arg3

UniProt ID: P31317
Organism: Schizosaccharomyces pombe 972h-
Review Status: COMPLETE
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Gene Description

arg3 (SPAC4G9.10) encodes ornithine carbamoyltransferase (OTCase, EC 2.1.3.3), the ortholog of S. cerevisiae ARG3. It transfers the carbamoyl group of carbamoyl phosphate to L-ornithine to form L-citrulline. Unlike the cytosolic budding-yeast enzyme, S. pombe arg3 carries a mitochondrial targeting sequence and acts in the mitochondrial matrix together with the arginine-specific carbamoyl-phosphate synthetase (arg5/arg4), so fission yeast exports citrulline rather than ornithine from mitochondria. arg3 deletion causes arginine auxotrophy. arg3 levels and OTCase activity depend on the mitochondrial thioredoxin Trx2, which associates with arg3 and supports its function independently of its active-site cysteines; arg3 overexpression suppresses the arginine requirement of trx2 mutants.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0000050 urea cycle
IC
GO_REF:0000111 		KEEP AS NON CORE
Summary: This enzyme performs a shared ornithine-to-arginine reaction within the fungal arginine/urea reaction network.
Reason: Live GO:0000050 defines ornithine-to-arginine synthesis followed by arginine cleavage to urea and regenerated ornithine; it does not require a ureotelic organism or nitrogen excretion. The target has the annotated OTC/ASS/ASL reaction and native fungal arginase supplies the return chemistry. Retain the existing process annotation as a contextual role, without asserting measured net full-cycle flux or a metazoan detoxification function. The primary role remains arginine biosynthesis. PMID:20435771 directly measures S. pombe Car1/Car3 arginase activity and urea production.
Supporting Evidence:
PMID:20435771
arginase catalyzes the degradation of arginine into urea and ornithine.
PMID:18849471
gene encoding ornithine carbamoyltransferase (OCTase) in the urea cycle of the
GO:0004585 ornithine carbamoyltransferase activity
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA for OTC activity with S. cerevisiae ARG3, rat Otc and arg3 itself among sources.
Reason: Core activity, experimentally grounded.
Supporting Evidence:
file:SCHPO/arg3/arg3-uniprot.txt
Reaction=carbamoyl phosphate + L-ornithine = L-citrulline + phosphate + H(+);
file:SCHPO/arg3/arg3-uniprot.txt
superfamily. OTCase family. {ECO:0000305}.
GO:0004585 ornithine carbamoyltransferase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: ARBA / Rhea 19513 / EC 2.1.3.3 mapping to ornithine carbamoyltransferase activity.
Reason: Correct activity.
Supporting Evidence:
file:SCHPO/arg3/arg3-uniprot.txt
Reaction=carbamoyl phosphate + L-ornithine = L-citrulline + phosphate + H(+);
GO:0004585 ornithine carbamoyltransferase activity
IMP
PMID:1313366
Cloning and sequencing of arg3 and arg11 genes of Schizosacc... 		ACCEPT
Summary: arg3 cloned by complementation of the S. pombe arg3 mutant (Van Huffel et al. 1992); UniProt cites the paper for experimental OTCase activity.
Reason: Deferred to the curator; strong genetic and sequence support.
Supporting Evidence:
PMID:1313366
were cloned by functional complementation of S. pombe arg3 and
PMID:1313366
carbamoyltransferase (arg3) and acetylglutamate kinase/acetylglutamyl-phosphate
GO:0004585 ornithine carbamoyltransferase activity
IMP
PMID:18849471
Thiol-independent action of mitochondrial thioredoxin to sup... 		ACCEPT
Summary: OTCase activity is reduced in trx2 mutants and arg3 overexpression rescues their arginine auxotrophy (Song et al. 2008).
Reason: Activity measurements tied to arg3 levels; correct activity.
Supporting Evidence:
PMID:18849471
arg3(+) transcript, Arg3 protein, and OCTase activity were all decreased in
PMID:18849471
found that the arg3(+) gene encoding ornithine carbamoyltransferase (OCTase) in the urea cycle of the arginine biosynthetic pathway rescued the arginine auxotrophy
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/arg3/arg3-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix {ECO:0000305|PubMed:1313366,
GO:0005737 cytoplasm
IEA
GO_REF:0000117 		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:1313366
in contrast to the S. pombe enzyme, more than 95% of the S. cerevisiae enzyme remains in the S. pombe cytoplasm
file:SCHPO/arg3/arg3-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix {ECO:0000305|PubMed:1313366,
GO:0005739 mitochondrion
IBA
GO_REF:0000033 		ACCEPT
Summary: arg3 has supported mitochondrial localization; the matrix assertion is retained separately.
Reason: The PAINT mitochondrial-location assertion is compatible with the native target targeting/localization evidence. A separately supported matrix location does not invalidate that inherited organelle claim. 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.
Propagation Review
Root cause: NO FAILURE CORE
Sources checked:
PANTHER:PTN000150427 SUPPORTS TRANSFER
The PAINT mitochondrial-location inference is supported for native S. pombe arg3 by the comparative localization in PMID:1313366 and Arg3-GFP mitochondrial localization in PMID:32896087. These target observations support retaining the inherited organelle claim; separately asserted matrix localization does not constitute a granularity failure. No new ancestral-node reconstruction or universal mitochondrial localization of OTC homologs is inferred from these experiments.
Supporting Evidence:
PMID:1313366
in contrast to the S. pombe enzyme, more than 95% of the S. cerevisiae enzyme remains in the S. pombe cytoplasm
GO:0005739 mitochondrion
IDA
PMID:1313366
Cloning and sequencing of arg3 and arg11 genes of Schizosacc... 		ACCEPT
Summary: arg3 has supported mitochondrial localization; the matrix assertion is retained separately.
