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KdgR DNA-binding transcriptional repressor

Synonyms: KdgR
The 2-Keto-3-deoxygluconate repressor, KdgR, is a DNA-binding transcription factor that represses transcription of the operons involved in transport and catabolism of 2-keto-3-deoxy gluconate (KDG) [1, 3, 4, 5]. Synthesis of these genes is induced when E. coli is grown in the presence of KDG and under high-temperature conditions, between 32 and 35°C.
Although little is known about the regulating mechanism of KdgR, it has been shown to act as a repressor that binds to a putative inverted repeat sequence [6, 7]. Comparative analysis of intergenic DNA sequences showed the consistent occurrence of KdgR possible binding sites upstream of the genes not related to the transport and catabolism of KDG [6, 8].

Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
KdgR     nd nd
Evolutionary Family: IclR
Connectivity class: Local Regulator
Gene name: kdgR
  Genome position: 1909308-1910099
  Length: 792 bp / 263 aa
Operon name: kdgR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) eda, edd
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Entner-Doudoroff (2)
carbon compounds (1)
glyoxylate degradation (1)
Regulated operon(s) edd-eda
First gene in the operon(s) eda, edd
Simple and complex regulons Cra,GntR,KdgR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  KdgR repressor edap1 nd 5.0 -349.0 eda
1933095 1933115 [BPP], [GEA], [HIBSCS] [1]
  KdgR repressor eddp1 Sigma70 -76.0 -185.0 edd, eda
1934779 1934799 [AIBSCS], [HIBSCS] [2]

Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [AIBSCS] Automated inference based on similarity to consensus sequences


 [1] Murray EL., Conway T., 2005, Multiple regulators control expression of the Entner-Doudoroff aldolase (Eda) of Escherichia coli., J Bacteriol. 187(3):991-1000

 [2] Kaleta C., Gohler A., Schuster S., Jahreis K., Guthke R., Nikolajewa S., 2010, Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis., BMC Syst Biol. 4:116

 [3] Pouyssegur J., Stoeber F., 1974, Genetic control of the 2-keto-3-deoxy-d-gluconate metabolism in Escherichia coli K-12: kdg regulon., J Bacteriol. 117(2):641-51

 [4] Pouyssegur J., Lagarde A., 1973, [2-Keto-3-deoxy-gluconate transport system in E. coli K 12: map location of a structural gene and of its operator], Mol Gen Genet. 121(2):163-80

 [5] Pouyssegur J., Stoeber F., 1972, [Physiologic and genetic control of metabolism of 2-keto-3-deoxy-gluconate in E. coli K 12. Regulon kdg], C R Acad Sci Hebd Seances Acad Sci D. 274(15):2249-52

 [6] Rodionov DA., Mironov AA., Rakhmaninova AB., Gelfand MS., 2000, Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria., Mol Microbiol. 38(4):673-83

 [7] Nasser W., Reverchon S., Condemine G., Robert-Baudouy J., 1994, Specific interactions of Erwinia chrysanthemi KdgR repressor with different operators of genes involved in pectinolysis., J Mol Biol. 236(2):427-40

 [8] Rodionov DA., Gelfand MS., Hugouvieux-Cotte-Pattat N., 2004, Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria., Microbiology. 150(Pt 11):3571-90