MdcD is the predicted beta subunit of the soluble, biotin-independent malonate decarboxylase system in Methylorubrum extorquens AM1. Together with MdcE it forms a crotonase-fold catalytic site that decarboxylates a malonyl group carried by the specialized acyl-carrier protein MdcC, regenerating acetyl-MdcC during malonate conversion to acetate and carbon dioxide. Its MdcD-specific family assignment and neighboring mdcA, mdcC and mdcE genes support this role; the detailed mechanism is inferred from experimentally characterized bacterial homologs.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003989 acetyl-CoA carboxylase activity | IEA GO_REF:0000118 | REMOVE | Summary: Retain rejection of the mismatched acetyl-CoA carboxylase assignment. Reason: The target has the MdcD-specific family assignment and neighboring mdcA/C/E genes. Its inferred reaction is decarboxylation of specialized ACP-bound malonyl substrate; it is not the ATP/biotin-dependent acetyl-CoA-to-malonyl-CoA reaction. Shared carboxyltransferase-fold ancestry does not establish retained substrate or pathway identity. Supporting Evidence: PMID:28757619 The malonyl-ACP is decarboxylated in the second step of the reaction to regenerate acetyl-ACP file:METEA/mdcD/mdcD-notes.md Thus the target is embedded among the characteristic malonate-decarboxylase components. file:METEA/mdcD/mdcD-uniprot.txt TIGR03133 |
| GO:0006633 fatty acid biosynthetic process | IEA GO_REF:0000118 | REMOVE | Summary: Retain rejection of the mismatched fatty acid biosynthesis assignment. Reason: MdcD acts in the malonate-degradation complex with a specialized MdcC carrier. It does not provide the malonyl-CoA-building reaction of acetyl-CoA carboxylase. The distinct substrate-carrier and target neighborhood, rather than simple absence of a native assay, argue against this inherited pathway assignment. Supporting Evidence: PMID:28757619 The malonyl-ACP is decarboxylated in the second step of the reaction to regenerate acetyl-ACP file:METEA/mdcD/mdcD-notes.md Thus the target is embedded among the characteristic malonate-decarboxylase components. file:METEA/mdcD/mdcD-uniprot.txt TIGR03133 |
| GO:2001295 malonyl-CoA biosynthetic process | IEA GO_REF:0000118 | REMOVE | Summary: Retain rejection of the mismatched malonyl-CoA biosynthesis assignment. Reason: The characterized homologous complex decarboxylates malonyl groups on specialized MdcC and regenerates acetyl-MdcC. It does not synthesize malonyl-CoA. The target MdcD-specific family and mdcA/C/E neighborhood support that pathway distinction. Supporting Evidence: PMID:28757619 The malonyl-ACP is decarboxylated in the second step of the reaction to regenerate acetyl-ACP file:METEA/mdcD/mdcD-notes.md Thus the target is embedded among the characteristic malonate-decarboxylase components. file:METEA/mdcD/mdcD-uniprot.txt TIGR03133 |
| GO:0004658 propionyl-CoA carboxylase activity | IEA GO_REF:0000003 | REMOVE | Summary: Retain rejection of the mismatched propionyl-CoA carboxylase assignment. Reason: The source EC6.4.1.3 mapping conflicts with the MdcD-specific family and malonate-decarboxylase gene neighborhood. The inferred ACP-bound decarboxylation does not carboxylate propionyl-CoA to methylmalonyl-CoA. No source EC field is rewritten. Supporting Evidence: PMID:28757619 The malonyl-ACP is decarboxylated in the second step of the reaction to regenerate acetyl-ACP file:METEA/mdcD/mdcD-notes.md Thus the target is embedded among the characteristic malonate-decarboxylase components. file:METEA/mdcD/mdcD-uniprot.txt TIGR03133 |
