sucB

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005829 cytosol	IEA GO_REF:0000118	ACCEPT	Summary: Cytosol annotation inferred from TreeGrafter phylogenetic analysis. For bacteria like Methylorubrum extorquens, the OGDH complex is located in the cytoplasm/cytosol as bacteria lack mitochondria. In eukaryotes, this enzyme is mitochondrial, but the bacterial homolog would indeed be cytosolic. Deep research confirms that in bacteria OGDHc operates in the cytosol as a soluble megacomplex. Reason: Appropriate cellular localization for a bacterial TCA cycle enzyme. Bacteria lack membrane-bound organelles, so the OGDH complex operates in the cytosol. The TreeGrafter annotation is consistent with expected bacterial cell biology. Supporting Evidence: UniProt:C5B053 E2 component of the 2-oxoglutarate dehydrogenase (OGDH) file:METEA/sucB/sucB-deep-research-falcon.md in bacteria it operates in the cytosol as a soluble megacomplex
GO:0004149 dihydrolipoyllysine-residue succinyltransferase activity	IEA GO_REF:0000120	ACCEPT	Summary: This is the precise molecular function for the E2 component of the OGDH complex. GO:0004149 catalyzes the reaction: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + succinyl-CoA = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[protein] + CoA. This corresponds exactly to EC 2.3.1.61 assigned to this protein. Reason: Core molecular function of the E2 subunit. UniProt assigns EC 2.3.1.61 with evidence from ARBA and RuleBase. The protein contains the characteristic lipoyl-binding domain (residues 2-77) required for this catalytic activity. InterPro signature IPR006255 (SucB) specifically identifies this as the E2 succinyltransferase component. Supporting Evidence: UniProt:C5B053 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex file:METEA/sucB/sucB-deep-research-falcon.md E2o catalyzes succinyl transfer to CoA (forming succinyl-CoA)
GO:0006099 tricarboxylic acid cycle	IEA GO_REF:0000120	ACCEPT	Summary: The OGDH complex is a central enzyme of the TCA cycle, catalyzing the conversion of 2-oxoglutarate to succinyl-CoA. This is one of the irreversible, regulated steps of the TCA cycle. Reason: Core biological process for this enzyme. The 2-oxoglutarate dehydrogenase complex is essential for TCA cycle function, converting 2-oxoglutarate (alpha-ketoglutarate) to succinyl-CoA. UniProt explicitly annotates this protein with the "Tricarboxylic acid cycle" keyword. This is a fundamental, evolutionarily conserved function. Supporting Evidence: UniProt:C5B053 Tricarboxylic acid cycle file:METEA/sucB/sucB-deep-research-falcon.md The OGDHc is a central TCA cycle enzyme producing succinyl-CoA and NADH
GO:0016740 transferase activity	IEA GO_REF:0000043	ACCEPT	Summary: This is the root transferase activity term, representing a very general classification. The protein does have transferase activity (it transfers succinyl groups), but GO:0004149 is far more informative. Reason: While this is a very general term, it is technically correct and derived from UniProtKB keyword mapping. The more specific term GO:0004149 is also annotated, so this general term provides correct hierarchical coverage. For IEA annotations from keyword mapping, general terms are acceptable as they are part of the standard annotation pipeline. Supporting Evidence: UniProt:C5B053 E2 component of the 2-oxoglutarate dehydrogenase (OGDH) complex which catalyzes file:METEA/sucB/sucB-deep-research-falcon.md E2o catalyzes succinyl transfer to CoA (forming succinyl-CoA)
GO:0016746 acyltransferase activity	IEA GO_REF:0000120	ACCEPT	Summary: Acyltransferase activity is an intermediate-level term between transferase activity and the specific dihydrolipoyllysine-residue succinyltransferase activity. The E2 subunit does transfer an acyl (succinyl) group. Reason: Correct intermediate-level molecular function. The protein is annotated with the "Acyltransferase" keyword in UniProt. The succinyl group transferred is indeed an acyl group, making this annotation accurate. InterPro signatures IPR001078 (2-oxoacid_DH_actylTfrase) and IPR004167 (PSBD) support this function. Supporting Evidence: UniProt:C5B053 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex file:METEA/sucB/sucB-deep-research-falcon.md E2o catalyzes succinyl transfer to CoA (forming succinyl-CoA)
GO:0033512 L-lysine catabolic process to acetyl-CoA via L-saccharopine	IEA GO_REF:0000120	KEEP AS NON CORE	Summary: This annotation derives from UniPathway UPA00868 which indicates the saccharopine pathway for lysine degradation. The OGDH complex can participate in lysine catabolism because 2-oxoglutarate is an intermediate, and the 2-oxoadipate dehydrogenase complex (structurally related to OGDH) uses the same E2 subunit in some organisms. Reason: This is a secondary metabolic role, not the core TCA cycle function. While the UniPathway annotation indicates step 6/6 in the lysine degradation pathway (glutaryl-CoA from L-lysine), this represents a peripheral function. The saccharopine pathway is more prominent in eukaryotes, and it is unclear how significant this pathway is in Methylorubrum extorquens. The core function remains TCA cycle participation. This annotation should be retained but recognized as non-core. Supporting Evidence: UniProt:C5B053 PATHWAY: Amino-acid degradation; L-lysine degradation via saccharopine
GO:0045252 oxoglutarate dehydrogenase complex	IEA GO_REF:0000120	ACCEPT	Summary: The E2 subunit is a structural and catalytic component of the OGDH complex. According to GO, the E2 forms the core of this multi-enzyme complex, onto which E1 and E3 components assemble. Reason: Core cellular component annotation. UniProt states that the protein "Forms a 24-polypeptide structural core with octahedral symmetry" and is "Part of the 2-oxoglutarate dehydrogenase (OGDH) complex composed of E1, E2 and E3." The InterPro signature IPR006255 (SucB) specifically identifies this as the OGDH E2 component. Supporting Evidence: UniProt:C5B053 Forms a 24-polypeptide structural core with octahedral file:METEA/sucB/sucB-deep-research-falcon.md E2o core: 24 subunits as eight homotrimers