Reason: The comparative targeting study distinguishes mitochondrial native S. pombe OTC from predominantly cytoplasmic S. cerevisiae OTC expressed in S. pombe. The native target mitochondrial observation remains valid. 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:1313366
in contrast to the S. pombe enzyme, more than 95% of the S. cerevisiae enzyme remains in the S. pombe cytoplasm
GO:0005739 mitochondrion
IDA
PMID:32896087
Mitochondrial respiration is required to provide amino acids... 		ACCEPT
Summary: arg3 has supported mitochondrial localization; the matrix assertion is retained separately.
Reason: The target fusion was observed in mitochondria in the native fission-yeast study. That imaging result supports mitochondrial localization without requiring matrix resolution. 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:32896087
fusion localises to mitochondria
GO:0005759 mitochondrial matrix
IC
GO_REF:0000111 		ACCEPT
Summary: PomBase IC placing the OTCase activity in the mitochondrial matrix.
Reason: Matrix location follows from mitochondrial import of a soluble enzyme that uses matrix-made carbamoyl phosphate; consistent with UniProt.
Supporting Evidence:
file:SCHPO/arg3/arg3-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix {ECO:0000305|PubMed:1313366,
GO:0005759 mitochondrial matrix
IEA
GO_REF:0000044 		ACCEPT
Summary: UniProt SubCell mapping (SL-0170 Mitochondrion matrix).
Reason: Correct location.
Supporting Evidence:
file:SCHPO/arg3/arg3-uniprot.txt
SUBCELLULAR LOCATION: Mitochondrion matrix {ECO:0000305|PubMed:1313366,
GO:0006520 amino acid metabolic process
IEA
GO_REF:0000002 		MODIFY
Summary: InterPro2GO (aspartate/ornithine carbamoyltransferase domains) mapping to amino acid metabolic process.
Reason: Uninformative; the enzyme functions in L-arginine biosynthesis.
Proposed replacements: L-arginine biosynthetic process
Supporting Evidence:
file:SCHPO/arg3/arg3-uniprot.txt
FUNCTION: Ornithine carbamoyltransferase involved in the synthesis of
GO:0006526 L-arginine biosynthetic process
EXP
PMID:32896087
Mitochondrial respiration is required to provide amino acids... 		ACCEPT
Summary: Malecki et al. 2020 showed an independently made arg3 deletion is an arginine auxotroph (the library strain was mis-annotated).
Reason: Direct phenotype.
Supporting Evidence:
PMID:32896087
Strain with arg3 gene deletion
GO:0006526 L-arginine biosynthetic process
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA for L-arginine biosynthetic process (node PTN000150424), arg3 among sources.
Reason: Correct and experimentally grounded.
Supporting Evidence:
file:SCHPO/arg3/arg3-uniprot.txt
FUNCTION: Ornithine carbamoyltransferase involved in the synthesis of
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/arg3/arg3-uniprot.txt
FUNCTION: Ornithine carbamoyltransferase involved in the synthesis of
GO:0006526 L-arginine biosynthetic process
IMP
PMID:1313366
Cloning and sequencing of arg3 and arg11 genes of Schizosacc... 		ACCEPT
Summary: Complementation of the arg3 mutant arginine requirement by the cloned gene (Van Huffel et al. 1992).
Reason: Direct genetic evidence.
Supporting Evidence:
PMID:1313366
were cloned by functional complementation of S. pombe arg3 and
GO:0006526 L-arginine biosynthetic process
IMP
PMID:18849471
Thiol-independent action of mitochondrial thioredoxin to sup... 		ACCEPT
Summary: arg3 overexpression suppresses the arginine auxotrophy of trx2 mutants (Song et al. 2008).
Reason: Genetic evidence placing arg3 activity in arginine synthesis.
Supporting Evidence:
PMID:18849471
found that the arg3(+) gene encoding ornithine carbamoyltransferase (OCTase) in the urea cycle of the arginine biosynthetic pathway rescued the arginine auxotrophy
GO:0006591 ornithine metabolic process
IEA
GO_REF:0000108 		ACCEPT
Summary: OTCase directly transforms ornithine during its core catalytic reaction.
Reason: Ornithine is a substrate, but the annotated entity is the enzyme that performs the chemical transformation. Participation in ornithine metabolism is therefore core, and is not peripheral simply because arginine biosynthesis also describes the reaction.
Supporting Evidence:
file:SCHPO/arg3/arg3-uniprot.txt
Reaction=carbamoyl phosphate + L-ornithine = L-citrulline + phosphate + H(+);
GO:0016597 amino acid binding
IEA
GO_REF:0000002 		ACCEPT
Summary: Ornithine substrate binding is a real component of ornithine carbamoyltransferase function.
Reason: The conserved substrate-binding domain supports amino acid binding, and budding-yeast OTCase mutagenesis directly alters ornithine affinity (PMID:12679340). The binding claim is not an over-annotation merely because catalysis requires it; no more specific ornithine-binding GO term was established in the live term search. The mutagenesis is comparative evidence from S. cerevisiae, not a direct assay on S. pombe Arg3.
Supporting Evidence:
file:SCHPO/arg3/arg3-uniprot.txt
superfamily. OTCase family. {ECO:0000305}.
PMID:12679340
mutations of putative ornithine binding residues, Asp-182, Asn-184, Asn-185, Cys-289, and Glu-256 greatly reduced the affinity for ornithine
GO:0016743 carboxyl- or carbamoyltransferase activity
IEA
GO_REF:0000002 		MODIFY
Summary: InterPro2GO mapping to carboxyl- or carbamoyltransferase activity.
Reason: Correct parent; the specific activity is ornithine carbamoyltransferase.
Supporting Evidence:
file:SCHPO/arg3/arg3-uniprot.txt
Reaction=carbamoyl phosphate + L-ornithine = L-citrulline + phosphate + H(+);
GO:0019240 L-citrulline biosynthetic process
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA for L-citrulline biosynthetic process (node PTN000150424), seeded by mammalian OTC.
Reason: OTC directly forms citrulline; in S. pombe citrulline is the product exported from mitochondria, as in the PomBase GO-CAM.
Supporting Evidence:
file:SCHPO/arg3/arg3-uniprot.txt
Reaction=carbamoyl phosphate + L-ornithine = L-citrulline + phosphate + H(+);

