MDH2

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005737 cytoplasm	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Phylogenetic (IBA) annotation to the broad location "cytoplasm". The mature MDH2 enzyme acts in the mitochondrial matrix, but MDH2 is synthesized as a cytosolic preprotein and a cytosolic RNA-binding pool has been documented (PMID:38609156). Broad cytoplasmic annotation is defensible but is not the primary/core site of the enzyme's catalytic action. Reason: The informative, core location is the mitochondrial matrix (GO:0005759). "cytoplasm" is a correct-but-general ancestor location; retained as non-core rather than removed.
GO:0005739 mitochondrion	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Phylogenetic (IBA) annotation to mitochondrion. Correct; MDH2 is a mitochondrial matrix enzyme. This is a valid but less specific version of the mitochondrial matrix location. Reason: Correct localization but subsumed by the more specific core location mitochondrial matrix (GO:0005759).
GO:0030060 L-malate dehydrogenase (NAD+) activity	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic (IBA) annotation to the specific catalytic activity of MDH2. This is the core molecular function, independently supported by direct and mutant-phenotype experimental evidence (PMID:16740313, PMID:27989324, PMID:6576816).
GO:0006099 tricarboxylic acid cycle	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic (IBA) annotation to the TCA cycle, the core biological process in which MDH2 catalyzes the malate-to-oxaloacetate step. Well-supported across evidence lines.
GO:0003824 catalytic activity	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: InterPro2GO (IEA) mapping to the root molecular-function term "catalytic activity". True but maximally general; the specific NAD-dependent malate dehydrogenase activity (GO:0030060) is the informative annotation. Reason: Uninformative high-level ancestor of the specific catalytic activity already annotated.
GO:0005759 mitochondrial matrix	IEA GO_REF:0000120	ACCEPT	Summary: Automated (IEA) annotation to the mitochondrial matrix, the correct and core subcellular location of MDH2 (consistent with UniProt SUBCELLULAR LOCATION "Mitochondrion matrix" and IDA evidence PMID:38609156).
GO:0006099 tricarboxylic acid cycle	IEA GO_REF:0000002	ACCEPT	Summary: InterPro2GO (IEA) annotation to the TCA cycle. Correct core process; redundant with the experimental/TAS/IBA annotations to the same term.
GO:0006108 malate metabolic process	IEA GO_REF:0000120	KEEP AS NON CORE	Summary: Automated (IEA) annotation to malate metabolic process. True (MDH2 oxidizes L-malate) but a general parent of the specific processes (TCA cycle, malate-aspartate shuttle) that better capture its role. Reason: Correct but general; the specific processes GO:0006099 and GO:0043490 are the core BP annotations.
GO:0016491 oxidoreductase activity	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: InterPro2GO (IEA) mapping to the broad "oxidoreductase activity" ancestor. True but uninformative relative to the specific L-malate dehydrogenase (NAD+) activity. Reason: General ancestor of GO:0030060; not informative on its own.
GO:0016615 malate dehydrogenase activity	IEA GO_REF:0000120	MODIFY	Summary: Automated (IEA) annotation to "malate dehydrogenase activity", the direct parent of the NAD+-specific term. MDH2 is specifically NAD-dependent (EC 1.1.1.37), so the more precise GO:0030060 should be used. Reason: Correct but less precise than the specific NAD+-dependent activity. Proposed replacements: L-malate dehydrogenase (NAD+) activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: InterPro2GO (IEA) mapping to a mid-level oxidoreductase ancestor. True but an over-general parent of the specific L-malate dehydrogenase (NAD+) activity. Reason: General ancestor of GO:0030060.
GO:0030060 L-malate dehydrogenase (NAD+) activity	IEA GO_REF:0000120	ACCEPT	Summary: Automated (IEA) annotation (from EC:1.1.1.37 / RHEA:21432) to the specific core molecular function. Correct and consistent with experimental evidence.
