KGD4 (YMR31/YFR049W) encodes a small mitochondrial protein that is a dedicated, non-catalytic subunit of the 2-oxoglutarate (alpha-ketoglutarate) dehydrogenase complex (OGDC/KGDH) of the citric acid cycle. Kgd4 binds the E1-E2 core (Kgd1-Kgd2) through its C-terminal region and the E3 dihydrolipoyl dehydrogenase Lpd1 through its N-terminal region, acting as a molecular adaptor that recruits E3 to the core and stabilises the assembled complex; without Kgd4 the catalytic subunits are stable but E3 dissociates and overall KGDH activity falls sharply. Kgd4 was first purified from mitochondrial small ribosomal subunit preparations (as YMR-31/MRPS36), but this assignment reflects co-sedimentation of the similarly sized, abundant KGDH complex. The protein is conserved in fungi and animals (human MRPS36/KGD4) and is absent from bacterial OGDH complexes. An alternative upstream UUG start codon produces a longer isoform (Kgd4L).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003735 structural constituent of ribosome | IDA PMID:2693936 Cloning and analysis of the nuclear genes for two mitochondr... | REMOVE | Summary: YMR-31 was purified as a mitochondrial small-subunit ribosomal protein by Matsushita et al. 1989 (N-terminal sequencing of a gradient-purified ribosomal fraction). Heublein et al. 2014 showed that Kgd4 co-purifies quantitatively with KGDH, not with ribosomal proteins, and that the KGDH complex co-sediments with and contaminates 28S ribosomal preparations. The ribosomal assignment is therefore contradicted by later direct evidence; UniProt also carries a CAUTION to this effect. Kgd4 is not a structural constituent of the mitoribosome. Reason: Contradicted by direct affinity-purification and gradient evidence (PMID:25165143) that the protein is a KGDH subunit and that its presence in mitoribosome preparations was contamination. Supporting Evidence: PMID:25165143 A number of independent lines of evidence support the notion that Kgd4 is a structural subunit of the KGDH complex and not a subunit of the mitochondrial ribosome. file:yeast/KGD4/KGD4-uniprot.txt CAUTION: Was originally identified in the small subunit (28S) of |
| GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity | IDA PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | ACCEPT | Summary: KGDH activity was measured photometrically in lysates of wild-type and kgd4-deleted mitochondria; activity was dramatically reduced without Kgd4 while MDH activity was unaffected. Kgd4 has no catalytic domain but is required for full activity of the E1-E2-E3 complex, which is exactly what contributes_to expresses for a non-catalytic complex subunit. Supporting Evidence: PMID:25165143 Robust KGDH activity was observed in lysates from wild-type cells, while KGDH activity was dramatically reduced in the absence of Kgd4 (Figure 2A). |
| GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity | IMP PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | ACCEPT | Summary: Same experiment read as a mutant phenotype: deletion of KGD4 sharply decreases KGDH activity without destabilising Kgd1, Kgd2 or Lpd1. Appropriate contributes_to annotation for a non-catalytic subunit that is required to recruit E3 to the E1-E2 core. Supporting Evidence: PMID:25165143 Robust KGDH activity was observed in lysates from wild-type cells, while KGDH activity was dramatically reduced in the absence of Kgd4 (Figure 2A). file:yeast/KGD4/KGD4-uniprot.txt DISRUPTION PHENOTYPE: Decreases OGDH activity in vitro without |
| GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways-to-GO-CAM conversion from the TCA-EUK-PWY frame. KGD4 is not listed as a gene on the YeastCyc 2-oxoglutarate dehydrogenase reaction in the cached YeastPathways export (KGD1, KGD2, LPD1 are), but the contributes_to OGDH activity statement is correct for Kgd4 and duplicates the experimental IDA/IMP rows. Supporting Evidence: PMID:25165143 Robust KGDH activity was observed in lysates from wild-type cells, while KGDH activity was dramatically reduced in the absence of Kgd4 (Figure 2A). |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: Gavin et al. 2006 TAP-MS co-complex with Lpd1 (E3). Real, but 'protein binding' is uninformative; the binding of Lpd1 is the mechanism of Kgd4's adaptor activity and its complex membership is captured by part_of oxoglutarate dehydrogenase complex. Reason: Removal does not dispute the interaction; uninformative protein binding from a high-throughput co-complex screen, function captured by GO:0030674 and GO:0045252. |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: Gavin et al. 2006 TAP-MS co-complex with Kgd1 (E1). Correct co-membership of KGDH but uninformative as an MF; captured by part_of GO:0045252 and the adaptor function. Reason: Removal does not dispute the interaction; uninformative protein binding from a high-throughput co-complex screen, complex membership already annotated. |
