LeuD

• Description: 3-isopropylmalate dehydratase (small subunit)
  
  

Gene name	leuD
Synonyms
Essential	no
Product	3-isopropylmalate dehydratase (small subunit)
Function	biosynthesis of leucine
Gene expression levels in SubtiExpress: leuD
Metabolic function and regulation of this protein in SubtiPathways: leuD
MW, pI	22 kDa, 4.582
Gene length, protein length	597 bp, 199 aa
Immediate neighbours	ysoA, leuC
Sequences	Protein DNA DNA_with_flanks
Genetic context This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

biosynthesis/ acquisition of amino acids

This gene is a member of the following regulons

CcpA regulon, CodY regulon, FsrA regulon, T-box, TnrA regulon

The gene

Basic information

• Locus tag: BSU28250

Database entries

• BsubCyc: BSU28250

• DBTBS entry: [1]

• SubtiList entry: [2]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity: (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmaleate + H₂O (according to Swiss-Prot)

• Protein family: LeuD type 1 subfamily (according to Swiss-Prot)

• Paralogous protein(s):

Extended information on the protein

• Kinetic information:

• Domains:

• Modification:

• Cofactors: contains an iron-sulfur cluster

• Effectors of protein activity:

• Interactions:

• Localization:

Database entries

• BsubCyc: BSU28250

• Structure: 2PKP (from Methanocaldococcus jannaschii dsm 2661, 38% identity, 53% similarity)

• UniProt: P94568

• KEGG entry: [3]

• E.C. number: 4.2.1.33

Additional information

• subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

• Operon: ilvB-ilvH-ilvC-leuA-leuB-leuC-leuD PubMed

• Expression browser: leuD PubMed

• Sigma factor: SigA PubMed

• Regulation:
  • for a complete overview on the regulation of the ilv operon, see Brinsmade et al.
  • repressed by casamino acids PubMed
  • expression is stimulated in the presence of glucose PubMed
  • repressed in the absence of good nitrogen sources (glutamine or ammonium) (TnrA) PubMed
  • repressed during growth in the presence of branched chain amino acids (CodY) PubMed
  • less expressed under conditions of extreme iron limitation (FsrA) PubMed

• Regulatory mechanism:
  • CodY: transcription repression PubMed
  • CcpA: transcription activation PubMed
  • repression by BCAA: tRNA-controlled RNA switch (T-box) that mediates termination/antitermination
  • TnrA: transcription repression PubMed
  • FsrA: translational repression PubMed

• Additional information: subject to Clp-dependent proteolysis upon glucose starvation PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium): 1251 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 5846 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 3609 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 2313 PubMed

Biological materials

• Mutant:

• Expression vector:

• lacZ fusion:

• GFP fusion:

• two-hybrid system:

• Antibody:

References

François Coutte, Joachim Niehren, Debarun Dhali, Mathias John, Cristian Versari, Philippe Jacques
Modeling leucine's metabolic pathway and knockout prediction improving the production of surfactin, a biosurfactant from Bacillus subtilis.
Biotechnol J: 2015, 10(8);1216-34
[PubMed:26220295] [WorldCat.org] [DOI] (I p)

Nicolas Mirouze, Elena Bidnenko, Philippe Noirot, Sandrine Auger
Genome-wide mapping of TnrA-binding sites provides new insights into the TnrA regulon in Bacillus subtilis.
Microbiologyopen: 2015, 4(3);423-35
[PubMed:25755103] [WorldCat.org] [DOI] (I p)

Yasutaro Fujita, Takenori Satomura, Shigeo Tojo, Kazutake Hirooka
CcpA-mediated catabolite activation of the Bacillus subtilis ilv-leu operon and its negation by either CodY- or TnrA-mediated negative regulation.
J Bacteriol: 2014, 196(21);3793-806
[PubMed:25157083] [WorldCat.org] [DOI] (I p)