GO:0016020 membrane	IEA GO_REF:0000107	REMOVE	Summary: Ensembl-Compara ortholog-transfer (IEA) annotation to "membrane". MDH2 is a soluble mitochondrial matrix enzyme (UniProt "SUBCELLULAR LOCATION: Mitochondrion matrix"; homodimer with a Rossmann fold), not a membrane protein. This is an erroneous electronic transfer. Reason: Clearly-wrong IEA: MDH2 is a soluble matrix enzyme, not membrane-localized.
GO:0042802 identical protein binding	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Ensembl (IEA) annotation to identical protein binding. MDH2 is a homodimer (UniProt "SUBUNIT: Homodimer"; confirmed by X-ray structures), so self-association is genuine. However, this is not an informative molecular function describing what the enzyme does. Reason: Homodimerization is real but not the core catalytic function; retained as non-core supporting information.
GO:0046554 L-malate dehydrogenase (NADP+) activity	IEA GO_REF:0000107	REMOVE	Summary: Ensembl ortholog-transfer (IEA) annotation to NADP-dependent malate dehydrogenase activity. MDH2 is the NAD-dependent enzyme (EC 1.1.1.37; catalytic reaction uses NAD(+), not NADP+). NADP+-dependent activity is not a documented function of human MDH2; this is an incorrect electronic transfer. Reason: Clearly-wrong IEA: MDH2 uses NAD+, not NADP+; contradicted by the documented catalytic activity.
GO:0006099 tricarboxylic acid cycle	TAS Reactome:R-HSA-71403	ACCEPT	Summary: Reactome traceable-author-statement placing MDH2 in the citric acid (TCA) cycle. Core biological process; consistent with all other evidence.
GO:0043490 malate-aspartate shuttle	TAS Reactome:R-HSA-9856872	ACCEPT	Summary: Reactome TAS placing MDH2 in the malate-aspartate shuttle, the mitochondrial arm of which is catalyzed by MDH2 (malate to oxaloacetate). Core biological process; also supported by IMP (PMID:37647199).
GO:0030060 L-malate dehydrogenase (NAD+) activity	EXP PMID:16740313 An NADH-tetrazolium-coupled sensitive assay for malate dehyd...	ACCEPT	Summary: Experimental annotation of the core catalytic activity. The cited paper is a sensitive spectrophotometric assay for mitochondrial malate dehydrogenase activity; Reactome uses it (with Eo et al.) as evidence for the MDH2 dimer dehydrogenating malate. Correct core molecular function.
GO:0003723 RNA binding	IDA PMID:38609156 Cytosolic RNA binding of the mitochondrial TCA cycle enzyme ...	KEEP AS NON CORE	Summary: Direct experimental demonstration (PNK, 2C, eCLIP, EMSA) that MDH2 binds RNA in cells, preferentially cytosolic tRNAs and mRNAs, via its Rossmann fold. This is a genuine moonlighting activity distinct from the enzyme's metabolic role, with an as-yet-unidentified physiological function. Reason: Well-supported moonlighting activity, but not the core metabolic function of MDH2.
GO:0005739 mitochondrion	IDA PMID:38609156 Cytosolic RNA binding of the mitochondrial TCA cycle enzyme ...	KEEP AS NON CORE	Summary: Direct evidence of mitochondrial localization from the RNA-binding study (subcellular fractionation / immunofluorescence). Correct; a less specific version of the core mitochondrial matrix location. Reason: Correct but subsumed by the more specific core location mitochondrial matrix (GO:0005759).
GO:0005759 mitochondrial matrix	IDA PMID:38609156 Cytosolic RNA binding of the mitochondrial TCA cycle enzyme ...	ACCEPT	Summary: Direct evidence (subcellular fractionation) that MDH2 localizes to and acts in the mitochondrial matrix. This is the core subcellular location of the enzyme. Supporting Evidence: PMID:38609156 imported into the mitochondrial matrix
GO:0005739 mitochondrion	IDA GO_REF:0000052	KEEP AS NON CORE	Summary: HPA immunofluorescence-based (IDA) annotation to mitochondrion. Correct; redundant with and less specific than the mitochondrial matrix core location. Reason: Correct but subsumed by mitochondrial matrix (GO:0005759).
GO:0005759 mitochondrial matrix	ISS GO_REF:0000024	ACCEPT	Summary: Sequence-similarity (ISS) transfer of mitochondrial matrix localization from an ortholog (P04636, rat MDH2). Correct core location, consistent with direct human evidence.
GO:0006099 tricarboxylic acid cycle	IMP PMID:37647199 The malate-aspartate shuttle is important for de novo serine...	ACCEPT	Summary: Mutant-phenotype (IMP) annotation from a study generating a panel of malate-aspartate-shuttle-deficient cell lines by genetically disrupting each MAS component, including MDH2. Supports MDH2 involvement in TCA-cycle / central carbon metabolism. Core process.
