arg4 (SPBC215.08c) encodes the large (synthetase, CarB-type) subunit of the arginine-specific carbamoyl-phosphate synthetase (CPSase A) of S. pombe, the ortholog of S. cerevisiae CPA2. It binds hydrogencarbonate, two ATP and ammonia (free or channelled from glutamine hydrolysed by the small subunit arg5) and makes carbamoyl phosphate, the carbamoyl donor for ornithine carbamoyltransferase (arg3). In S. pombe CPSase A is mitochondrial and repressed by arginine, and its carbamoyl phosphate is kept separate from the cytosolic pyrimidine-pathway pool made by ura1; in S. cerevisiae the equivalent enzyme is cytosolic. arg4 mutants require arginine. Note the nomenclature trap: S. pombe arg4 is not the ortholog of S. cerevisiae ARG4 (argininosuccinate lyase, which in S. pombe is arg41/arg7).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004087 carbamoyl-phosphate synthase (ammonia) activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for carbamoyl-phosphate synthase (ammonia) activity, sources include mammalian CPS1 and S. cerevisiae CPA2. Reason: The large subunit carries out the ammonia-dependent ATP-coupled synthetase reaction. Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt Reaction=hydrogencarbonate + NH4(+) + 2 ATP = carbamoyl phosphate + 2 ADP + phosphate + 2 H(+); file:SCHPO/arg4/arg4-uniprot.txt FUNCTION: Large subunit of the arginine-specific carbamoyl phosphate |
| GO:0004087 carbamoyl-phosphate synthase (ammonia) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Rhea 18029 / EC 6.3.4.16 mapping to carbamoyl-phosphate synthase (ammonia) activity. Reason: Correct activity of the large subunit. Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt Reaction=hydrogencarbonate + NH4(+) + 2 ATP = carbamoyl phosphate + 2 ADP + phosphate + 2 H(+); |
| GO:0004087 carbamoyl-phosphate synthase (ammonia) activity | ISS GO_REF:0000024 | ACCEPT | Summary: PomBase ISS from Neurospora CPA2/arg-3 large subunit (Q7SH52). Reason: Orthologous arginine-specific large subunit; activity is the core synthetase reaction. Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt Reaction=hydrogencarbonate + NH4(+) + 2 ATP = carbamoyl phosphate + 2 ADP + phosphate + 2 H(+); file:SCHPO/arg4/arg4-uniprot.txt FUNCTION: Large subunit of the arginine-specific carbamoyl phosphate |
| GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Rhea 18633 / EC 6.3.5.5 mapping of the glutamine-dependent overall CPSase reaction to the large subunit. Reason: The glutamine-dependent reaction is the activity of the arg5-arg4 heterodimer; arg4 provides the synthetase sites. Strictly a contributes_to activity for this subunit, as captured in core_functions; accepted as in the S. cerevisiae CPA2 review. Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt Reaction=hydrogencarbonate + L-glutamine + 2 ATP + H2O = carbamoyl phosphate + L-glutamate + 2 ADP + phosphate + 2 H(+); file:SCHPO/arg4/arg4-uniprot.txt SUBUNIT: Heterodimer composed of 2 chains; the small (or glutamine) |
| GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity | ISS GO_REF:0000024 | ACCEPT | Summary: PomBase ISS from Neurospora CPA2/arg-3 (Q7SH52) for glutamine-dependent CPSase activity. Reason: Correct complex-level activity to which arg4 contributes (see core_functions). Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt Reaction=hydrogencarbonate + L-glutamine + 2 ATP + H2O = carbamoyl phosphate + L-glutamate + 2 ADP + phosphate + 2 H(+); file:SCHPO/arg4/arg4-uniprot.txt SUBUNIT: Heterodimer composed of 2 chains; the small (or glutamine) |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: ATP substrate binding is intrinsic to the core catalytic reaction. Reason: This experimentally established or conserved substrate/cofactor interaction is part of the core enzyme mechanism. Being required for catalysis or already implied by a catalytic activity does not make it a peripheral function. Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt Reaction=hydrogencarbonate + NH4(+) + 2 ATP = carbamoyl phosphate + 2 ADP + phosphate + 2 H(+); |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | MODIFY | Summary: The cytoplasm annotation is compatible with the more specific supported cellular compartment. Reason: Cytoplasm includes the relevant organelle/cytosolic compartment in GO. Refine this broad true term to mitochondrial matrix, supported by the combined localization evidence; do not call the broad term a contradictory location or infer tag interference without examining the original images. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000150222 SUPPORTS TRANSFER The broad inherited cellular location remains true. Refinement uses target-specific localization and does not allege faulty ancestral placement or a change from cytoplasm to a non-cytoplasmic organelle. Proposed replacements: mitochondrial matrix Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt it is localized to mitochondria and repressed by arginine. |
| GO:0005739 mitochondrion | EXP PMID:200419 Change in location of ornithine carbamoyltransferase and car... | ACCEPT | Summary: arg4 has supported mitochondrial localization; the matrix assertion is retained separately. Reason: The original experimental annotation is corroborated by publication-linked curated UniProt mitochondrial localization. The cached 1977 paper lacks accessible abstract and full text, so no independent re-reading or matrix-resolving experiment is claimed for it. The root-organelle policy preserves mitochondrion as an informative claim. Matrix localization was checked and remains a separate annotation, with its own experimental or inference basis. Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:16823372, |
