arg5

UniProt ID: O60060
Organism: Schizosaccharomyces pombe 972h-
Review Status: COMPLETE
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Gene Description

arg5 (SPBC56F2.09c, also cpa1) encodes the small (glutamine amidotransferase, CarA-type) subunit of the arginine-specific carbamoyl-phosphate synthetase (CPSase A) of S. pombe, the ortholog of S. cerevisiae CPA1. It hydrolyses L-glutamine and passes the released ammonia to the large subunit arg4, which makes carbamoyl phosphate for ornithine carbamoyltransferase (arg3). The protein has an N-terminal mitochondrial transit peptide and CPSase A is mitochondrial and repressed by arginine in S. pombe, separate from the cytosolic pyrimidine-pathway CPSase within ura1. arg5 mutants require arginine. Note the nomenclature trap: S. pombe arg5 is not the ortholog of S. cerevisiae ARG5,6 (which corresponds to S. pombe arg11).

Existing Annotations Review

GO Term Evidence Action Reason
GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA, qualifier contributes_to, for glutamine-dependent CPSase activity (node PTN000150382), sources include S. cerevisiae CPA1 and E. coli CarA.
Reason: The small subunit contributes the glutaminase half-reaction to the heterodimer activity; the contributes_to qualifier is correct.
Supporting Evidence:
file:SCHPO/arg5/arg5-uniprot.txt
Reaction=hydrogencarbonate + L-glutamine + 2 ATP + H2O = carbamoyl phosphate + L-glutamate + 2 ADP + phosphate + 2 H(+);
file:SCHPO/arg5/arg5-uniprot.txt
SUBUNIT: Heterodimer composed of 2 chains; the small (or glutamine)
GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
IEA
GO_REF:0000120 		ACCEPT
Summary: Rhea 18633 / EC 6.3.5.5 and InterPro (IPR006274) mapping of the overall CPSase reaction to arg5.
Reason: Correct complex-level activity (arg5 contributes to it; see core_functions); accepted as in the S. cerevisiae CPA1 review.
Supporting Evidence:
file:SCHPO/arg5/arg5-uniprot.txt
Reaction=hydrogencarbonate + L-glutamine + 2 ATP + H2O = carbamoyl phosphate + L-glutamate + 2 ADP + phosphate + 2 H(+);
GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
ISS
GO_REF:0000024 		ACCEPT
Summary: PomBase ISS from Neurospora crassa arg-2 (P22572).
Reason: Orthologous small subunit; correct complex activity. Donor identity was verified against UniProt P22572; it is the Neurospora arginine-specific CPS small chain, not S. cerevisiae CPA1 (P07258).
Supporting Evidence:
file:SCHPO/arg5/arg5-uniprot.txt
Reaction=hydrogencarbonate + L-glutamine + 2 ATP + H2O = carbamoyl phosphate + L-glutamate + 2 ADP + phosphate + 2 H(+);
file:SCHPO/arg5/arg5-uniprot.txt
FUNCTION: Small subunit of the arginine-specific carbamoyl phosphate
GO:0004359 glutaminase activity
IEA
GO_REF:0000116 		ACCEPT
Summary: Rhea 15889 mapping to glutaminase activity (the small-subunit half-reaction).
Reason: Correct intrinsic activity of the CarA-type subunit.
Supporting Evidence:
file:SCHPO/arg5/arg5-uniprot.txt
Reaction=L-glutamine + H2O = L-glutamate + NH4(+);
GO:0004359 glutaminase activity
ISS
GO_REF:0000024 		ACCEPT
Summary: PomBase ISS from Neurospora crassa arg-2 (P22572) for glutaminase activity.
Reason: Correct. Donor identity was verified against UniProt P22572; it is the Neurospora arginine-specific CPS small chain, not S. cerevisiae CPA1 (P07258).
Supporting Evidence:
file:SCHPO/arg5/arg5-uniprot.txt
Reaction=L-glutamine + H2O = L-glutamate + NH4(+);
file:SCHPO/arg5/arg5-uniprot.txt
FUNCTION: Small subunit of the arginine-specific carbamoyl phosphate
GO:0005737 cytoplasm
HDA
PMID:16823372
ORFeome cloning and global analysis of protein localization ... 		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. The ORFeome cytoplasm call alone does not establish a separate cytosolic population.
Proposed replacements: mitochondrial matrix
Supporting Evidence:
PMID:16823372
we determined the localization of 4,431 proteins
file:SCHPO/arg5/arg5-uniprot.txt
Cytoplasm {ECO:0000269|PubMed:16823372}.
file:SCHPO/arg5/arg5-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:200419}.
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. The ORFeome cytoplasm call alone does not establish a separate cytosolic population.
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/arg5/arg5-uniprot.txt
it is localized to mitochondria and repressed by arginine.
GO:0005737 cytoplasm
IEA
GO_REF:0000120 		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. The ORFeome cytoplasm call alone does not establish a separate cytosolic population.
Proposed replacements: mitochondrial matrix
Supporting Evidence:
file:SCHPO/arg5/arg5-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: arg5 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/arg5/arg5-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:200419}.
GO:0005739 mitochondrion
IEA
GO_REF:0000044 		ACCEPT
Summary: arg5 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/arg5/arg5-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:200419}.
GO:0005759 mitochondrial matrix
IC
GO_REF:0000024 		ACCEPT
Summary: PomBase IC from complex membership placing CPSase A in the mitochondrial matrix with arg3 OTC.
Reason: Appropriate specific location for the soluble mitochondrial enzyme.
Supporting Evidence:
file:SCHPO/arg5/arg5-uniprot.txt
it is localized to mitochondria and repressed by arginine.
GO:0005951 carbamoyl-phosphate synthase complex
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA for carbamoyl-phosphate synthase complex (node PTN000150382).
Reason: arg5 is the small subunit of the arg5-arg4 heterodimer.
Supporting Evidence:
file:SCHPO/arg5/arg5-uniprot.txt
SUBUNIT: Heterodimer composed of 2 chains; the small (or glutamine)
file:SCHPO/arg5/arg5-uniprot.txt
linked to the arginine pathway and is designated CPSase A (arg5-arg4),
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
IEA
GO_REF:0000002 		REMOVE
Summary: InterPro2GO (IPR006274, CarA family) mapping to de novo pyrimidine nucleobase biosynthesis.
Reason: The mapping suits bacterial CarA shared between pathways. In S. pombe the pyrimidine-pathway CPSase is the cytosolic ura1 multifunctional protein, and the carbamoyl phosphate of each synthase is channelled to its own pathway; there is no evidence that arg5 contributes to pyrimidine synthesis.
Supporting Evidence:
file:SCHPO/arg5/arg5-uniprot.txt
one, CPSase P, is part of a multifunctional protein (ura1) encoding 3
file:SCHPO/arg5/arg5-uniprot.txt
synthase is channeled to its respective pathway, in contrast to
GO:0006526 L-arginine biosynthetic process
EXP
PMID:17248775
Genetic Mapping in SCHIZOSACCHAROMYCES POMBE by Mitotic and ... 		ACCEPT
Summary: Classical arg5 mutant mapped as an arginine-requiring marker (Kohli et al. 1977, abstract-only).
Reason: Deferred to the curator; long-established arginine auxotroph.
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; arg5 and S. cerevisiae CPA1 among sources.
Reason: Correct and experimentally grounded.
Supporting Evidence:
file:SCHPO/arg5/arg5-uniprot.txt
FUNCTION: Small subunit of the arginine-specific carbamoyl phosphate
GO:0006526 L-arginine biosynthetic process
IEA
GO_REF:0000041 		ACCEPT
Summary: UniPathway UPA00068 mapping to L-arginine biosynthetic process.
Reason: Correct pathway.
Supporting Evidence:
file:SCHPO/arg5/arg5-uniprot.txt
FUNCTION: Small subunit of the arginine-specific carbamoyl phosphate
GO:0006541 L-glutamine metabolic process
IEA
GO_REF:0000002 		MODIFY
Summary: The small CPS subunit directly hydrolyzes glutamine to supply ammonia.
Reason: Refine L-glutamine metabolism to L-glutamine catabolism. This gene product performs the hydrolysis itself; it is not merely a substrate consumed by another enzyme. The glutaminase half-reaction is a catalytic component of the core CPS function.
Proposed replacements: L-glutamine catabolic process
Supporting Evidence:
file:SCHPO/arg5/arg5-uniprot.txt
Reaction=L-glutamine + H2O = L-glutamate + NH4(+);