GO:0043490 malate-aspartate shuttle	IMP PMID:37647199 The malate-aspartate shuttle is important for de novo serine...	ACCEPT	Summary: Mutant-phenotype (IMP) evidence: MDH2-deficient HEK293 cells were part of the MAS-deficient panel used to show the shuttle's role in serine biosynthesis and cytosolic NAD+ regeneration. MDH2 is the mitochondrial MDH of the malate-aspartate shuttle. Core process.
GO:0005739 mitochondrion	HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an...	KEEP AS NON CORE	Summary: High-throughput mitochondrial-proteome (HTP) detection of MDH2 in mitochondria. Consistent with the established localization; less specific than mitochondrial matrix. Reason: Correct but subsumed by mitochondrial matrix (GO:0005759).
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-70979	ACCEPT	Summary: Reactome TAS (reaction "MDH2 dimer dehydrogenates MAL") placing the active enzyme in the mitochondrial matrix. Core location.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9838035	ACCEPT	Summary: Reactome TAS (mitochondrial protein-degradation pathway; CLPXP binds matrix proteins) locating MDH2 in the mitochondrial matrix. Correct core location, captured here as a substrate of the matrix quality-control machinery.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9838081	ACCEPT	Summary: Reactome TAS (LONP1 degrades matrix proteins) locating MDH2 in the mitochondrial matrix. Correct core location.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9838093	ACCEPT	Summary: Reactome TAS (LONP1 binds matrix proteins) locating MDH2 in the mitochondrial matrix. Correct core location.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9838289	ACCEPT	Summary: Reactome TAS (CLPXP degrades matrix proteins) locating MDH2 in the mitochondrial matrix. Correct core location.
GO:0009060 aerobic respiration	IDA PMID:27989324 Mutations in MDH2, Encoding a Krebs Cycle Enzyme, Cause Earl...	KEEP AS NON CORE	Summary: MDH2 supports cellular respiration; DEE51-causing variants show severe defects in aerobic respiration when assayed in a heterologous (yeast) system, and loss of MDH2 disrupts the TCA cycle that feeds the respiratory chain. Legitimate but a broad downstream process relative to the direct TCA-cycle role. Reason: Correct contribution but downstream/general; the core BP annotations are the TCA cycle and malate-aspartate shuttle.
GO:0030060 L-malate dehydrogenase (NAD+) activity	IDA PMID:27989324 Mutations in MDH2, Encoding a Krebs Cycle Enzyme, Cause Earl...	ACCEPT	Summary: Direct experimental evidence: patient fibroblasts lacking MDH2 show MDH enzymatic activity close to null, restored by WT MDH2 cDNA, establishing the NAD-dependent malate dehydrogenase activity of MDH2. Core molecular function. Supporting Evidence: PMID:27989324 showed both an apparently complete loss of MDH2 levels and MDH2 enzymatic
GO:0070062 extracellular exosome	HDA PMID:23533145 In-depth proteomic analyses of exosomes isolated from expres...	MARK AS OVER ANNOTATED	Summary: High-throughput exosome/secretome proteomics detection. MDH2 is an abundant mitochondrial matrix enzyme frequently detected as a background contaminant in exosome/extracellular-vesicle preparations; it has no established secreted or extracellular function. Reason: Recurrent proteomics contaminant location; not a functional extracellular localization of this matrix enzyme.
GO:0005634 nucleus	HDA PMID:21630459 Proteomic characterization of the human sperm nucleus.	MARK AS OVER ANNOTATED	Summary: High-throughput sperm-nucleus proteomics detection. There is no established nuclear function for MDH2; this most likely reflects proteomic contamination of the nuclear fraction rather than a functional nuclear pool. Reason: Isolated high-throughput proteomics hit with no functional support; likely contamination of a matrix enzyme.
GO:0003723 RNA binding	HDA PMID:22658674 Insights into RNA biology from an atlas of mammalian mRNA-bi...	KEEP AS NON CORE	Summary: High-throughput mRNA-interactome capture identifying MDH2 as an RNA-binding protein. Consistent with the directly validated moonlighting RNA-binding activity (PMID:38609156), but not the core metabolic function. Reason: Corroborates the non-core moonlighting RNA-binding activity.
