leu1

UniProt ID: P18869
Organism: Schizosaccharomyces pombe 972h-
Review Status: COMPLETE
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Gene Description

3-isopropylmalate dehydrogenase (beta-IPM dehydrogenase, EC 1.1.1.85) of fission yeast, encoded by SPBC1A4.02c. It is a homodimeric enzyme of the isocitrate/isopropylmalate dehydrogenase family that needs Mg2+ or Mn2+. Using NAD+, it oxidatively decarboxylates (2R,3S)-3-isopropylmalate to 4-methyl-2-oxopentanoate (2-oxoisocaproate), the third step of the leucine branch. The aminotransferase eca39 then converts 2-oxoisocaproate to leucine. The enzyme is cytosolic. The cloned gene complements E. coli leuB and S. cerevisiae leu2 mutants. The leu1-32 allele (a G46E helix-capping substitution) is the standard fission-yeast leucine auxotrophic marker. Despite the shared name, S. pombe leu1 is the counterpart of S. cerevisiae LEU2, not LEU1.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0000287 magnesium ion binding
IEA
GO_REF:0000002 		KEEP AS NON CORE
Summary: InterPro (IPR019818) mapping to magnesium ion binding; IPMDH binds one Mg2+ or Mn2+ per subunit for catalysis.
Reason: Cofactor binding underlying catalysis; non-core.
Supporting Evidence:
file:SCHPO/leu1/leu1-uniprot.txt
Note=Binds 1 Mg(2+) or Mn(2+) ion per subunit. {ECO:0000250};
PMID:35325114
This catalytic reaction requires NAD+ and divalent cations (Mn2+ or Mg2+)
GO:0003862 3-isopropylmalate dehydrogenase activity
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA from PTN000216982 (LeuB clade); donors include S. pombe leu1 itself (its IGI annotation), S. cerevisiae LEU2 and E. coli LeuB. Core MF.
Supporting Evidence:
PMID:35325114
In S. pombe, 3-isopropylmalate dehydrogenase is encoded by leu1+, and S. pombe leu1+ can complement the Escherichia coli leuB mutation and S. cerevisiae leu2 mutation
file:SCHPO/leu1/leu1-uniprot.txt
Reaction=(2R,3S)-3-isopropylmalate + NAD(+) = 4-methyl-2-oxopentanoate
GO:0003862 3-isopropylmalate dehydrogenase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: Combined IEA (ARBA, IPR004429, RHEA:32271, EC 1.1.1.85); correct.
Supporting Evidence:
file:SCHPO/leu1/leu1-uniprot.txt
Reaction=(2R,3S)-3-isopropylmalate + NAD(+) = 4-methyl-2-oxopentanoate
GO:0003862 3-isopropylmalate dehydrogenase activity
IGI
PMID:3063400
The primary structure of the leu1+ gene of Schizosaccharomyc... 		ACCEPT
Summary: Kikuchi et al. cloned leu1 by complementation of E. coli leuB and showed the fragment also complements S. cerevisiae leu2 (IPMDH) mutants; cross-species complementation of characterised IPMDH mutants supports the activity. Abstract-only; defer to the curator.
Supporting Evidence:
PMID:3063400
A DNA fragment which carries the leu1 gene encoding beta-isopropylmalate dehydrogenase in Schizosaccharomyces pombe has been isolated by complementation of an E. coli leuB mutation.
PMID:3063400
This 1.5 kb DNA fragment complements not only the S. pombe leu1 mutation, but also the S. cerevisiae leu2 mutation.
GO:0005737 cytoplasm
IEA
GO_REF:0000044 		ACCEPT
Summary: UniProt subcellular-location mapping (Cytoplasm); correct, although cytosol is more precise.
Supporting Evidence:
file:SCHPO/leu1/leu1-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm.
GO:0005829 cytosol
HDA
PMID:16823372
ORFeome cloning and global analysis of protein localization ... 		ACCEPT
Summary: ORFeome-wide YFP localisation placed leu1 in the cytosol, as cited by the 2022 review; correct.
Supporting Evidence:
PMID:35325114
Leu1 is localized in the cytosol (Kikuchi et al. 1988, Matsuyama et al. 2006).
GO:0005829 cytosol
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA for is_active_in cytosol, consistent with the S. pombe HDA and with the cytosolic leucine branch.
Supporting Evidence:
PMID:35325114
Leu1 is localized in the cytosol (Kikuchi et al. 1988, Matsuyama et al. 2006).
GO:0005829 cytosol
IGI
PMID:3063400
The primary structure of the leu1+ gene of Schizosaccharomyc... 		ACCEPT
Summary: PomBase IGI for cytosol from the same complementation study (with S. cerevisiae LEU2). Complementation of a cytosolic enzyme is indirect evidence for location, but the location is independently supported by the HDA and the IBA, and the review cites Kikuchi et al. for cytosolic localisation.
Supporting Evidence:
PMID:35325114
Leu1 is localized in the cytosol (Kikuchi et al. 1988, Matsuyama et al. 2006).
PMID:3063400
This 1.5 kb DNA fragment complements not only the S. pombe leu1 mutation, but also the S. cerevisiae leu2 mutation.
GO:0009098 L-leucine biosynthetic process
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA for L-leucine biosynthesis; correct.
Supporting Evidence:
PMID:35325114
In S. pombe, 3-isopropylmalate dehydrogenase is encoded by leu1+, and S. pombe leu1+ can complement the Escherichia coli leuB mutation and S. cerevisiae leu2 mutation
PMID:35325114
Among the Leu biosynthetic pathway, a mutation of leu1+, leu1-32, is widely used, which causes Leu auxotrophy.
GO:0009098 L-leucine biosynthetic process
IEA
GO_REF:0000120 		ACCEPT
Summary: Combined IEA (ARBA, IPR004429, UniPathway UPA00048 step 3/4); correct.
Supporting Evidence:
file:SCHPO/leu1/leu1-uniprot.txt
FUNCTION: Catalyzes the oxidation of 3-carboxy-2-hydroxy-4-
GO:0009098 L-leucine biosynthetic process
IGI
PMID:3063400
The primary structure of the leu1+ gene of Schizosaccharomyc... 		ACCEPT
Summary: Complementation of S. pombe leu1, S. cerevisiae leu2 and E. coli leuB leucine auxotrophs by the cloned gene; correct.
Supporting Evidence:
PMID:3063400
This 1.5 kb DNA fragment complements not only the S. pombe leu1 mutation, but also the S. cerevisiae leu2 mutation.
PMID:3063400
A DNA fragment which carries the leu1 gene encoding beta-isopropylmalate dehydrogenase in Schizosaccharomyces pombe has been isolated by complementation of an E. coli leuB mutation.
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
IEA
GO_REF:0000002 		TOO GENERAL
Summary: InterPro mapping to the parent class of NAD(P)-dependent CH-OH oxidoreductases; correct but less specific than GO:0003862.
Reason: Parent of the core MF; non-core.
Supporting Evidence:
file:SCHPO/leu1/leu1-uniprot.txt
Reaction=(2R,3S)-3-isopropylmalate + NAD(+) = 4-methyl-2-oxopentanoate
GO:0051287 NAD binding
IEA
GO_REF:0000002 		KEEP AS NON CORE
Summary: InterPro mapping to NAD binding; NAD+ is the cosubstrate of IPMDH.
Reason: Cosubstrate binding; non-core.
Supporting Evidence:
PMID:35325114
This catalytic reaction requires NAD+ and divalent cations (Mn2+ or Mg2+)

