MDH3 encodes the peroxisomal isozyme of NAD+-dependent malate dehydrogenase (EC 1.1.1.37), a homodimer targeted to the peroxisomal matrix by a C-terminal SKL (PTS1); dimerisation precedes import. Although its sequence is closest to mitochondrial Mdh1p, Mdh3p acts inside peroxisomes, where it interconverts malate and oxaloacetate to reoxidise NADH generated during fatty acid beta-oxidation, because the peroxisomal membrane is impermeable to NAD(H). mdh3 mutants have impaired beta-oxidation in intact cells and cannot grow on oleate, while growth on other non-fermentable carbon sources is normal or only mildly slowed (acetate). Mdh3p contributes about 10% of cellular MDH activity in acetate-grown cells and has also been detected binding mRNAs in a proteome-wide screen.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003729 mRNA binding | IDA PMID:21124907 A screen for RNA-binding proteins in yeast indicates dual fu... | KEEP AS NON CORE | Summary: IDA: Scherrer et al. confirmed reproducible mRNA association of Mdh3p by RIP-Chip, with enrichment for messages encoding NTPase/helicase proteins. A real observation but with no demonstrated function; Mdh3p is a peroxisomal matrix enzyme, so physiological relevance is unclear. Supporting Evidence: PMID:21124907 We tested four (Gre3, Dfr1, Mdh1, Mdh3) NAD binding proteins for association with cellular RNA with RIP-Chip and found that all of them were reproducibly associated with mRNAs |
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: IEA from InterPro2GO (IPR015955) mapping to the generic term "catalytic activity". Correct for MDH3 but uninformative; the specific NAD+-dependent L-malate dehydrogenase activity is established for this isozyme. Proposed replacements: L-malate dehydrogenase (NAD+) activity Supporting Evidence: file:yeast/MDH3/MDH3-uniprot.txt Reaction=(S)-malate + NAD(+) = oxaloacetate + NADH + H(+); |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA from PTN000166149 (deep MDH node incl. cytosolic MDH). GO cytoplasm technically includes peroxisomes, but Mdh3p is a PTS1-targeted peroxisomal matrix enzyme and "is_active_in cytoplasm" is uninformative/misleading. Reason: Uninformative relative to the established peroxisomal matrix location. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000166149 SUPPORTS SOURCE BUT NOT TARGET Deep MDH node whose cytoplasm assertion is driven by cytosolic MDHs (e.g. mouse Mdh1, yeast Mdh2). MDH3 is an organellar isozyme (peroxisomal matrix); cytoplasm is only true via part_of and is uninformative. Supporting Evidence: PMID:8824293 We observed efficient import of MDH3 into peroxisomes with a large variety of PTS1 tripeptides. |
| GO:0005737 cytoplasm | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: IEA from ARBA00026971 (cytoplasm). Same consideration as the IBA row. Reason: Uninformative relative to peroxisomal matrix. Supporting Evidence: PMID:8824293 We observed efficient import of MDH3 into peroxisomes with a large variety of PTS1 tripeptides. |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | REMOVE | Summary: IBA from PTN000899493, the mitochondrial MDH clade seeded by Mdh1p and S. pombe Mdh1. Although Mdh3p is sequence-closer to Mdh1p than to Mdh2p, it has diverged in targeting: it carries a C-terminal SKL PTS1, is imported into peroxisomes as a dimer, and is found in the peroxisomal matrix by fractionation. There is no evidence for a mitochondrial pool. This is target-specific evidence of loss of the inherited location. Reason: Inherited mitochondrial location contradicted by experimental peroxisomal localisation of Mdh3p. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000899493 SUPPORTS SOURCE BUT NOT TARGET Mitochondrial MDH clade node. Placement is sound for Mdh1p and S. pombe Mdh1, but MDH3 acquired a PTS1 and relocated to peroxisomes, so the mitochondrial/TCA assertion does not hold for this descendant. SGD:S000001568 SUPPORTS SOURCE BUT NOT TARGET MDH1, the experimentally grounded yeast donor; its mitochondrial TCA role is not shared by MDH3. Supporting Evidence: PMID:1447211 The MDH3 sequence was found to contain a carboxyl-terminal SKL tripeptide, characteristic of many peroxisomal enzymes, and immunochemical analysis was used to confirm organellar localization of the MDH3 isozyme. PMID:8824293 We observed efficient import of MDH3 into peroxisomes with a large variety of PTS1 tripeptides. |
