SucC is the beta subunit of the soluble cytosolic succinyl-CoA synthetase complex in Pseudomonas putida KT2440. With the SucD alpha subunit, it catalyzes the reversible Mg2+-dependent interconversion of succinyl-CoA and succinate in the tricarboxylic acid cycle (EC 6.2.1.5), coupling succinyl-CoA cleavage to ATP or GTP synthesis at the only substrate-level phosphorylation step of the cycle and running in reverse to supply succinyl-CoA for biosynthesis. SucC contributes nucleotide and succinate specificity through its ATP-grasp and dicarboxylate-binding domains, while SucD provides the CoA- and phosphate-binding sites.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: Succinyl-CoA synthetase requires Mg2+ as a cofactor; UniProt annotates one Mg2+ per beta subunit with two binding residues (positions 199 and 213). Reason: Correct. The HAMAP rule records Mg2+ as the cofactor for Q88FB2, with one Mg2+ ion bound per beta subunit. Cofactor binding is part of the core reaction, not a function in its own right, so the row is kept as non-core. Supporting Evidence: file:PSEPK/sucC/sucC-uniprot.txt Note=Binds 1 Mg(2+) ion per subunit. |
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: Root-level catalytic activity term; the specific succinate-CoA ligase activity is captured by more precise terms. Reason: True but uninformative: GO:0004775 succinate-CoA ligase (ADP-forming) activity and GO:0004776 succinate-CoA ligase (GDP-forming) activity, both accepted in this review, entail it. Supporting Evidence: file:PSEPK/sucC/sucC-uniprot.txt Reaction=succinate + ATP + CoA = succinyl-CoA + ADP + phosphate; |
| GO:0004775 succinate-CoA ligase (ADP-forming) activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the canonical molecular function of SucC/SucD - EC 6.2.1.5, the ADP-forming succinate-CoA ligase, mapped via RHEA:17661 and EC:6.2.1.5. Reason: Core molecular function. The exact ADP-forming succinate-CoA ligase reaction is recorded in UniProt and supported by conserved bacterial SCS family/domain evidence; the OpenScientist report found no direct PP_4186 enzyme assay, so the assignment remains homology based. Supporting Evidence: file:PSEPK/sucC/sucC-uniprot.txt Reaction=succinate + ATP + CoA = succinyl-CoA + ADP + phosphate; file:PSEPK/sucC/sucC-deep-research-openscientist.md All catalytic, kinetic, and structural conclusions are transferred by homology from *E. coli*, *T. aquaticus*, and mammalian SCS. There is no published crystal structure, purified-enzyme kinetics, or Km/kcat measurement specifically for Q88FB2. |
| GO:0004776 succinate-CoA ligase (GDP-forming) activity | IEA GO_REF:0000116 | ACCEPT | Summary: The HAMAP rule records the GDP-forming reaction (RHEA:22120) beside the ADP-forming one; GTP use is shown for the P. aeruginosa enzyme and has not been assayed for the KT2440 enzyme. Reason: The HAMAP rule records both the ATP and the GTP reaction for Q88FB2. Nucleotide preference has not been measured for the KT2440 enzyme. The nearest assayed enzyme, P. aeruginosa SucCD (beta subunit 94% identical, 363 of 388 residues), formed ATP and GTP in about equal amounts from an equimolar mixture of ADP and GDP (PMID:10671455) and carries experimental annotations for both activities, so neither activity is ranked above the other here. That result is an end-point observation without kinetic constants in the abstract, and the same abstract notes that the enzyme copurifies with nucleoside diphosphate kinase, so it does not show equal intrinsic specificity. The E. coli tenfold preference for ATP (beta subunit 77% identical) is not assumed to transfer. Supporting Evidence: file:PSEPK/sucC/sucC-uniprot.txt Reaction=GTP + succinate + CoA = succinyl-CoA + GDP + phosphate; file:PSEPK/sucC/sucC-uniprot.txt coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP PMID:10671455 Scs synthesizes essentially an equimolar amount of ATP and GTP |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: The beta subunit ATP-grasp domain binds ATP; UniProt annotates multiple ATP-binding residues (e.g., 46, 53-55, 99, 102, 107). Reason: Correct. Substrate binding is part of the core reaction, not a function in its own right, so the row is kept as non-core. The beta subunit provides the nucleotide-binding chemistry of SCS. Support is the HAMAP MF_00558 rule: its curated function statement assigns nucleotide specificity to the beta subunit, and it maps an ATP-grasp domain with ATP-binding residues (46, 53-55, 99, 102, 107) onto Q88FB2. These are rule-based family transfers, not a KT2440 binding assay. Supporting Evidence: file:PSEPK/sucC/sucC-uniprot.txt The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate file:PSEPK/sucC/sucC-uniprot.txt BINDING 46 /ligand="ATP" file:PSEPK/sucC/sucC-uniprot.txt DR PROSITE; PS50975; ATP_GRASP; 1. |