Allison Kriel, Shaun R Brinsmade, Jessica L Tse, Ashley K Tehranchi, Alycia N Bittner, Abraham L Sonenshein, Jue D Wang
GTP dysregulation in Bacillus subtilis cells lacking (p)ppGpp results in phenotypic amino acid auxotrophy and failure to adapt to nutrient downshift and regulate biosynthesis genes.
J Bacteriol: 2014, 196(1);189-201
[PubMed:24163341] [WorldCat.org] [DOI] (I p)

Shaun R Brinsmade, Roelco J Kleijn, Uwe Sauer, Abraham L Sonenshein
Regulation of CodY activity through modulation of intracellular branched-chain amino acid pools.
J Bacteriol: 2010, 192(24);6357-68
[PubMed:20935095] [WorldCat.org] [DOI] (I p)

Ana Gutiérrez-Preciado, Tina M Henkin, Frank J Grundy, Charles Yanofsky, Enrique Merino
Biochemical features and functional implications of the RNA-based T-box regulatory mechanism.
Microbiol Mol Biol Rev: 2009, 73(1);36-61
[PubMed:19258532] [WorldCat.org] [DOI] (I p)

Ahmed Gaballa, Haike Antelmann, Claudio Aguilar, Sukhjit K Khakh, Kyung-Bok Song, Gregory T Smaldone, John D Helmann
The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins.
Proc Natl Acad Sci U S A: 2008, 105(33);11927-32
[PubMed:18697947] [WorldCat.org] [DOI] (I p)

Shigeo Tojo, Takenori Satomura, Kanako Kumamoto, Kazutake Hirooka, Yasutaro Fujita
Molecular mechanisms underlying the positive stringent response of the Bacillus subtilis ilv-leu operon, involved in the biosynthesis of branched-chain amino acids.
J Bacteriol: 2008, 190(18);6134-47
[PubMed:18641142] [WorldCat.org] [DOI] (I p)

Shigeo Tojo, Takenori Satomura, Kaori Morisaki, Ken-Ichi Yoshida, Kazutake Hirooka, Yasutaro Fujita
Negative transcriptional regulation of the ilv-leu operon for biosynthesis of branched-chain amino acids through the Bacillus subtilis global regulator TnrA.
J Bacteriol: 2004, 186(23);7971-9
[PubMed:15547269] [WorldCat.org] [DOI] (P p)

Ulrike Mäder, Susanne Hennig, Michael Hecker, Georg Homuth
Transcriptional organization and posttranscriptional regulation of the Bacillus subtilis branched-chain amino acid biosynthesis genes.
J Bacteriol: 2004, 186(8);2240-52
[PubMed:15060025] [WorldCat.org] [DOI] (P p)

Virginie Molle, Yoshiko Nakaura, Robert P Shivers, Hirotake Yamaguchi, Richard Losick, Yasutaro Fujita, Abraham L Sonenshein
Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis.
J Bacteriol: 2003, 185(6);1911-22
[PubMed:12618455] [WorldCat.org] [DOI] (P p)

Holger Ludwig, Christoph Meinken, Anastasija Matin, Jörg Stülke
Insufficient expression of the ilv-leu operon encoding enzymes of branched-chain amino acid biosynthesis limits growth of a Bacillus subtilis ccpA mutant.
J Bacteriol: 2002, 184(18);5174-8
[PubMed:12193635] [WorldCat.org] [DOI] (P p)

Ulrike Mäder, Georg Homuth, Christian Scharf, Knut Büttner, Rüdiger Bode, Michael Hecker
Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability.
J Bacteriol: 2002, 184(15);4288-95
[PubMed:12107147] [WorldCat.org] [DOI] (P p)

Christine Eymann, Georg Homuth, Christian Scharf, Michael Hecker
Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis.
J Bacteriol: 2002, 184(9);2500-20
[PubMed:11948165] [WorldCat.org] [DOI] (P p)

F J Grundy, T M Henkin
Conservation of a transcription antitermination mechanism in aminoacyl-tRNA synthetase and amino acid biosynthesis genes in gram-positive bacteria.
J Mol Biol: 1994, 235(2);798-804
[PubMed:8289305] [WorldCat.org] [DOI] (P p)