SucD (PA1589) is the 288-residue alpha subunit of succinyl-CoA synthetase (succinate-CoA ligase, SCS) of Pseudomonas aeruginosa PAO1, encoded in the sucCD operon downstream of the beta-subunit gene sucC. In the alpha2beta2 enzyme the alpha subunit binds CoA and phosphate and carries the catalytic histidine that is transiently phosphorylated during the reaction, while the beta subunit binds succinate and the nucleotide. SCS catalyses the substrate-level phosphorylation step of the tricarboxylic acid cycle, converting succinyl-CoA, phosphate and NDP into succinate, CoA and NTP. The P. aeruginosa enzyme makes ATP and GTP about equally from an equimolar ADP/GDP mixture and, at higher NDP concentrations, also UTP and CTP. SCS copurifies with nucleoside diphosphate kinase (Ndk), and the SCS-12-kDa Ndk complex makes little CTP.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO catalytic activity. Reason: True but uninformative; GO:0004775 and GO:0004776, accepted in this review, are descendants of catalytic activity. Supporting Evidence: PMID:10671455 In this reaction the Scs enzyme converted succinate, CoA, and [Ξ³- 32 P]ATP to succinyl-CoA, ADP, and P i . |
| GO:0004550 nucleoside diphosphate kinase activity | IDA PMID:10671455 Succinyl coenzyme A synthetase of Pseudomonas aeruginosa wit... | MARK AS OVER ANNOTATED | Summary: PseudoCAP IDA NDP kinase activity; purified SCS transferred the gamma-phosphate of ATP to GDP (and of GTP to ADP). Reason: Full text read. The transphosphorylation is real in vitro, probably through the alpha-subunit phosphohistidine, but its physiological relevance is unknown and P. aeruginosa has a dedicated nucleoside diphosphate kinase (ndk). Much of what the paper calls NDP kinase activity is the normal SCS reaction run with different NDP acceptors, which the ligase terms already cover. Same action as on the sibling sucC row from this paper. Supporting Evidence: PMID:10671455 As shown in Fig. 4 A and B, the Scs complex transferred the terminal phosphate from [Ξ³- 32 P]ATP to GDP to form GTP |
| GO:0004775 succinate-CoA ligase (ADP-forming) activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA ADP-forming SCS activity from PTN000122012, seeded by E. coli SucD, human SUCLG1, rat Suclg1, two tomato alpha subunits and P. aeruginosa SucD. Reason: SCS alpha subunits are shared by the ADP- and GDP-forming enzymes, so both ligase terms suit the alpha-subunit clade; SucD's own seed is direct biochemistry and appears in WITH/FROM as expected. Supporting Evidence: PMID:10671455 In the presence of inorganic orthophosphate, succinyl-CoA, and an equimolar amount of ADP and GDP, Scs synthesizes essentially an equimolar amount of ATP and GTP. |
| GO:0004775 succinate-CoA ligase (ADP-forming) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (UniRule, RHEA:17661, EC 6.2.1.5). Reason: Consistent with the biochemistry. Supporting Evidence: PMID:10671455 In the presence of inorganic orthophosphate, succinyl-CoA, and an equimolar amount of ADP and GDP, Scs synthesizes essentially an equimolar amount of ATP and GTP. |
| GO:0004775 succinate-CoA ligase (ADP-forming) activity | IDA PMID:10671455 Succinyl coenzyme A synthetase of Pseudomonas aeruginosa wit... | ACCEPT | Summary: PseudoCAP IDA ADP-forming SCS activity; a seed of the PTN000122012 IBD. A mixture of purified SucC and SucD converted succinate, CoA and ATP to succinyl-CoA, ADP and Pi, and made ATP from succinyl-CoA, Pi and ADP. Reason: Full text read. Direct assays with purified subunits in both directions. SucD is the CoA/phosphate-binding, phosphohistidine subunit of the heterotetramer, so it contributes to the activity together with SucC. Supporting Evidence: PMID:10671455 In this reaction the Scs enzyme converted succinate, CoA, and [Ξ³- 32 P]ATP to succinyl-CoA, ADP, and P i . |
| GO:0004776 succinate-CoA ligase (GDP-forming) activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA GDP-forming SCS activity from PTN000122012. Reason: The P. aeruginosa enzyme makes GTP as readily as ATP. Supporting Evidence: PMID:10671455 In the presence of inorganic orthophosphate, succinyl-CoA, and an equimolar amount of ADP and GDP, Scs synthesizes essentially an equimolar amount of ATP and GTP. |
