ECM31 (YBR176W) encodes the mitochondrial 3-methyl-2-oxobutanoate (ketopantoate) hydroxymethyltransferase of S. cerevisiae, the PanB-family enzyme that transfers a hydroxymethyl group from 5,10-methylenetetrahydrofolate to 3-methyl-2-oxobutanoate (alpha-ketoisovalerate, a valine-biosynthesis intermediate) to form 2-dehydropantoate (ketopantoate). This is the first committed step of pantoate and hence pantothenate (vitamin B5) synthesis; ketopantoate is subsequently reduced to pantoate and condensed with beta-alanine by Pan6. ecm31 deletion mutants cannot grow on beta-alanine and require pantothenate. Large-scale proteomic and localisation studies consistently place Ecm31 in mitochondria. The ECM ('extracellular mutant') name derives from a cell-wall screen and does not reflect its function.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA (PTN000466854; E. coli PanB P31057, M. tuberculosis PanB). Bacterial ketopantoate hydroxymethyltransferases are Mg2+-dependent and Ecm31 retains the PanB fold; Mg2+ binding is a plausible inherited cofactor property, but it is a cofactor detail rather than the core function and has not been tested for the yeast enzyme. Reason: Plausible inherited cofactor binding, not core. Supporting Evidence: file:yeast/ECM31/ECM31-uniprot.txt SIMILARITY: Belongs to the PanB family. |
| GO:0003864 3-methyl-2-oxobutanoate hydroxymethyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA (PTN000466854) with bacterial PanB enzymes; Ecm31 is the sole PanB-family protein in yeast and is required for de novo pantothenate synthesis. Core MF. Supporting Evidence: file:yeast/ECM31/ECM31-uniprot.txt SIMILARITY: Belongs to the PanB family. PMID:11154694 Furthermore, yeast genes ECM31 and YIL145c, which both have structural homology to genes of the bacterial pantothenic acid pathway, were also required for pantothenic acid biosynthesis. |
| GO:0003864 3-methyl-2-oxobutanoate hydroxymethyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA from InterPro IPR003700 / RHEA:11824 / EC 2.1.2.11. Correct for this PanB-family enzyme. Supporting Evidence: file:yeast/ECM31/ECM31-uniprot.txt Reaction=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + 3-methyl-2- |
| GO:0003864 3-methyl-2-oxobutanoate hydroxymethyltransferase activity | IMP PMID:11154694 Saccharomyces cerevisiae is capable of de Novo pantothenic a... | ACCEPT | Summary: IMP (White et al. 2001): ecm31 deletion blocks pantothenate synthesis from beta-alanine, consistent with loss of the ketopantoate hydroxymethyltransferase step. The activity itself is inferred from PanB homology plus the auxotrophy (UniProt: 'Probable', EC by ECO:0000305), but there is no reason to doubt it. Supporting Evidence: PMID:11154694 Furthermore, yeast genes ECM31 and YIL145c, which both have structural homology to genes of the bacterial pantothenic acid pathway, were also required for pantothenic acid biosynthesis. PMID:19266201 we show that deletion of ECM31 and PAN6 results in mutants requiring pantothenate |
| GO:0003864 3-methyl-2-oxobutanoate hydroxymethyltransferase activity | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways PANTOSYN2-PWY assigning Ecm31 to the EC 2.1.2.11 step (5,10-methylene-THF + 3-methyl-2-oxobutanoate -> 2-dehydropantoate). Correct assignment. Supporting Evidence: file:yeast/ECM31/ECM31-uniprot.txt Reaction=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + 3-methyl-2- |
| GO:0005739 mitochondrion | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: HDA (Huh et al. 2003 GFP localisation). Consistent with multiple independent mitochondrial proteome datasets for Ecm31. |
| GO:0005739 mitochondrion | HDA PMID:14576278 The proteome of Saccharomyces cerevisiae mitochondria. | ACCEPT | Summary: HDA (Sickmann et al. 2003 mitochondrial proteome). Independent support for mitochondrial location. |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: HDA (Reinders et al. 2006 mitochondrial proteome). Independent support for mitochondrial location. |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | ACCEPT | Summary: HDA (Renvoise et al. 2014 quantitative mitochondrial proteome). Independent support for mitochondrial location. |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: IBA (PTN000466856, including plant mitochondrial KPHMTs AT2G46110/AT3G61530). Plant and fungal ketopantoate hydroxymethyltransferases are mitochondrial; consistent with yeast proteomics. |