GO:0003723 RNA binding	HDA PMID:22681889 The mRNA-bound proteome and its global occupancy profile on ...	KEEP AS NON CORE	Summary: High-throughput mRNA-bound-proteome capture identifying MDH2 as an RNA-binding protein. Corroborates the moonlighting RNA-binding activity; not the core function. Reason: Corroborates the non-core moonlighting RNA-binding activity.
GO:0005739 mitochondrion	HDA PMID:20833797 Phosphoproteome analysis of functional mitochondria isolated...	KEEP AS NON CORE	Summary: High-throughput phosphoproteomics of isolated mitochondria detecting MDH2. Correct localization; less specific than the mitochondrial matrix core location. Reason: Correct but subsumed by mitochondrial matrix (GO:0005759).
GO:0070062 extracellular exosome	HDA PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos...	MARK AS OVER ANNOTATED	Summary: High-throughput urinary-exosome proteomics detection. As above, MDH2 is a recurrent background hit in vesicle/exosome proteomics with no functional extracellular role. Reason: Recurrent proteomics contaminant location; not a functional extracellular localization.
GO:0070062 extracellular exosome	HDA PMID:20458337 MHC class II-associated proteins in B-cell exosomes and pote...	MARK AS OVER ANNOTATED	Summary: High-throughput B-cell exosome proteomics detection. As above, background detection of an abundant mitochondrial enzyme; no functional secreted role. Reason: Recurrent proteomics contaminant location; not a functional extracellular localization.
GO:0005739 mitochondrion	IDA PMID:16740313 An NADH-tetrazolium-coupled sensitive assay for malate dehyd...	KEEP AS NON CORE	Summary: IDA annotation to mitochondrion associated with the malate dehydrogenase assay in isolated mitochondria. Correct localization; less specific than the mitochondrial matrix core location. Reason: Correct but subsumed by mitochondrial matrix (GO:0005759).
GO:0006108 malate metabolic process	IDA PMID:16740313 An NADH-tetrazolium-coupled sensitive assay for malate dehyd...	KEEP AS NON CORE	Summary: IDA annotation to malate metabolic process from measurement of mitochondrial malate dehydrogenase activity. True but a general parent of the specific processes (TCA cycle, malate-aspartate shuttle). Reason: Correct but general; core BP terms are GO:0006099 and GO:0043490.
GO:0006108 malate metabolic process	IMP PMID:6576816 Studies on mitochondrial and cytoplasmic malate dehydrogenas...	KEEP AS NON CORE	Summary: Mutant/dosage-phenotype (IMP) evidence: reduced mitochondrial malate dehydrogenase activity in cells with monosomy 7 (the MDH2 locus is on chromosome 7), linking MDH2 gene dosage to malate metabolism. Correct but a general parent of the specific core processes. Reason: Correct but general; core BP terms are GO:0006099 and GO:0043490.
GO:0030060 L-malate dehydrogenase (NAD+) activity	IDA PMID:16740313 An NADH-tetrazolium-coupled sensitive assay for malate dehyd...	ACCEPT	Summary: Direct assay of mitochondrial malate dehydrogenase (NAD-coupled) activity. Core molecular function of MDH2.
GO:0030060 L-malate dehydrogenase (NAD+) activity	IMP PMID:6576816 Studies on mitochondrial and cytoplasmic malate dehydrogenas...	ACCEPT	Summary: Mutant/dosage (IMP) evidence: monosomy-7 cells show reduced mitochondrial malate dehydrogenase activity, supporting MDH2 as the enzyme responsible for this NAD-dependent activity. Core molecular function.

Gene Description

Existing Annotations Review

Core Functions

Mitochondrial NAD-dependent L-malate dehydrogenase that catalyzes the reversible oxidation of L-malate to oxaloacetate (EC 1.1.1.37) in the mitochondrial matrix, completing the final step of the tricarboxylic acid cycle.

Mitochondrial arm of the malate-aspartate shuttle: MDH2 reoxidizes malate to oxaloacetate within the matrix, transferring reducing equivalents delivered from the cytosol and helping maintain the cytosolic/mitochondrial NAD+/NADH redox balance.

References

📚 Additional Documentation

Notes

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