| GO:0005777 peroxisome | IDA PMID:1447211 Isolation and characterization of the yeast gene encoding th... | ACCEPT | Summary: IDA: immunochemical analysis confirmed organellar (peroxisomal) localization of Mdh3p, which has a C-terminal SKL. Core location. Supporting Evidence: PMID:1447211 The MDH3 sequence was found to contain a carboxyl-terminal SKL tripeptide, characteristic of many peroxisomal enzymes, and immunochemical analysis was used to confirm organellar localization of the MDH3 isozyme. |
| GO:0005777 peroxisome | IDA PMID:7628449 The membrane of peroxisomes in Saccharomyces cerevisiae is i... | ACCEPT | Summary: IDA: van Roermund et al. studied Mdh3p as the peroxisomal MDH (abstract-only; deferring to curator on the localization data). Correct. Supporting Evidence: PMID:7628449 Disruption of the peroxisomal malate dehydrogenase 3 gene (MDH3) resulted in impaired beta-oxidation capacity as measured in intact cells |
| GO:0005777 peroxisome | IEA GO_REF:0000044 | ACCEPT | Summary: IEA from UniProt subcellular location (SL-0204 Peroxisome). Correct. Supporting Evidence: file:yeast/MDH3/MDH3-uniprot.txt SUBCELLULAR LOCATION: Peroxisome. |
| GO:0005782 peroxisomal matrix | IDA PMID:8824293 Analysis of the carboxyl-terminal peroxisomal targeting sign... | ACCEPT | Summary: IDA: subcellular fractionation showing PTS1-dependent import of Mdh3p into the peroxisomal matrix. Most specific location; core. Supporting Evidence: PMID:8824293 We observed efficient import of MDH3 into peroxisomes with a large variety of PTS1 tripeptides. PMID:8824293 Because we show that dimerization of MDH3 precedes import into the organelle |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA (glyoxylate cycle, GLYOXYLATE-BYPASS) placing the MDH step in the cytosol and attaching Mdh3p. Mdh3p is peroxisomal; the cytosolic MDH of the yeast glyoxylate cycle is Mdh2p. Reason: Compartment contradicted by peroxisomal matrix localisation of Mdh3p. Supporting Evidence: PMID:8824293 We observed efficient import of MDH3 into peroxisomes with a large variety of PTS1 tripeptides. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA from the TCA/glyoxylate superpathway (PWY3O-94) placing MDH in the cytosol. Same artefact for the peroxisomal isozyme. Reason: Compartment contradicted by peroxisomal matrix localisation of Mdh3p. Supporting Evidence: PMID:1447211 The MDH3 sequence was found to contain a carboxyl-terminal SKL tripeptide, characteristic of many peroxisomal enzymes, and immunochemical analysis was used to confirm organellar localization of the MDH3 isozyme. |
| GO:0006097 glyoxylate cycle | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: YeastPathways RCA from glyoxylate cycle. Steffan & McAlister-Henn observed slower growth of mdh3 mutants on acetate, consistent with a glyoxylate-cycle contribution, but van Roermund et al. found mdh3 mutants grow normally on non-fermentable carbon sources other than oleate and concluded that Mdh3p mainly reoxidises beta-oxidation NADH rather than acting in the glyoxylate cycle. Plausible, minor/contested role. Supporting Evidence: PMID:1447211 Disruption of the chromosomal MDH3 locus produced a reduction in cellular growth rates on acetate, consistent with the presumed function of this isozyme in the glyoxylate pathway of yeast. PMID:7628449 suggesting that MDH3 is involved in the reoxidation of NADH generated during fatty acid beta-oxidation rather than functioning as part of the glyoxylate cycle |
