merge of terms for EC:1.1.1.87 and EC:1.1.1.155

[gocentral]

Hi,

This should not be acted upon until and, of course unless, it becomes official, but I wanted to post it now while I've got all the emails, included in this suggestion, in front of me. Some literature and web research I did suggested that EC:1.1.1.87 and EC:1.1.1.155 are identical. I emailed one of the EC people and she's responded saying that the proposed merge of 1.1.1.155 into 1.1.1.87 will be put on the EC's page for public comments and will take 2 months after that before it would be made final, assuming it is accepted. More info, including emails, below.

thanks,

-Karen

Of the two current GO terms, below, the name of GO:0047984, "homoisocitrate dehydrogenase activity", should definitely be kept as a synonym name since it seems to be the more commonly used name. I suppose though that for consistency, we should probably make whichever one is kept as the main EC number into the main term name (currently proposed to make 1.1.1.87 the main EC

).

[Term] id: GO:0047984 name: homoisocitrate dehydrogenase activity namespace: function def: "Catalysis of the reaction: (-)-1-hydroxy-1\,2\,4- butanetricarboxylate + NAD+ = 2-oxoadipate + CO2 + NADH." [MetaCyc:HOMOISOCITRATE-DEHYDROGENASE- RXN, EC:1.1.1.155] xref_analog: EC:1.1.1.155 xref_analog: MetaCyc:HOMOISOCITRATE- DEHYDROGENASE-RXN is_a: GO:0016616

[Term] id: GO:0047046 name: 3-carboxy-2-hydroxyadipate dehydrogenase activity namespace: function def: "Catalysis of the reaction: NAD+ + 3-carboxy-2- hydroxyadipate = NADH + CO2 + 2-keto-adipate." [MetaCyc:1.1.1.87-RXN, EC:1.1.1.87] xref_analog: EC:1.1.1.87 xref_analog: MetaCyc:1.1.1.87-RXN is_a: GO:0016616

Email I sent:

Date: Tue, 6 Apr 2004 16:38:31 -0700 (PDT) From: Karen Christie <kchris@fafner.Stanford.EDU> To: sboyce@tcd.ie Cc: Karen Christie <kchris@genome.stanford.edu> Subject: REPORT FORM FOR AN ERROR OR UPDATE IN AN EXISTING ENZYME ENTRY Parts/Attachments: 1 Shown 63 lines Text 2 OK 307 KB Application, "pdf file"

Hi,

I was trying to send you this report using the web submission form for enzyme updates "http://us.expasy.org/ enzyme/enz_update_form.html", but I tried 3-4 times with 2 different browsers and kept getting error messages like this one: "Your email address "phone=1-650-725-3062" is not valid. Please go back and correct it." so I've sent the possible update report directly along with a pdf file for the Zabriskie reference I mention.

I was wondering if there is really a difference between 1.1.1.87 and 1.1.1.155? I am trying to reconcile two sources of information, the pathway diagram and EC number (1.1.1.155) used in SGD's MetaCyc derived pathway for lysine biosynthesis and the one given (1.1.1.87) for the same reaction in Zabriskie, T.M. and M.D. Jackson (2000). Nat. Prod. Rep. 17(1):85-97. Lysine biosynthesis and metabolism in fungi (pdf sent separately).

I've looked at both the PAREO (PAthway RElational Organisation) site in France and the Metacyc site and it appears that 1.1.1.87 and 1.1.1.155 may represent the same enzymatic reaction, differing only by the name used for one of the compounds, "3-carboxy-2-hydroxyadipate" in 1.1.1.87 versus "(-)1-1-hydroxy-1,2,4-butanetricarboxylate in 1.1.1.155. From what I can find in both the PAREO and MetaCyc web sites, these two names appear to represent the same thing. Therefore, I was wondering if 1.1.1.87 and 1.1.1.155 should be merged.

Best Regards,

-Karen

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Karen Christie, Ph.D., Database Curator Saccharomyces Genome Database Stanford University Medical Center Department of Genetics Stanford, CA 94305-5120 USA phone: 650-725-3062 fax: 650-723-7016 e-mail: yeast-curator@genome.stanford.edu WWW: http://genome-www.stanford.edu/

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SGD page for lysine biosynthesis

http://pathway.yeastgenome.org:8555/YEAST/new- image?type=PATHWAY&object=LYSINE-AMINOAD-PWY&de tail-level=2

PAREO site page for homoisocitrate:

http://genome.jouy.inra.fr/cgi-bin/pareo/ compound.cgi?compound_id=C05662

MetaCyc entry for 1.1.1.155

http://BioCyc.org/META/NEW- IMAGE?type=REACTION&object=HOMOISOCITRATE- DEHYDROGENASE-RXN

MetaCyc entry for 1.1.1.87

http://BioCyc.org/META/NEW- IMAGE?type=REACTION&object=1.1.1.87-RXN

Response I received:

Date: Thu, 8 Apr 2004 15:25:31 +0100 From: "[iso-8859-1] Siniad Boyce" <sboyce@tcd.ie> To: Karen Christie <kchris@genome.stanford.edu> Subject: Re: REPORT FORM FOR AN ERROR OR UPDATE IN AN EXISTING ENZYME ENTRY

Dear Karen,

Many thanks for your very helpful e-mail and sorry that you had trouble with the update form. I will pass on your comments about the errors you encountered to Elisabeth Gasteiger of SWISS-PROT, who hosts the form for us.

You are of course correct that the two enzymes are identical. What I propose doing is to delete EC 1.1.1.155 from the Enzyme list and incorporate the names from EC 1.1.1.155 into the entry for EC 1.1.1.87. I will also add the reference you cited. As this change involves the deletion of an enzyme, it will go through our public-review process, which will begin at http://www.chem.qmul.ac.uk/iubmb/ enzyme/newenz.html within the next couple of weeks and takes 2 months before the changes are made official.

If you come across any other errors, please don't hesistate to pass them on.

with best wishes, Sinead

--

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Sinead Boyce, Ph.D. Department of Biochemistry, Trinity College, Dublin 2, Ireland.

For enzyme nomenclature, see http:// www.chem.qmul.ac.uk/iubmb/enzyme/

Reported by: krchristie

Original Ticket: "geneontology/ontology-requests/1654":https://sourceforge.net/p/geneontology/ontology-requests/1654

[gocentral]

Logged In: YES user_id=473796

Merged GO:0047984 into homoisocitrate dehydrogenase activity ; GO: 0047046.

Original comment by: girlwithglasses

[gocentral]

• milestone: 224411 --> TermGenie
• assigned_to: nobody --> girlwithglasses
• status: open --> closed-fixed

Original comment by: girlwithglasses