Core Functions

Glutamine amidotransferase (small) subunit of the mitochondrial arginine-specific carbamoyl-phosphate synthetase (arg5-arg4, CPSase A): hydrolyses glutamine and channels ammonia to arg4 for carbamoyl-phosphate synthesis feeding matrix OTC. Same activity as S. cerevisiae CPA1 but located in mitochondria in S. pombe.

Molecular Function:
glutaminase activity
Directly Involved In:
L-arginine biosynthetic process
Cellular Locations:
mitochondrial matrix
In Complex:
carbamoyl-phosphate synthase complex
Supporting Evidence:
  • file:SCHPO/arg5/arg5-uniprot.txt
    FUNCTION: Small subunit of the arginine-specific carbamoyl phosphate
  • file:SCHPO/arg5/arg5-uniprot.txt
    Reaction=L-glutamine + H2O = L-glutamate + NH4(+);
  • file:SCHPO/arg5/arg5-uniprot.txt
    linked to the arginine pathway and is designated CPSase A (arg5-arg4),
  • file:SCHPO/arg5/arg5-uniprot.txt
    it is localized to mitochondria and repressed by arginine.

References

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Suggested Questions for Experts

Q: Does S. pombe Arg5 have a separate soluble cytosolic population in addition to its mitochondrial CPS complex, and under which growth conditions? The broad GO cytoplasm term alone cannot distinguish these locations.

Suggested Experiments

Experiment: Localise endogenously C-terminally tagged arg5 and arg4 together with a matrix marker, and test protease protection of arg5 in isolated mitochondria.

📚 Additional Documentation

Notes

(arg5-notes.md)

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