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YpdB DNA-binding transcriptional activator

Synonyms: YpdB-phosphorylated
YpdB belongs to the LytTR response regulator (RR) of the two-component system |CITS:[12034833]| that participates in the carbon control network and may participate in nutrient scavenging before entry into stationary phase |CITS:[23222720]|. It is composed of an N-terminal CheY-like receiver domain and a C-terminal LytTR-like effector domain with DNA-binding affinity |CITS:[23222720]|. Chromatography analysis showed that YpdB is present as a monomeric form in solution |CITS:[27013338]|.
A mimic of the phosphorylated form of YpdB has a higher capacity for binding to DNA compared to its unphosphorylated form |CITS:[27013338]|.
YpdB binds to two direct repeats of the motif GGCATTTCAT, separated by an 11-bp spacer, in the yhjX promoter |CITS:[23222720]|. The YpdB-binding sites in the yhjX promoter have different affinities; the YpdB-binding site, with its higher affinity, is important for the stability and for the binding of a second YpdN molecule to the lower-affinity site, and together they probably enhance the protein-DNA interactions |CITS:[27013338]|.
Based on genome scanning and microarray analysis, it has been determined that yhjX is the sole target gene regulated by the YpdA/YpdB system, and it is modulated by the sequence-dependent structure of the surrounding DNA |CITS:[23222720]|.
Based on microarray analyses of Escherichia coli, 2,3-butanedione (2,3-BD) and glyoxylic acid (GA), volatile organic compounds (VOCs) emitted from Bacillus subtilis, mediated global changes in gene expression related to motility and antibiotic resistance phenotypes that affected the expression of more than 100 genes |CITS:[23651997]|.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
YpdB-phosphorylated     nd nd
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: ypdB
  Genome position: 2500383-2501117
  Length: 735 bp / 244 aa
Operon name: ypdABC
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) yhjX
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Porters (Uni-, Sym- and Antiporters) (1)
membrane (1)
Regulated operon(s) yhjX
First gene in the operon(s) yhjX
Simple and complex regulons YpdB
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
  YpdB-phosphorylated activator yhjXp Sigma70 -73.5 -109.5 yhjX
3712112 3712121 [BPP], [SM] [1]
  YpdB-phosphorylated activator yhjXp Sigma70 -52.5 -88.5 yhjX
3712091 3712100 [BPP], [SM] [1]

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

 [SM] Site mutation


 [1] Fried L., Behr S., Jung K., 2013, Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli., J Bacteriol. 195(4):807-15