leu3

UniProt ID: O59736
Organism: Schizosaccharomyces pombe 972h-
Review Status: COMPLETE
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Gene Description

2-isopropylmalate synthase (alpha-IPM synthase, EC 2.3.3.13) of fission yeast, encoded by SPBC3E7.16c. It belongs to the LeuA type-2 (fungal-type) subfamily and corresponds to S. cerevisiae LEU4/LEU9. It condenses acetyl-CoA with 2-oxoisovalerate to form (2S)-2-isopropylmalate, the first committed step of the leucine branch, and is allosterically inhibited by leucine. leu3 is the only known IPMS in S. pombe, and the deletion is a leucine auxotroph. The protein localises to mitochondria, where 2-oxoisovalerate is made. Its product must be exported to the cytosol for the isomerase (leu2) and dehydrogenase (leu1) steps; the predicted exporter is the carrier oac1.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003824 catalytic activity
IEA
GO_REF:0000002 		MODIFY
Summary: InterPro (IPR000891, pyruvate carboxyltransferase/HMGL-like domain) mapped to root catalytic activity; true but uninformative.
Reason: Replace with the specific 2-isopropylmalate synthase activity.
Supporting Evidence:
file:SCHPO/leu3/leu3-uniprot.txt
FUNCTION: Catalyzes the condensation of the acetyl group of acetyl-CoA
GO:0003852 2-isopropylmalate synthase activity
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA (PTN000814652, seeded by S. cerevisiae LEU4 and LEU9) for 2-isopropylmalate synthase activity. leu3 is a LeuA type-2 (fungal) IPMS (TIGR00970). Core MF.
Supporting Evidence:
file:SCHPO/leu3/leu3-uniprot.txt
FUNCTION: Catalyzes the condensation of the acetyl group of acetyl-CoA
PMID:35325114
The gene leu3+ encodes 2-isopropylmalate synthase, which uses acetyl-CoA to acetylate 3-methyl-2-oxobutanoate to produce (2S)-2-isopropylmalate
GO:0003852 2-isopropylmalate synthase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: Combined IEA (IPR005668/IPR013709, RHEA:21524, EC 2.3.3.13); correct.
Supporting Evidence:
file:SCHPO/leu3/leu3-uniprot.txt
FUNCTION: Catalyzes the condensation of the acetyl group of acetyl-CoA
GO:0003852 2-isopropylmalate synthase activity
ISS
GO_REF:0000024 		ACCEPT
Summary: ISS from M. tuberculosis LeuA (P9WQB3), a structurally and biochemically characterised IPMS; supported in S. pombe by the leu3 deletion phenotype and by rescue with Phycomyces leuA (an IPMS).
Supporting Evidence:
PMID:20657649
Of six deletion strains tested, all were unable to grow on medium that lacked leucine, implicating this gene as functioning in the leucine biosynthesis pathway of S. pombe.
PMID:20657649
whereas transformation with the plasmid containing the P. blakesleeanus leuA gene partially rescues this phenotype
PMID:35325114
The gene leu3+ encodes 2-isopropylmalate synthase, which uses acetyl-CoA to acetylate 3-methyl-2-oxobutanoate to produce (2S)-2-isopropylmalate
GO:0005739 mitochondrion
HDA
PMID:16823372
ORFeome cloning and global analysis of protein localization ... 		ACCEPT
Summary: ORFeome-wide YFP localisation placed leu3 in mitochondria, as cited by the 2022 review. UniProt annotates no transit peptide, but the HDA is consistent with the mitochondrial alpha-IPM synthesis seen in other fungi.
Supporting Evidence:
PMID:35325114
Leu3 is localized to the mitochondria (Matsuyama et al. 2006).
GO:0005739 mitochondrion
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA (PTN000814652; S. cerevisiae LEU4/LEU9 donors) for mitochondrion; agrees with the S. pombe HDA.
Supporting Evidence:
PMID:35325114
Leu3 is localized to the mitochondria (Matsuyama et al. 2006).
GO:0005759 mitochondrial matrix
IC
GO_REF:0000111 		ACCEPT
Summary: PomBase curator inference (from GO:0003852) of matrix activity; consistent with mitochondrial localisation and with the use of the matrix 2-oxoisovalerate pool made by ilv3.
Supporting Evidence:
PMID:35325114
Leu3 is localized to the mitochondria (Matsuyama et al. 2006).
GO:0009098 L-leucine biosynthetic process
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA for L-leucine biosynthesis; donors include S. pombe leu3 itself (its IMP/IGI annotations), which marks experimental grounding on the target.
Supporting Evidence:
PMID:20657649
Of six deletion strains tested, all were unable to grow on medium that lacked leucine, implicating this gene as functioning in the leucine biosynthesis pathway of S. pombe.
GO:0009098 L-leucine biosynthetic process
IEA
GO_REF:0000120 		ACCEPT
Summary: Combined IEA (ARBA, InterPro, UniPathway UPA00048 step 1/4); correct.
Supporting Evidence:
file:SCHPO/leu3/leu3-uniprot.txt
PATHWAY: Amino-acid biosynthesis; L-leucine biosynthesis; L-leucine
GO:0009098 L-leucine biosynthetic process
IGI
PMID:20657649
Two origins for the gene encoding alpha-isopropylmalate synt... 		ACCEPT
Summary: Larson & Idnurm partially rescued the S. pombe leu3 deletion leucine auxotrophy with Phycomyces blakesleeanus leuA (E2D2C5), an IPMS; correct IGI.
Supporting Evidence:
PMID:20657649
whereas transformation with the plasmid containing the P. blakesleeanus leuA gene partially rescues this phenotype
PMID:20657649
Of six deletion strains tested, all were unable to grow on medium that lacked leucine, implicating this gene as functioning in the leucine biosynthesis pathway of S. pombe.
GO:0009098 L-leucine biosynthetic process
IMP
PMID:20657649
Two origins for the gene encoding alpha-isopropylmalate synt... 		ACCEPT
Summary: All six leu3 deletion strains were leucine auxotrophs; leu3 catalyses the first committed step of the leucine branch.
Supporting Evidence:
PMID:20657649
Of six deletion strains tested, all were unable to grow on medium that lacked leucine, implicating this gene as functioning in the leucine biosynthesis pathway of S. pombe.
PMID:35325114
A loss-of-function mutation of any of leu1+, leu2+, or leu3+ leads to Leu auxotrophy (Kohli et al. 1977).
GO:0046912 acyltransferase activity, acyl groups converted into alkyl on transfer
IEA
GO_REF:0000002 		TOO GENERAL
Summary: InterPro (IPR002034, alpha-IPM/homocitrate synthase signature) mapping to the parent acyltransferase class; correct but less specific than GO:0003852.
Reason: Parent of the core MF; non-core.
Supporting Evidence:
file:SCHPO/leu3/leu3-uniprot.txt
FUNCTION: Catalyzes the condensation of the acetyl group of acetyl-CoA