| GO:0005739 mitochondrion | IDA PMID:17054397 Assessing systems properties of yeast mitochondria through a... | ACCEPT | Summary: IDA (Perocchi et al. 2006 mitochondrial localisation/interaction map). The full text cached does not name ECM31 in the main text (likely in supplementary data); defer to the curator, consistent with the other mitochondrial evidence. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: RCA from YeastPathways PANTOSYN2-PWY, which places the whole pantothenate/CoA superpathway in the cytosol. For Ecm31 this compartment default conflicts with four independent mitochondrial proteome/localisation datasets and the mitochondrial IBA; there is no evidence for a cytosolic pool of Ecm31. Reason: Pathway-level compartment default contradicted by consistent mitochondrial localisation data for this protein. |
| GO:0015937 coenzyme A biosynthetic process | RCA GO_REF:0000123 | MARK AS OVER ANNOTATED | Summary: RCA from YeastPathways superpathway PANTOSYN2-PWY ('pantothenate and coenzyme A biosynthesis'). Ecm31 makes ketopantoate, a precursor of pantothenate; it does not catalyse any step of the CoA pathway proper (pantothenate -> CoA, Cab1-Cab5). In GO, pantothenate biosynthetic process is not part_of CoA biosynthetic process, so this is superpathway inflation. Reason: Superpathway-inherited BP; Ecm31's step is in pantothenate (vitamin B5) synthesis, upstream of CoA synthesis. Supporting Evidence: PMID:11154694 Furthermore, yeast genes ECM31 and YIL145c, which both have structural homology to genes of the bacterial pantothenic acid pathway, were also required for pantothenic acid biosynthesis. |
| GO:0015940 pantothenate biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA (PTN000466854) with bacterial PanB. Ketopantoate hydroxymethyltransferase catalyses the first committed step of pantoate/pantothenate synthesis. Core BP. Supporting Evidence: PMID:11154694 Furthermore, yeast genes ECM31 and YIL145c, which both have structural homology to genes of the bacterial pantothenic acid pathway, were also required for pantothenic acid biosynthesis. |
| GO:0015940 pantothenate biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: IEA from InterPro IPR003700 / UniPathway UPA00028 (pantothenate biosynthesis). Correct. Supporting Evidence: file:yeast/ECM31/ECM31-uniprot.txt SIMILARITY: Belongs to the PanB family. |
| GO:0015940 pantothenate biosynthetic process | IMP PMID:11154694 Saccharomyces cerevisiae is capable of de Novo pantothenic a... | ACCEPT | Summary: IMP (White et al. 2001): ECM31 is required for pantothenic acid biosynthesis; independently confirmed by Olzhausen et al. 2009. Supporting Evidence: PMID:11154694 Furthermore, yeast genes ECM31 and YIL145c, which both have structural homology to genes of the bacterial pantothenic acid pathway, were also required for pantothenic acid biosynthesis. PMID:19266201 we show that deletion of ECM31 and PAN6 results in mutants requiring pantothenate |
| GO:0072330 monocarboxylic acid biosynthetic process | IEA GO_REF:0000117 | MODIFY | Summary: IEA from ARBA rule ARBA00027175 (monocarboxylic acid biosynthetic process). Correct but very general; pantothenate biosynthetic process (an is_a child) is the informative term and is already annotated. Proposed replacements: pantothenate biosynthetic process Supporting Evidence: PMID:11154694 Furthermore, yeast genes ECM31 and YIL145c, which both have structural homology to genes of the bacterial pantothenic acid pathway, were also required for pantothenic acid biosynthesis. |
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Download this section (compressed HTML)Q: YeastPathways places the pantothenate branch in the cytosol, but Ecm31 is mitochondrial; how is 2-dehydropantoate (or pantoate) exported from mitochondria to meet beta-alanine and Pan6 (pantothenate synthetase), and which ketopantoate reductase acts in yeast?
Experiment: Purify recombinant Ecm31 and measure 5,10-methylene-THF-dependent ketopantoate formation directly, including Mg2+ dependence, to convert the homology/auxotrophy-based activity assignment into direct biochemical evidence.
Ketopantoate hydroxymethyltransferase; required for pantothenic acid biosynthesis, converts 2-oxoisovalerate into 2-dehydropantoate
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