LEU4/YNL104C Summary Help

Standard Name LEU4 1
Systematic Name YNL104C
Feature Type ORF, Verified
Description Alpha-isopropylmalate synthase (2-isopropylmalate synthase); the main isozyme responsible for the first step in the leucine biosynthesis pathway; LEU4 has a paralog, LEU9, that arose from the whole genome duplication (2, 3, 4 and see Summary Paragraph)
Name Description LEUcine biosynthesis 5
Chromosomal Location
ChrXIV:426754 to 424895 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: -76 cM
Gene Ontology Annotations All LEU4 GO evidence and references
  View Computational GO annotations for LEU4
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 8 genes
Classical genetics
Large-scale survey
40 total interaction(s) for 33 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 9
  • Affinity Capture-RNA: 3
  • Biochemical Activity: 1
  • PCA: 1
  • Reconstituted Complex: 4
  • Two-hybrid: 3

Genetic Interactions
  • Dosage Rescue: 1
  • Negative Genetic: 15
  • Phenotypic Suppression: 1
  • Synthetic Growth Defect: 2

Expression Summary
Length (a.a.) 619
Molecular Weight (Da) 68,408
Isoelectric Point (pI) 5.89
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrXIV:426754 to 424895 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Genetic position: -76 cM
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..1860 426754..424895 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | E.C. | Entrez Gene | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000005048

LEU4 and LEU9 encode alpha-isopropylmalate synthase, the enzyme that catalyzes the conversion of 2-keto-isovalerate into alpha-isopropylmalate (5, 6 and reviewed in 7). This reaction is the first step in leucine biosynthesis (see pathway diagram). Leu4p and Leu9p are 83% identical; Leu4p is the major isozyme (6), accounting for about 80% of total alpha-isopropylmalate synthase activity in wild-type cells (8).

Like the other genes in the leucine biosynthesis pathway, LEU4 is transcriptionally regulated in the presence of isopropylmalate, a process mediated by binding of the transcriptional regulator Leu3p to the upstream activation site UASLEU (9, 10). LEU4 expression is also upregulated through general amino acid control via two Gcn4p binding sites in the LEU4 promoter. The LEU4 promoter also contains a Bas Response Element (BRE), the binding site for the global transcription factor Pho2p; LEU4 gene expression decreases upon removal of the BRE or under increased concentrations of inorganic phosphate (9).

Translation of the LEU4 transcript from both the first and second in-frame AUG codons results in two alternate gene products, a full-length and an N-terminally shortened form, both of which function as dimers (2, 11). The full-length form of Leu4p contains a mitochondrial matrix targeting sequence at its N-terminus while the shorter form lacks this mitochondrial import sequence and thus remains in the cytoplasm (2). The majority of alpha-isopropylmalate synthesis occurs in the mitochondria, however, and it remains unknown why alpha-isopropylmalate synthase is also necessary in the cytoplasm (12). It has been speculated that this may be due to the loss of mitochondrial function and inaccessibility of the mitochondrially located enzymes during anaerobic growth (reviewed in 7).

Leu4p enzyme activity is inactivated by the small molecules leucine and coenzyme A (CoA) (13). Regulation by leucine is via feedback inhibition and it has been shown that amino acid Asp578 is key to this process (14). Inactivation by CoA is more complicated as it depends on Zn2+ as well as binding of CoA to two sites in Leu4p (11). In the absence of zinc, CoA binds to the substrate/product site and acts as a competitive inhibitor with acetyl-CoA. In the presence of zinc, a second CoA binding site opens up and binding of CoA to this second site causes rapid inactivation of Leu4p (11).

Although leu4 deletion strains are still able to grow in the absence of leucine due to redundant Leu9p activity, cells lacking Leu4p are sensitive to the leucine analog trifluoroleucine and are impaired for growth on non-fermentable carbon sources (8, 6). LEU4 dominant mutants are resistant to 5,5,5-trifluoro-DL-leucine, insensitive to feedback inhibition by leucine, and produce increased levels of isoamyl alcohol (1).

Last updated: 2006-08-08 Contact SGD

References cited on this page View Complete Literature Guide for LEU4
1) Baichwal VR, et al.  (1983) Leucine biosynthesis in yeast : Identification of two genes (LEU4, LEU5) that affect alpha-Isopropylmalate synthase activity and evidence that LEU1 and LEU2 gene expression is controlled by alpha-Isopropylmalate and the product of a regulatory gene. Curr Genet 7(5):369-77
2) Beltzer JP, et al.  (1988) Yeast LEU4 encodes mitochondrial and nonmitochondrial forms of alpha-isopropylmalate synthase. J Biol Chem 263(1):368-74
3) Drain P and Schimmel P  (1988) Multiple new genes that determine activity for the first step of leucine biosynthesis in Saccharomyces cerevisiae. Genetics 119(1):13-20
4) Byrne KP and Wolfe KH  (2005) The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res 15(10):1456-61
5) Chang LF, et al.  (1984) Cloning and characterization of yeast Leu4, one of two genes responsible for alpha-isopropylmalate synthesis. Genetics 108(1):91-106
6) Casalone E, et al.  (2000) Identification by functional analysis of the gene encoding alpha-isopropylmalate synthase II (LEU9) in Saccharomyces cerevisiae. Yeast 16(6):539-45
7) Kohlhaw GB  (2003) Leucine biosynthesis in fungi: entering metabolism through the back door. Microbiol Mol Biol Rev 67(1):1-15, table of contents
8) Chang LF, et al.  (1985) Total deletion of yeast LEU4: further evidence for a second alpha-isopropylmalate synthase and evidence for tight LEU4-MET4 linkage. Gene 33(3):333-9
9) Peters MH, et al.  (1990) Expression of the yeast LEU4 gene is subject to four different modes of control. Arch Biochem Biophys 276(1):294-8
10) Friden P and Schimmel P  (1987) LEU3 of Saccharomyces cerevisiae encodes a factor for control of RNA levels of a group of leucine-specific genes. Mol Cell Biol 7(8):2708-17
11) Tracy JW and Kohlhaw GB  (1977) Evidence for two distinct CoA binding sites on yeast alpha-isopropylmalate synthase. J Biol Chem 252(12):4085-91
12) Ryan ED, et al.  (1973) Subcellular localization of the leucine biosynthetic enzymes in yeast. J Bacteriol 116(1):222-5
13) Cavalieri D, et al.  (1999) Trifluoroleucine resistance and regulation of alpha-isopropyl malate synthase in Saccharomyces cerevisiae. Mol Gen Genet 261(1):152-60
14) Oba T, et al.  (2005) Asp578 in LEU4p is one of the key residues for leucine feedback inhibition release in sake yeast. Biosci Biotechnol Biochem 69(7):1270-3