| GO:0005515 protein binding | IPI PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | MODIFY | Summary: Heublein et al. 2014 showed by native purification, including from kgd1-deleted mitochondria and with an N-terminal Kgd4 fragment, that Kgd4 binds Lpd1 directly via its N-terminal domain. This binding is the substance of Kgd4's function as an adaptor that bridges E3 to the E1-E2 core, so the informative replacement is protein-macromolecule adaptor activity. Proposed replacements: protein-macromolecule adaptor activity Supporting Evidence: PMID:25165143 Taken together, these purification experiments confirmed that Lpd1 cannot stably incorporate into KGDH in the absence of Kgd4 and showed that Kgd4 directly binds to Lpd1. |
| GO:0005515 protein binding | IPI PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | MODIFY | Summary: Kgd4 (via its C-terminal domain) binds the assembled Kgd1-Kgd2 core; a Kgd4 fragment lacking the N-terminus co-purified Kgd1 and Kgd2 but not Lpd1. Together with its Lpd1 binding this defines a bridging adaptor; replace protein binding with protein-macromolecule adaptor activity. Proposed replacements: protein-macromolecule adaptor activity Supporting Evidence: PMID:25165143 This demonstrates that the C-terminal domain of Kgd4 directly interacts with the assembled Kgd1-Kgd2 core |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Michaelis et al. 2023 quantitative affinity-enrichment MS interactome recovers Kgd4 with Lpd1. Confirms complex membership; protein binding adds nothing beyond GO:0045252 and the adaptor activity established in PMID:25165143. Reason: Removal does not dispute the interaction; uninformative high-throughput protein binding, captured by complex membership and adaptor activity. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Michaelis et al. 2023 affinity-enrichment MS recovers Kgd4 with Kgd1. Consistent with Kgd4 being a KGDH subunit; protein binding term is uninformative. Reason: Removal does not dispute the interaction; uninformative high-throughput protein binding, captured by complex membership. |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: Reinders et al. 2006 mitochondrial proteome (multidimensional LC-MS of purified mitochondria) detects Kgd4. Consistent with its role as a matrix KGDH subunit. |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | ACCEPT | Summary: Renvoise et al. 2014 quantitative mitochondrial proteome of fermenting and respiring cells detects Kgd4 in mitochondria. Consistent with its KGDH membership. |
| GO:0005739 mitochondrion | IDA PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | ACCEPT | Summary: Kgd4 was purified from isolated mitochondria together with KGDH subunits and migrates with the complex on sucrose gradients of mitochondrial lysates. Correct location; the complex is in the matrix. Supporting Evidence: PMID:25165143 Importantly, Kgd4 quantitatively comigrated with the KGDH complex and not with smaller particles. |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell (SL-0173 Mitochondrion) mapping; the UniProt location is experimentally grounded (PMID:14562095, 14576278, 25165143). Correct. Supporting Evidence: file:yeast/KGD4/KGD4-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14562095, |
| GO:0005739 mitochondrion | RCA GO_REF:0000123 | ACCEPT | Summary: is_active_in mitochondrion from the YeastPathways TCA-EUK-PWY conversion. Correct: the KGDH complex acts in the mitochondrial matrix, unlike many YeastCyc conversions that default to cytosol. |
| GO:0005761 mitochondrial ribosome | IDA PMID:2693936 Cloning and analysis of the nuclear genes for two mitochondr... | REMOVE | Summary: Location in the mitochondrial ribosome rests on the 1989 isolation of YMR-31 from ribosomal fractions. Heublein et al. 2014 show this reflects co-sedimentation of KGDH with the small ribosomal subunit; Kgd4 comigrates quantitatively with KGDH. The ribosome location is contradicted; the protein is a mitochondrial (matrix) KGDH subunit. Reason: Contradicted by PMID:25165143: Kgd4 copurifies with KGDH and not with ribosomal proteins, and KGDH contaminates ribosomal preparations made by sequential centrifugation. Supporting Evidence: PMID:25165143 typically uses sequential centrifugation steps that do not allow separating the small ribosomal subunit from the KGDH, because both have a similar size; the highly abundant KGDH is therefore found to contaminate ribosomal preparations |
