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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, 2]. 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 [4]. 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 [4].

Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
KdgR Functional   [IEP], [IMP] [1], [2]
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 regulation    

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] [3]

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


 [IEP] Inferred from expression pattern

 [IMP] Inferred from mutant phenotype

 [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] 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

 [3] 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

 [4] 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