Core Functions

2-isopropylmalate synthase (EC 2.3.3.13) that condenses acetyl-CoA with 2-oxoisovalerate to form (2S)-2-isopropylmalate, the first committed and leucine-feedback-inhibited step of leucine biosynthesis; the only known IPMS of S. pombe and localised to mitochondria.

Molecular Function:
2-isopropylmalate synthase activity
Directly Involved In:
L-leucine biosynthetic process
Cellular Locations:
mitochondrion
Supporting Evidence:
  • PMID:35325114
    The gene leu3+ encodes 2-isopropylmalate synthase, which uses acetyl-CoA to acetylate 3-methyl-2-oxobutanoate to produce (2S)-2-isopropylmalate
  • PMID:20657649
    Of six deletion strains tested, all were unable to grow on medium that lacked leucine, implicating this gene as functioning in the leucine biosynthesis pathway of S. pombe.
  • PMID:35325114
    Leu3 is localized to the mitochondria (Matsuyama et al. 2006).
  • PMID:35325114
    While in S. pombe, Leu3 is the only known 2-isopropylmalate synthase

References

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Suggested Questions for Experts

Q: Does S. pombe leu3, unlike S. cerevisiae LEU4, lack any cytosolic form (no alternative start or dual targeting), which would make alpha-isopropylmalate export by oac1 essential for leucine prototrophy?

Suggested Experiments

Experiment: Measure leucine-sensitive IPMS activity in mitochondrial versus cytosolic fractions of S. pombe and test whether an oac1 deletion alone causes leucine auxotrophy.

📚 Additional Documentation

Notes

(leu3-notes.md)

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