| GO:0006099 tricarboxylic acid cycle | IMP PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | ACCEPT | Summary: Loss of Kgd4 strongly reduces KGDH activity, a TCA-cycle step. Kgd4 is an integral subunit of the enzyme that performs the 2-oxoglutarate to succinyl-CoA step, so it participates in the cycle (not just upstream of it). Supporting Evidence: PMID:25165143 In this paper, we have identified a novel subunit of the mitochondrial KGDH. |
| GO:0006099 tricarboxylic acid cycle | NAS PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | ACCEPT | Summary: Author statement that Kgd4 is a subunit of a key citric acid cycle enzyme. Redundant with the IMP row but correct. Supporting Evidence: PMID:25165143 A central enzyme of the citric acid cycle is Ξ±-ketoglutarate dehydrogenase (Ξ±-KGDH), which catalyzes the oxidative decarboxylation of Ξ±-ketoglutarate to succinyl-CoA and the concomitant formation of NADH and CO2. |
| GO:0006103 2-oxoglutarate metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT node PTN002055411 seeded by yeast Kgd4 and mouse/human KGD4 (MRPS36). The Kgd4 family is restricted to fungi and animals and its experimentally characterised members function in OGDC, so the inherited 2-oxoglutarate metabolic process is sound. The term is broader than the TCA cycle step but correct. |
| GO:0006103 2-oxoglutarate metabolic process | IDA PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | ACCEPT | Summary: Direct assay of 2-oxoglutarate dehydrogenase activity in mitochondrial lysates with and without Kgd4. Correct; the TCA cycle annotation is the more informative process. Supporting Evidence: PMID:25165143 Robust KGDH activity was observed in lysates from wild-type cells, while KGDH activity was dramatically reduced in the absence of Kgd4 (Figure 2A). |
| GO:0006103 2-oxoglutarate metabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO from IPR020373 (Kgd4/MRPS36 family). The family mapping to 2-oxoglutarate metabolism reflects the reassignment of the family to OGDC; correct for this protein. |
| GO:0006103 2-oxoglutarate metabolic process | IMP PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | ACCEPT | Summary: kgd4 deletion reduces 2-oxoglutarate dehydrogenase activity. Correct, overlapping the IDA row. Supporting Evidence: PMID:25165143 Robust KGDH activity was observed in lysates from wild-type cells, while KGDH activity was dramatically reduced in the absence of Kgd4 (Figure 2A). |
| GO:0009060 aerobic respiration | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: Aerobic respiration inherited from the YeastPathways TCA-EUK-PWY frame. The TCA cycle is part of aerobic respiration in GO, so this is a correct but broader superprocess of the TCA cycle annotation; non-core. |
| GO:0045252 oxoglutarate dehydrogenase complex | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT node seeded by yeast Kgd4 and mammalian KGD4; the OGDC subunit role is experimentally shown in yeast and in murine cells (PMID:25165143). Sound inheritance. Supporting Evidence: PMID:25165143 In this paper, we have identified a novel subunit of the mitochondrial KGDH. |
| GO:0045252 oxoglutarate dehydrogenase complex | IDA PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | ACCEPT | Summary: Kgd4 co-purifies with His-tagged Kgd1 and Lpd1 and comigrates quantitatively with the complex on sucrose gradients. Core cellular component. Supporting Evidence: PMID:25165143 In summary, these data show that Kgd4 quantitatively associates with the core of KGDH formed by Kgd1 and Kgd2. |
| GO:0045252 oxoglutarate dehydrogenase complex | IPI PMID:25165143 The novel component Kgd4 recruits the E3 subunit to the mito... | ACCEPT | Summary: Same paper, interaction-based evidence (co-purification with KGDH subunits). Correct. Supporting Evidence: PMID:25165143 Importantly, Kgd4 quantitatively comigrated with the KGDH complex and not with smaller particles. |
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Download this section (compressed HTML)Q: Does the long, UUG-initiated Kgd4L isoform differ from Kgd4S in import, KGDH assembly or any non-KGDH role?
Q: Does Kgd4 also bridge E3 to other 2-oxoacid dehydrogenase complexes in yeast (e.g. the 2-oxoadipate route via Kgd1/Kgd2 in lysine degradation), or is it strictly OGDC-specific?
Experiment: Cryo-EM of the yeast KGDH holo-complex with and without Kgd4 to map the Kgd4-Lpd1 and Kgd4-E1/E2 interfaces and test the adaptor model at structural resolution.
Type: structural biology
Subunit of the mitochondrial alpha-ketoglutarate dehydrogenase; recruits E3 subunit (Lpd1p) to the E1-E2 (Kgd1p, Kgd2p) core; exists in two forms derived from a single mRNA translated from two alternative start sites; evolutionarily conserved role in the organization of mitochondrial Ξ±-KGDH complexes; homolog of human KGD4
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