| GO:0005829 cytosol | IEA GO_REF:0000118 | ACCEPT | Summary: As a soluble TCA-cycle enzyme in a Gram-negative bacterium, SucC acts in the cytoplasm/cytosol. Reason: The bacterial SucCD complex is a soluble cytosolic TCA-cycle enzyme. The Q88FB2 record has no SIGNAL or TRANSMEM feature and no CC SUBCELLULAR LOCATION line, and the protein belongs to the HAMAP MF_00558 bacterial succinyl-CoA synthetase beta-subunit family. The cytosol call rests on that family membership plus the absence of export or membrane features; it is not an experimental localization. Supporting Evidence: file:PSEPK/sucC/sucC-uniprot.txt DR HAMAP; MF_00558; Succ_CoA_beta; 1. file:PSEPK/sucC/sucC-uniprot.txt Belongs to the succinate/malate CoA ligase beta subunit family. |
| GO:0006099 tricarboxylic acid cycle | IEA GO_REF:0000120 | ACCEPT | Summary: Succinyl-CoA synthetase catalyzes the succinyl-CoA to succinate step, the substrate-level phosphorylation step of the TCA cycle. Reason: Core biological process. The UniProt HAMAP-based pathway statement places Q88FB2 in the ligase-route conversion of succinyl-CoA to succinate, the SCS step of the TCA cycle. Supporting Evidence: file:PSEPK/sucC/sucC-uniprot.txt succinate from succinyl-CoA (ligase route): step 1/1. |
| GO:0006104 succinyl-CoA metabolic process | IEA GO_REF:0000118 | ACCEPT | Summary: The enzyme directly interconverts succinyl-CoA and succinate, so it participates in succinyl-CoA metabolism. Reason: The enzyme interconverts succinyl-CoA and succinate in both directions, and the term names the direct process of the reaction. It is as precise as warranted for a reversible enzyme. GO:0006104 is not an ancestor of GO:0006099 tricarboxylic acid cycle, so the TCA-cycle row does not entail it. Supporting Evidence: file:PSEPK/sucC/sucC-uniprot.txt succinate from succinyl-CoA (ligase route): step 1/1. |
| GO:0042709 succinate-CoA ligase complex | IEA GO_REF:0000120 | ACCEPT | Summary: SucC is the beta subunit of the succinate-CoA ligase complex, a heterotetramer of two alpha and two beta subunits. Reason: Correct complex membership. The HAMAP rule describes the enzyme as a heterotetramer of two alpha and two beta subunits. The generic complex term is the one that covers an enzyme forming ATP or GTP, and this gene carries no row for the ADP-forming child term GO:0009361, so the row is not too general here. The P. aeruginosa ortholog is annotated to this term by IDA. Supporting Evidence: file:PSEPK/sucC/sucC-uniprot.txt Heterotetramer of two alpha and two beta subunits. |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | MODIFY | Summary: General metal-ion binding term; the relevant metal here is Mg2+, captured specifically by GO:0000287. Reason: Correct but general. The metal is Mg2+, and the protein carries GO:0000287 magnesium ion binding in this review; that descendant is the term to use. Proposed replacements: magnesium ion binding Supporting Evidence: file:PSEPK/sucC/sucC-uniprot.txt Note=Binds 1 Mg(2+) ion per subunit. |
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Download this section (compressed HTML)Q: Has the KT2440 SucC/SucD complex been purified directly, and what is its ADP/GDP nucleotide preference in the succinyl-CoA cleavage and succinyl-CoA synthesis directions?
Experiment: Co-express and purify PP_4186/PP_4185 SucC/SucD, then measure Mg2+-dependent succinyl-CoA ligase and synthetase activity with ADP/ATP versus GDP/GTP to establish KT2440 nucleotide preference and reversibility.
Type: enzyme-complex reconstitution
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