mdh1

Summary: Generic InterPro-derived parent of the specific activity, which is already annotated.

Reason: Catalytic activity is correct but general. Mdh1 belongs to the MDH type 1 family (NCBIfam TIGR01772, eukaryotic/ gamma-proteobacterial MDH) and UniProt curates the NAD-dependent (S)-malate/oxaloacetate reaction; the activity rests on family membership, not an S. pombe enzyme assay. Refine to the specific descendant GO:0030060 L-malate dehydrogenase (NAD+) activity, which the gene already carries (IBA, IEA).

Proposed replacements: L-malate dehydrogenase (NAD+) activity

Summary: PAINT inference of cytoplasm; true in GO's sense (the mitochondrion is part of the cytoplasm) but general, since mdh1 is the mitochondrial-matrix isozyme.

Reason: The IBA node (PTN000166149) groups Mdh1 with mitochondrial MDHs such as human MDH2 (P40926) and mouse Mdh2, so the claim is not contested; in GO the mitochondrial matrix is part_of the mitochondrion, which is part_of the cytoplasm. Mdh1 carries a predicted mitochondrial transit peptide, and the S. pombe ORFeome localization study (PMID:16823372) places it in the mitochondrial matrix, so the correct-but-general cytoplasm term is refined to GO:0005759 mitochondrial matrix, which the gene already carries (IEA, ISS).

Proposed replacements: mitochondrial matrix

Summary: ORFeome YFP screen: mitochondrion.

Summary: PAINT inference of mitochondrial location.

Reason: Root organelle term kept per policy; the claim holds. UniProt curates a mitochondrial matrix location from the S. pombe ORFeome localization study (PubMed:16823372) and annotates an N-terminal mitochondrial transit peptide; the matrix sub-compartment is carried by the GO:0005759 rows.

Summary: Matrix location of this TCA enzyme (inference or mapping); consistent.

Reason: The SubCell mapping comes from UniProt's curated matrix location, which is tied to the S. pombe ORFeome localization study (PubMed:16823372); the entry also has a mitochondrial transit peptide.

Summary: Matrix location of this TCA enzyme (inference or mapping); consistent.

Reason: The ISS source is S. cerevisiae Mdh1 (P17505). The claim is independently supported for S. pombe by UniProt's curated matrix location from the ORFeome localization study (PubMed:16823372) and by the annotated mitochondrial transit peptide.

Summary: 13C tracing in S. pombe versus S. japonicus shows that S. pombe runs a respiratory, oxidative TCA cycle (curator, full text).

Summary: PAINT inference; TCA cycle step.

Reason: Mdh1 is a type 1 (mitochondrial-clade) malate dehydrogenase whose curated reaction, (S)-malate to oxaloacetate with NAD+, is the TCA-cycle step that regenerates oxaloacetate, and it is located in the matrix where the cycle runs. The enzyme activity rests on family classification and by-similarity active-site annotation, not on an S. pombe assay.

Summary: InterPro/UniPathway mapping; consistent.

Reason: The mapping rests on IPR010097 (malate dehydrogenase type 1) membership; the family's reaction, (S)-malate to oxaloacetate with NAD+, is a TCA-cycle step, and the protein is in the mitochondrial matrix.

Summary: Generic InterPro-derived parent of the specific activity, which is already annotated.

Reason: Oxidoreductase activity is correct but general. Mdh1 belongs to the MDH type 1 family (NCBIfam TIGR01772, eukaryotic/ gamma-proteobacterial MDH) and UniProt curates the NAD-dependent (S)-malate/oxaloacetate reaction; the activity rests on family membership, not an S. pombe enzyme assay. Refine to the specific descendant GO:0030060 L-malate dehydrogenase (NAD+) activity, which the gene already carries (IBA, IEA).

Proposed replacements: L-malate dehydrogenase (NAD+) activity

Summary: Generic InterPro-derived parent of the specific activity, which is already annotated.

Reason: This CH-OH/NAD(P) oxidoreductase term is correct but general. Mdh1 belongs to the MDH type 1 family (NCBIfam TIGR01772, eukaryotic/ gamma-proteobacterial MDH) and UniProt curates the NAD-dependent (S)-malate/oxaloacetate reaction; the activity rests on family membership, not an S. pombe enzyme assay. Refine to the specific descendant GO:0030060 L-malate dehydrogenase (NAD+) activity, which the gene already carries (IBA, IEA).

Proposed replacements: L-malate dehydrogenase (NAD+) activity

Summary: NAD-malate dehydrogenase activity (PAINT/EC).

Reason: Supported by family membership (MDH type 1, NCBIfam TIGR01772 eukaryotic/gamma-proteobacterial MDH), UniProt's curated reaction, and a by-similarity proton-acceptor active site. No S. pombe enzyme assay is cached; the activity is inferred from the family.

Summary: NAD-malate dehydrogenase activity (PAINT/EC).

Reason: The EC/Rhea mapping derives from UniProt's curated reaction, which rests on MDH type 1 family membership (InterPro IPR010097) rather than an S. pombe assay.

Summary: Curator inference of the malate-aspartate shuttle; mitochondrial MDH is part of it in principle, but the shuttle has not been shown in S. pombe.

Reason: PomBase curator inference (IC from GO:0030060). The supporting facts are family-level and localization evidence, not a shuttle experiment in S. pombe; Mdh1 is an MDH type 1 enzyme catalysing the reversible NAD-dependent malate/oxaloacetate reaction and resides in the mitochondrial matrix (ORFeome localization, PMID:16823372), which is the matrix half of the malate-aspartate shuttle in other eukaryotes. Plausible but peripheral to its TCA-cycle role, so kept as non-core; the support is thin.