| GO:0005739 mitochondrion | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | ACCEPT | Summary: arg4 has supported mitochondrial localization; the matrix assertion is retained separately. Reason: The curated HDA assignment is from the fission-yeast ORFeome localization screen. The linked UniProt location and other target evidence are compatible; the screen-level quotation alone does not distinguish matrix from other mitochondrial subcompartments. The root-organelle policy preserves mitochondrion as an informative claim. Matrix localization was checked and remains a separate annotation, with its own experimental or inference basis. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins file:SCHPO/arg4/arg4-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:16823372, |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: arg4 has supported mitochondrial localization; the matrix assertion is retained separately. Reason: The electronic compartment assignment agrees with the publication-linked curated target localization and existing experimental mitochondrial annotations. Its source stops at the organelle and is retained at that level. The root-organelle policy preserves mitochondrion as an informative claim. Matrix localization was checked and remains a separate annotation, with its own experimental or inference basis. Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:16823372, |
| GO:0005759 mitochondrial matrix | IC GO_REF:0000111 | ACCEPT | Summary: PomBase IC from the complex membership: the CPSase A complex acts in the matrix with arg3 OTC. Reason: Soluble mitochondrial enzyme feeding matrix OTC; matrix is the appropriate specific location. Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt it is localized to mitochondria and repressed by arginine. |
| GO:0005759 mitochondrial matrix | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA (ARBA00028628) mapping to mitochondrial matrix. Reason: Correct location. Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt it is localized to mitochondria and repressed by arginine. |
| GO:0005951 carbamoyl-phosphate synthase complex | ISO GO_REF:0000024 | ACCEPT | Summary: ISO from S. cerevisiae CPA2 (SGD:S000003870) membership of the CPA1-CPA2 carbamoyl-phosphate synthase complex. Reason: arg4 and arg5 form the equivalent heterodimer (CPSase A). Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt SUBUNIT: Heterodimer composed of 2 chains; the small (or glutamine) file:SCHPO/arg4/arg4-uniprot.txt linked to the arginine pathway and is designated CPSase A (arg5-arg4), |
| GO:0006526 L-arginine biosynthetic process | EXP PMID:17248775 Genetic Mapping in SCHIZOSACCHAROMYCES POMBE by Mitotic and ... | ACCEPT | Summary: Classical arg4 mutant used as a mapped arginine-requiring marker (Kohli et al. 1977, abstract-only). Reason: Deferred to the curator; arg4 mutants are long-established arginine auxotrophs. Supporting Evidence: PMID:17248775 118 genetic markers have been assigned to 3 linkage groups |
| GO:0006526 L-arginine biosynthetic process | EXP PMID:32896087 Mitochondrial respiration is required to provide amino acids... | ACCEPT | Summary: Deletion-library arginine-auxotrophy screen (Malecki et al. 2020). Reason: Consistent with the mutant phenotype. Supporting Evidence: PMID:32896087 This screen identified 31 mutants that grew substantially better when supplemented with arginine PMID:32896087 eight were identified in our screen |
| GO:0006526 L-arginine biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for L-arginine biosynthetic process, arg4 and S. cerevisiae CPA2 among sources. Reason: Correct and experimentally grounded. Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt FUNCTION: Large subunit of the arginine-specific carbamoyl phosphate |
| GO:0006526 L-arginine biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: ARBA/UniPathway mapping to L-arginine biosynthetic process. Reason: Correct pathway. Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt FUNCTION: Large subunit of the arginine-specific carbamoyl phosphate |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | MODIFY | Summary: The CPS synthetase domains bind divalent magnesium or manganese ions. Reason: Refine metal ion binding to magnesium ion binding and manganese ion binding, both specified by the curated PROSITE/ProRule-supported cofactor assignment. These are catalytic cofactors, not peripheral functions; the assignment is a domain-based inference rather than a new target-specific stoichiometric binding measurement. Proposed replacements: magnesium ion binding manganese ion binding Supporting Evidence: file:SCHPO/arg4/arg4-uniprot.txt Note=Binds 4 Mg(2+) or Mn(2+) ions per subunit. |
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Download this section (compressed HTML)Q: Is carbamoyl phosphate made by mitochondrial CPSase A strictly channelled to arg3, and does arginine repression of arg5/arg4 explain the separate control of the arginine and pyrimidine pools?
Experiment: Measure CPSase A and OTC activities in mitochondria from arg4 and ura1 mutants to test cross-feeding between the arginine and pyrimidine carbamoyl-phosphate pools.
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