26118] (linked from IntEnz) so that we can be sure we're using the correct nomenclature.
Names and synonyms: KEGG and EC both give us "(2E,6E)-farnesyl-diphosphate diphosphate-lyase (8-epi-cedrol-forming)", which is the systematic name, according to EC. We also have "8-epicedrol synthase" and "epicedrol synthase".
Parentage: find the GO term for the category EC:4.2.3; if any of the children are relevant, use them as the parent.
name: epi-cedrol synthase activity
def: "Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate + H2O = epi-cedrol + diphosphate." [RHEA:26118]
synonym: "(2E,6E)-farnesyl-diphosphate diphosphate-lyase (8-epi-cedrol-forming) activity" EXACT systematic_synonym [EC:]
synonym: "8-epicedrol synthase activity" EXACT []
synonym: "epicedrol synthase activity" EXACT []
xref: EC:
xref: MetaCyc:RXN-10004
xref: KEGG:R09140
xref: RHEA:26118
is_a: GO:0016838 ! carbon-oxygen lyase activity, acting on phosphates
==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. (N.b. a 'prenol kinase' term was later added which would be a more appropriate parent)
*Reaction equation: NTP and NDP are referred to in ChEBI as nucleoside triphosphate and nucleoside diphosphate.
name: farnesol kinase activity
def: "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.-
is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor
*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:, so go to IntEnz and look up [http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=]. 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
def: "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
is_a: GO:0008170 ! N-methyltransferase activity

Latest revision as of 08:09, 9 February 2021