Closed gocentral closed 9 years ago
gocentral
commented
13 years ago Also to be noted: GO:50983 should be renamed as being deoxyhypusine biosynthesis from spermidine, rather than spermidine catabolism to deoxyhypusine.
Original comment by: girlwithglasses
gocentral
commented
12 years ago Back at ID: 1840593 Peter D\'Eustachio ( deustp01 ) pointed out that "the larger purpose of the process is not to degrade spermidine but to synthesize a derivative of a specific protein, eIF5A, by rearranging a specific lysine residue first to a deoxyhypusine residue (the reaction under discussion here) and then adding oxygen to that to form a hypusine residue (molecular function GO:0019135 "deoxyhypusine monooxygenase activity"). The whole two-step (or five-step, depending how one counts) process appears to be a good fit to biological_process term GO:0046515 "hypusine biosynthetic process" Actually, the purpose is not "to synthesize a derivative of a specific protein, eIF5A, by rearranging a specific lysine residue first to a deoxyhypusine residue..." but "to modify a specific protein, eIF5A, by modifying (adding fragment of spermidine to) a specific lysine residue first to a deoxyhypusine residue...". But, I agree completely with Peter that "the larger purpose of the process is not to degrade spermidine". Whoever defined the term as a spermidine catabolic process must have made a mistake in creating that definition without considering the context, because no one but GO refers to it that way. After all, when S-adenosylmethionine is used to methylate a lysine, it is not referred to as an "S-adenosylmethionine catabolic process", is it? I hope not. I think GO:0050983 is a red herring that should be obsoleted. Deoxyhypusine is not biosynthesized as a separate molecule, as Amelia suggests. It is a modified lysine produced in eIF5-A by the enzyme. In addition, GO:0034038 (as it is) should get an xref to RESID:AA0546. The reciprocal xref will go into the next release. Technically, RESID:AA0546 represents the deoxyhypusine modification of lysine either in the transient intermediate in the enzyme, or in the metabolic intermediate in the maturation of eIF5A, whereas GO is focused only on the modification produced in eIF5-A by the enzyme.
Original comment by: jsgaravelli
gocentral
commented
12 years ago The premise behind this item is wrong, anyway, because the two terms aren't equivalent in terms of end products. I have not done any further work on it for that reason, and I'm going to close this item.
Regarding term nomenclature and "X catabolism to Y" vs "Y biosynthesis from X", editors are often asked to add terms to represent a certain process without any background on the process or suggestion as to whether it is the start, end, or even an intermediate product that is "important", and how the term should be named. The process term has now been renamed in terms of deoxyhypusine biosynthesis. If there are other examples where terms are inappropriately named, feel free to suggest new names for them. Thanks!
Original comment by: girlwithglasses
gocentral
commented
12 years ago Original comment by: girlwithglasses
Wir haben:
id: GO:0034038 name: deoxyhypusine synthase activity (molecular function) def: "Catalysis of the reaction: [eIF5A-precursor]-lysine + spermidine = [eIF5A-precursor]-deoxyhypusine + propane-1,3-diamine. Four sub-reactions have been identified,in which the intermediates remain tightly associated with the enzyme: spermidine + NAD+ = dehydrospermidine + NADH; dehydrospermidine + [enzyme]-lysine = N-(4-aminobutylidene)-[enzyme]-lysine + propane-1,3-diamine; N-(4-aminobutylidene)-[enzyme]-lysine + [eIF5A-precursor]-lysine = N-(4-aminobutylidene)-[eIF5A-precursor]-lysine + [enzyme]-lysine; N-(4-aminobutylidene)-[eIF5A-precursor]-lysine + NADH + H+ = [eIF5A-precursor]-deoxyhypusine + NAD+." [EC:2.5.1.46, GOC:pde, MetaCyc:2.5.1.46-RXN] xref: EC:2.5.1.46 xref: MetaCyc:2.5.1.46-RXN
und
id: GO:0050983 name: spermidine catabolic process to deoxyhypusine, using deoxyhypusine synthase (biological process) def: "The chemical reactions resulting in the breakdown of spermidine to form deoxyhypusine by the enzyme [eIF-5A]-deoxyhypusine synthase. The reaction occurs in four steps:
The nomenclature used in the defs is slightly different, but these two terms are essentially identical. The comment for the former term says, "Note that this term is equivalent to the obsolete molecular function term 'deoxyhypusine synthase activity ; GO:0004171' and corresponds closely to the biological process term 'spermidine catabolic process to deoxyhypusine, using deoxyhypusine synthase ; GO:0050983'."
I don't see the logic in creating GO:0034038 when (1) a previous function term to represent the set of reactions was obsoleted, and (2) a process term representing the reactions exists. I suggest merging GO:0034038 into GO:0050983 because they represent the same set of reactions.
Reported by: girlwithglasses
Original Ticket: geneontology/ontology-requests/8778