Core Functions

Cytosolic NAD+-dependent 3-isopropylmalate dehydrogenase (EC 1.1.1.85) that oxidatively decarboxylates (2R,3S)-3-isopropylmalate to 4-methyl-2-oxopentanoate, step 3 of the leucine branch; functional equivalent of S. cerevisiae LEU2 and E. coli LeuB.

Molecular Function:
3-isopropylmalate dehydrogenase activity
Directly Involved In:
L-leucine biosynthetic process
Cellular Locations:
cytosol
Supporting Evidence:
  • PMID:35325114
    In S. pombe, 3-isopropylmalate dehydrogenase is encoded by leu1+, and S. pombe leu1+ can complement the Escherichia coli leuB mutation and S. cerevisiae leu2 mutation
  • PMID:3063400
    This 1.5 kb DNA fragment complements not only the S. pombe leu1 mutation, but also the S. cerevisiae leu2 mutation.
  • file:SCHPO/leu1/leu1-uniprot.txt
    Reaction=(2R,3S)-3-isopropylmalate + NAD(+) = 4-methyl-2-oxopentanoate
  • PMID:35325114
    Leu1 is localized in the cytosol (Kikuchi et al. 1988, Matsuyama et al. 2006).

References

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📚 Additional Documentation

Notes

(leu1-notes.md)

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