| GO:0006099 tricarboxylic acid cycle | IBA GO_REF:0000033 | REMOVE | Summary: IBA from PTN000899493 (mitochondrial MDH clade). The TCA cycle is mitochondrial and Mdh3p is peroxisomal; mdh3 mutants have no defect on respiratory carbon sources other than oleate. The inherited TCA role was lost along with mitochondrial targeting in this paralog. Reason: Target-specific evidence (peroxisomal location, phenotype) against the inherited TCA-cycle role. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000899493 SUPPORTS SOURCE BUT NOT TARGET Mitochondrial MDH clade node. Placement is sound for Mdh1p and S. pombe Mdh1, but MDH3 acquired a PTS1 and relocated to peroxisomes, so the mitochondrial/TCA assertion does not hold for this descendant. SGD:S000001568 SUPPORTS SOURCE BUT NOT TARGET MDH1, the experimentally grounded yeast donor; its mitochondrial TCA role is not shared by MDH3. Supporting Evidence: PMID:7628449 suggesting that MDH3 is involved in the reoxidation of NADH generated during fatty acid beta-oxidation rather than functioning as part of the glyoxylate cycle PMID:1447211 The MDH3 sequence was found to contain a carboxyl-terminal SKL tripeptide, characteristic of many peroxisomal enzymes, and immunochemical analysis was used to confirm organellar localization of the MDH3 isozyme. |
| GO:0006099 tricarboxylic acid cycle | IEA GO_REF:0000002 | REMOVE | Summary: IEA from InterPro IPR010097 (MDH type 1) to TCA cycle; over-propagated family mapping inapplicable to the peroxisomal isozyme. Reason: Family-level IEA inapplicable to the peroxisomal paralog. Supporting Evidence: PMID:7628449 suggesting that MDH3 is involved in the reoxidation of NADH generated during fatty acid beta-oxidation rather than functioning as part of the glyoxylate cycle |
| GO:0006108 malate metabolic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: IEA from InterPro IPR001252. True but general. Supporting Evidence: file:yeast/MDH3/MDH3-uniprot.txt Reaction=(S)-malate + NAD(+) = oxaloacetate + NADH + H(+); |
| GO:0006635 fatty acid beta-oxidation | IMP PMID:7628449 The membrane of peroxisomes in Saccharomyces cerevisiae is i... | ACCEPT | Summary: IMP: mdh3 disruption impaired beta-oxidation in intact cells (not in lysates) and abolished growth on oleate. Mdh3p is part of the peroxisomal malate/oxaloacetate redox shuttle that regenerates intraperoxisomal NAD+ consumed by the 3-hydroxyacyl-CoA dehydrogenase step, so it supplies a cofactor that a beta-oxidation step depends on. Retained as the physiological process context of Mdh3p. Supporting Evidence: PMID:7628449 Disruption of the peroxisomal malate dehydrogenase 3 gene (MDH3) resulted in impaired beta-oxidation capacity as measured in intact cells PMID:7628449 suggesting that MDH3 is involved in the reoxidation of NADH generated during fatty acid beta-oxidation rather than functioning as part of the glyoxylate cycle |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | MODIFY | Summary: IEA from InterPro2GO (IPR001236) mapping to the generic term "oxidoreductase activity". Correct for MDH3 but uninformative; the specific NAD+-dependent L-malate dehydrogenase activity is established for this isozyme. Proposed replacements: L-malate dehydrogenase (NAD+) activity Supporting Evidence: file:yeast/MDH3/MDH3-uniprot.txt Reaction=(S)-malate + NAD(+) = oxaloacetate + NADH + H(+); |
| GO:0016615 malate dehydrogenase activity | IEA GO_REF:0000002 | MODIFY | Summary: IEA from InterPro2GO (IPR001252) mapping to the generic term "malate dehydrogenase activity". Correct for MDH3 but uninformative; the specific NAD+-dependent L-malate dehydrogenase activity is established for this isozyme. Proposed replacements: L-malate dehydrogenase (NAD+) activity Supporting Evidence: file:yeast/MDH3/MDH3-uniprot.txt Reaction=(S)-malate + NAD(+) = oxaloacetate + NADH + H(+); |
| GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | IEA GO_REF:0000002 | MODIFY | Summary: IEA from InterPro2GO (IPR001557/IPR015955/IPR022383) mapping to the generic term "oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor". Correct for MDH3 but uninformative; the specific NAD+-dependent L-malate dehydrogenase activity is established for this isozyme. Proposed replacements: L-malate dehydrogenase (NAD+) activity Supporting Evidence: file:yeast/MDH3/MDH3-uniprot.txt Reaction=(S)-malate + NAD(+) = oxaloacetate + NADH + H(+); |
| GO:0030060 L-malate dehydrogenase (NAD+) activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000166149 (NAD+-MDH node). Correct; Mdh3p has its own biochemical evidence. Supporting Evidence: file:yeast/MDH3/MDH3-uniprot.txt Reaction=(S)-malate + NAD(+) = oxaloacetate + NADH + H(+); |
| GO:0030060 L-malate dehydrogenase (NAD+) activity | IDA PMID:1447211 Isolation and characterization of the yeast gene encoding th... | ACCEPT | Summary: IDA: Mdh3p was purified as residual MDH activity from an mdh1 mdh2 strain, and the triple mutant lacks detectable MDH activity. Core activity. Supporting Evidence: PMID:1447211 The MDH3 isozyme of Saccharomyces cerevisiae was purified from a haploid strain containing disruptions in genomic loci encoding the mitochondrial MDH1 and nonmitochondrial MDH2 isozymes. PMID:1447211 Combined disruption of MDH1, MDH2, and MDH3 loci in a haploid strain resulted in the absence of detectable cellular malate dehydrogenase activity. |
| GO:0030060 L-malate dehydrogenase (NAD+) activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA (GO_REF:0000120) from ARBA, InterPro IPR010097, RHEA:21432, EC 1.1.1.37. Correct. Supporting Evidence: file:yeast/MDH3/MDH3-uniprot.txt Reaction=(S)-malate + NAD(+) = oxaloacetate + NADH + H(+); |
| GO:0030060 L-malate dehydrogenase (NAD+) activity | IMP PMID:1986231 Isolation, nucleotide sequence analysis, and disruption of t... | ACCEPT | Summary: IMP: residual MDH activity in mdh1 mdh2 double mutants revealed a third isozyme (later identified as Mdh3p). Supports the activity. Supporting Evidence: PMID:1986231 The detection of residual malate dehydrogenase activity in the latter strain confirmed the existence of at least three isozymes in yeast cells. |
| GO:0030060 L-malate dehydrogenase (NAD+) activity | IMP PMID:7628449 The membrane of peroxisomes in Saccharomyces cerevisiae is i... | ACCEPT | Summary: IMP from van Roermund et al.: mdh3 mutant phenotypes in peroxisomal NADH reoxidation (abstract-only; deferring to the curator). Activity well established. Supporting Evidence: PMID:7628449 suggesting that MDH3 is involved in the reoxidation of NADH generated during fatty acid beta-oxidation rather than functioning as part of the glyoxylate cycle |
| GO:0030060 L-malate dehydrogenase (NAD+) activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (glyoxylate cycle) assigning EC 1.1.1.37. Activity correct for Mdh3p. Supporting Evidence: file:yeast/MDH3/MDH3-uniprot.txt Reaction=(S)-malate + NAD(+) = oxaloacetate + NADH + H(+); |
| GO:0030060 L-malate dehydrogenase (NAD+) activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA (TCA/glyoxylate superpathway) assigning EC 1.1.1.37. Activity correct. Supporting Evidence: file:yeast/MDH3/MDH3-uniprot.txt Reaction=(S)-malate + NAD(+) = oxaloacetate + NADH + H(+); |
| GO:0070013 intracellular organelle lumen | IEA GO_REF:0000117 | MODIFY | Summary: IEA from ARBA00027917 (intracellular organelle lumen). Correct for Mdh3p (peroxisomal matrix is an organelle lumen) but much less specific than the IDA-supported peroxisomal matrix. Proposed replacements: peroxisomal matrix Supporting Evidence: PMID:8824293 We observed efficient import of MDH3 into peroxisomes with a large variety of PTS1 tripeptides. |
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Experiment: 13C-acetate flux analysis in mdh3 versus wild type, combined with a peroxisome-targeted NAD+/NADH sensor, to separate glyoxylate-cycle and redox-shuttle roles.
Peroxisomal malate dehydrogenase; catalyzes interconversion of malate and oxaloacetate; involved in the glyoxylate cycle; mutation in human homolog MDH2 causes early-onset severe encephalopathy
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