| GO:0005975 carbohydrate metabolic process | IEA GO_REF:0000002 | REMOVE | Summary: Malonate utilization is not established carbohydrate metabolism. Reason: The prior KEEP_AS_NON_CORE rationale cited only the possibility that acetate feeds central carbon metabolism. Malonate is a dicarboxylic acid and MdcD directly decarboxylates its ACP-bound derivative; no carbohydrate-processing step performed by MdcD is established. A downstream metabolite connection is insufficient for involvement in GO:0005975 as defined. This is a pathway-scope distinction, not rejection for breadth. Supporting Evidence: PMID:28757619 The malonyl-ACP is decarboxylated in the second step of the reaction to regenerate acetyl-ACP file:METEA/mdcD/mdcD-notes.md Thus the target is embedded among the characteristic malonate-decarboxylase components. file:METEA/mdcD/mdcD-uniprot.txt TIGR03133 |
| GO:0016740 transferase activity | IEA GO_REF:0000043 | REMOVE | Summary: Retain rejection of the mismatched transferase assignment. Reason: The actual MdcD-MdcE reaction releases CO2 without transferring the carboxyl group to an acceptor. MdcA supplies the separate ACP-transferase step. A homologous carboxyltransferase fold and membership in a complex containing a transferase do not confer transferase activity on MdcD. Supporting Evidence: PMID:28757619 The malonyl-ACP is decarboxylated in the second step of the reaction to regenerate acetyl-ACP file:METEA/mdcD/mdcD-notes.md Thus the target is embedded among the characteristic malonate-decarboxylase components. file:METEA/mdcD/mdcD-uniprot.txt TIGR03133 |
| GO:0016831 carboxy-lyase activity | IEA GO_REF:0000002 | ACCEPT | Summary: Retain carboxy-lyase activity as the catalytic class contributed by MdcD. Reason: The target-specific family and gene neighborhood support MdcD identity, while primary homolog structures place decarboxylation at the MdcD-MdcE interface. A broad but correct catalytic class is appropriate; the function is executed together with MdcE. Supporting Evidence: PMID:28757619 The malonyl-ACP is decarboxylated in the second step of the reaction to regenerate acetyl-ACP file:METEA/mdcD/mdcD-notes.md Thus the target is embedded among the characteristic malonate-decarboxylase components. file:METEA/mdcD/mdcD-uniprot.txt TIGR03133 file:METEA/mdcD/mdcD-deep-research-falcon.md conclusions for AM1 are inferred from conserved function across mdcD orthologs. |
| GO:0016874 ligase activity | IEA GO_REF:0000043 | REMOVE | Summary: Retain rejection of the mismatched ligase assignment. Reason: The inferred MdcD-MdcE reaction is a biotin-independent decarboxylation, not energy-dependent joining of substrates. The target is a catalytic component of the malonate-degradation complex; related ACC/PCC ligase chemistry is not retained merely because of shared fold. Supporting Evidence: PMID:28757619 The malonyl-ACP is decarboxylated in the second step of the reaction to regenerate acetyl-ACP file:METEA/mdcD/mdcD-notes.md Thus the target is embedded among the characteristic malonate-decarboxylase components. file:METEA/mdcD/mdcD-uniprot.txt TIGR03133 |
| GO:0090410 malonate catabolic process | ISS file:METEA/mdcD/mdcD-deep-research-falcon.md | NEW | Summary: This biological process annotation should be added. MdcD is part of the malonate decarboxylase complex (EC 4.1.1.88) which catalyzes the catabolism of malonate to acetate and CO2. This is the core biological process in which MdcD participates. Reason: The MdcD-specific family assignment and independently checked mdcA/C/D/E neighborhood in AM1 support transfer of the experimentally characterized bacterial malonate-degradation role. MdcD contributes the decarboxylation step itself, so this is participation rather than merely necessity or downstream metabolic association. The evidence remains ISS; no AM1 assay is claimed. Supporting Evidence: PMID:28757619 The malonyl-ACP is decarboxylated in the second step of the reaction to regenerate acetyl-ACP file:METEA/mdcD/mdcD-notes.md Thus the target is embedded among the characteristic malonate-decarboxylase components. file:METEA/mdcD/mdcD-uniprot.txt TIGR03133 |
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