| GO:0004776 succinate-CoA ligase (GDP-forming) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA GDP-forming SCS activity (RHEA:22120). Reason: Consistent with the biochemistry. Supporting Evidence: PMID:10671455 In the presence of inorganic orthophosphate, succinyl-CoA, and an equimolar amount of ADP and GDP, Scs synthesizes essentially an equimolar amount of ATP and GTP. |
| GO:0004776 succinate-CoA ligase (GDP-forming) activity | EXP PMID:10671455 Succinyl coenzyme A synthetase of Pseudomonas aeruginosa wit... | ACCEPT | Summary: UniProt EXP GDP-forming SCS activity. Reason: Full text read; GTP synthesis from succinyl-CoA, Pi and GDP by purified SCS. Supporting Evidence: PMID:10671455 In the presence of inorganic orthophosphate, succinyl-CoA, and an equimolar amount of ADP and GDP, Scs synthesizes essentially an equimolar amount of ATP and GTP. |
| GO:0006099 tricarboxylic acid cycle | IBA GO_REF:0000033 | ACCEPT | Summary: IBA TCA cycle from PTN000122012. Reason: SCS catalyses the succinyl-CoA to succinate step of the TCA cycle. Supporting Evidence: PMID:10671455 It is involved in the only step in the tricarboxylic acid (TCA) cycle where a molecule of GTP or ATP is generated by substrate level phosphorylation. |
| GO:0006099 tricarboxylic acid cycle | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA TCA cycle (UniRule, UniPathway). Reason: As for the IBA row. Supporting Evidence: PMID:10671455 It is involved in the only step in the tricarboxylic acid (TCA) cycle where a molecule of GTP or ATP is generated by substrate level phosphorylation. |
| GO:0009142 nucleoside triphosphate biosynthetic process | IDA PMID:10671455 Succinyl coenzyme A synthetase of Pseudomonas aeruginosa wit... | KEEP AS NON CORE | Summary: PseudoCAP IDA NTP biosynthesis; SCS generates ATP, GTP, UTP and CTP from succinyl-CoA, Pi and the corresponding NDPs. Reason: Full text read. The products are NTPs, so the term is true; NTP supply is a consequence of the TCA step rather than the gene's main process. Same action as on the sibling sucC row. Supporting Evidence: PMID:10671455 In the presence of inorganic orthophosphate, succinyl-CoA, and an equimolar amount of ADP and GDP, Scs synthesizes essentially an equimolar amount of ATP and GTP. |
| GO:0009361 succinate-CoA ligase complex (ADP-forming) | IBA GO_REF:0000033 | ACCEPT | Summary: IBA ADP-forming SCS complex from PTN000122012, seeded by E. coli SucD. Reason: Bacterial SCS is the alpha2beta2 complex, and the P. aeruginosa enzyme forms ATP, so membership of the ADP-forming complex is true. Because the same enzyme is equally GDP-forming, the general GO:0042709 rows are kept as accurate rather than marked TOO_GENERAL. Supporting Evidence: PMID:10671455 In order to test the activity of Scs Ξ² subunit, an Scs enzymatic reaction was performed with succinate, CoA, and a mixture of purified Scs Ξ± and Ξ² subunits |
| GO:0042709 succinate-CoA ligase complex | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA SCS complex. Reason: The enzyme is a dual-specificity alpha/beta complex; the general term describes it accurately. Supporting Evidence: PMID:10671455 In order to test the activity of Scs Ξ² subunit, an Scs enzymatic reaction was performed with succinate, CoA, and a mixture of purified Scs Ξ± and Ξ² subunits |
| GO:0042709 succinate-CoA ligase complex | IDA PMID:10671455 Succinyl coenzyme A synthetase of Pseudomonas aeruginosa wit... | ACCEPT | Summary: PseudoCAP IDA SCS complex; activity required the mixture of separately purified SucC and SucD. Reason: Full text read. Reconstitution of activity from the two subunits supports the complex. Same action as on the sibling sucC row. Supporting Evidence: PMID:10671455 In order to test the activity of Scs Ξ² subunit, an Scs enzymatic reaction was performed with succinate, CoA, and a mixture of purified Scs Ξ± and Ξ² subunits |
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