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#11810 BP for glo3
Hi,
I wonder what BP should be used for glyoxalase III enzymes? Glyoxalase III converts methylglyoxal to D-lactate without GSH
There is another system comprising glyoxalase I & II which uses GSH for which this BP exists:
GO:0019243 methylglyoxal catabolic process to D-lactate
The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, into D-lactate via the intermediate S-lactoyl-glutathione. Glutathione is used in the first step of the pathway and then regenerated in the second step.
So I guess I'd want a term for GSH-independent methylglyoxal catabolic process to D-lactate?
eg PMID:24758716
note to self 134ecf3bebd24e1a
Hi Antonia,
It seems that there are a lot of annotations to the current pathway that are not to hydroxyacylglutathione hydrolase or lactoylglutathione lyase. These should be the only enzymes in the pathway that proceeds via S-lactoyl-glutathione. As far as I can tell, there are at least two other pathways that can convert methylglyoxal to lactate. First is the direct conversion via glyoxalase III and second is the one through lactaldehyde.
There are two things I can possibly do. First, I can relax the definition of the existing term so that it includes any catabolic process that converts methylglyoxal to lactate. This would presumably leave the current annotations correct and would make the current logical definition and child correct. I can then create two new children for the direct pathway (a one enzymatic step pathway!) and the one through S-lactoyl-glutathione. Those would all be easy to define using the same pattern that I used for glycolysis.
Second, I could rename the current term to be 'methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione' to reflect the textual definition. Then I could create the generic term and redo the logical definitions and sort out the Metacyc xrefs and and children. I suspect this will make a lot of existing annotations incorrect.
I will think about it some more, but I am leaning towards the first option.
-David
Hi Antonia,
After conferring with Tanya, I have decided to go with option 2. I have renamed the current term to match its textual definition. I also made a new generic term ' methylglyoxal catabolic process to D-lactate' with no constraints other than the inputs and outputs in the logical definition. I also refined the logical definition of the existing term. I made glyoxalase III a part_of the new generic process. This should work fine because every time the reaction occurs, it satisfies the process. I will work on the other subtypes and cross-references tomorrow, so I will not close this item yet.
-David
Thanks for the quick reply!
OK. I finished cleaning up what we had. When the time comes to add the remaining pathways, hopefully it will be straightforward. Here is the diff if you care to look and see if there is anything odd.
name:methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione (not in the diff)
namespace: biological_process
def: "The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, into D-lactate via the intermediate S-lactoyl-glutathione. Glutathione is used in the first step of the pathway and then regenerated in the second step." [GOC:ai, GOC:dph, PMID:2198020]
subset: gosubset_prok
-synonym: "D-lactate biosynthesis from methylglyoxal" EXACT []
-synonym: "D-lactate biosynthetic process from methylglyoxal" EXACT []
+synonym: "D-lactate biosynthesis from methylglyoxal" BROAD []
+synonym: "D-lactate biosynthetic process from methylglyoxal" BROAD []
synonym: "glyoxalase system" RELATED []
-synonym: "methylglyoxal breakdown to D-lactate" EXACT []
-synonym: "methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione" EXACT []
+synonym: "methylglyoxal breakdown to D-lactate" BROAD []
synonym: "methylglyoxal catabolism to D-lactate via S-lactoyl-glutathione" EXACT []
-synonym: "methylglyoxal degradation to D-lactate" EXACT []
+synonym: "methylglyoxal degradation to D-lactate" BROAD []
synonym: "methylglyoxal detoxification" RELATED []
-xref: MetaCyc:PWY-901
+xref: MetaCyc:PWY-5386
is_a: GO:0006089 {is_inferred="true"} ! lactate metabolic process
is_a: GO:0061727 ! methylglyoxal catabolic process to lactate
intersection_of: GO:0009056 ! catabolic process
@@ -177164,7 +177163,7 @@
id: GO:0019248
name: D-lactate biosynthetic process from methylglyoxal via (R)-lactaldehyde
namespace: biological_process
-def: "The chemical reactions and pathways resulting in the formation of D-lactate from other compounds, including methylglyoxal, via the intermediate (R)-lactaldehyde." [GOC:go_curators]
+def: "The chemical reactions and pathways resulting in the formation of D-lactate from methylglyoxal, via the intermediate (R)-lactaldehyde." [GOC:dph, GOC:go_curators, MetaCyc:MGLDLCTANA-PWY]
subset: gosubset_prok
synonym: "D-lactate anabolism from methylglyoxal via (R)-lactaldehyde" EXACT []
synonym: "D-lactate formation from methylglyoxal via (R)-lactaldehyde" EXACT []
@@ -177173,9 +177172,11 @@
is_a: GO:0019249 {is_inferred="true"} ! lactate biosynthetic process
is_a: GO:0061727 ! methylglyoxal catabolic process to lactate
intersection_of: GO:0009058 ! biosynthetic process
+intersection_of: ends_with GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
intersection_of: has_input CHEBI:17158 ! methylglyoxal
intersection_of: has_intermediate CHEBI:17167 ! (R)-lactaldehyde
intersection_of: has_output CHEBI:16004 ! (R)-lactate
+intersection_of: starts_with GO:0019170 ! methylglyoxal reductase (NADH-dependent) activity
name:methylglyoxal catabolic process (not in the actual diff)
synonym: "methylglyoxal breakdown" EXACT []
synonym: "methylglyoxal catabolism" EXACT []
synonym: "methylglyoxal degradation" EXACT []
+xref: MetaCyc:METHGLYUT-PWY
+xref: MetaCyc:Methylglyoxal-Detoxification
is_a: GO:0009438 {is_inferred="true"} ! methylglyoxal metabolic process
is_a: GO:0042182 {is_inferred="true"} ! ketone catabolic process
is_a: GO:0046185 {is_inferred="true"} ! aldehyde catabolic process