Core Functions

Mitochondrial ornithine carbamoyltransferase: carbamoylation of L-ornithine to L-citrulline in the matrix, using carbamoyl phosphate from the matrix arginine-specific CPSase. Same activity as S. cerevisiae ARG3, but S. pombe-specific evidence places it in mitochondria rather than the cytosol.

Molecular Function:
ornithine carbamoyltransferase activity
Directly Involved In:
L-arginine biosynthetic process L-citrulline biosynthetic process
Cellular Locations:
mitochondrial matrix
Supporting Evidence:
  • file:SCHPO/arg3/arg3-uniprot.txt
    Reaction=carbamoyl phosphate + L-ornithine = L-citrulline + phosphate + H(+);
  • PMID:1313366
    in contrast to the S. pombe enzyme, more than 95% of the S. cerevisiae enzyme remains in the S. pombe cytoplasm
  • PMID:1313366
    were cloned by functional complementation of S. pombe arg3 and
  • PMID:18849471
    arg3(+) transcript, Arg3 protein, and OCTase activity were all decreased in

References

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Suggested Questions for Experts

Q: How does Trx2 support arg3 levels independently of its catalytic cysteines: chaperoning import or folding, or stabilising the matrix enzyme?

Q: Should GO record a mitochondrial citrulline export step in S. pombe, given the transporter (SPBC365.16) modelled in the PomBase GO-CAM?

Suggested Experiments

Experiment: Measure arg3 import and matrix stability (pulse-chase, protease protection) in trx2 deletion and cysteine-less trx2 strains.

📚 Additional Documentation

Notes

(arg3-notes.md)

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