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RtcR DNA-binding transcriptional activator

Synonyms: RtcR
Summary:
RtcR , "RNA terminal phosphate cyclase regulator," regulates the expression of genes involved in the ATP-dependent conversion of a 3'-phosphate at the end of RNA to 2',3'-cyclic phosphodiester [1] RtcR belongs to the group of σ54-dependent transcriptional regulators, which contain three domains: the sensory domain located in the N terminus, the central domain involved in ATP hydrolysis and interaction with σ54, and the C-terminal domain, which contains a helix-turn-helix motif. Although the C-terminal domain and the central domain from RtcR are similar to those of other members of this group, its N-terminal domain is not [1] The rtcR gene is transcribed divergently from the genes it regulates [1]


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
RtcR Functional   nd nd nd
Evolutionary Family: EBP
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: rtcR
  Genome position: 3558268-3559866
  Length: 1599 bp / 532 aa
Operon name: rtcR
TU(s) encoding the TF:
Transcription unit        Promoter
rtcR
rtcRp


Regulon       
Regulated gene(s) rtcA, rtcB
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
RNA modification (1)
DNA related (1)
RNA related (1)
Regulated operon(s) rtcBA
First gene in the operon(s) rtcB
Simple and complex regulons IHF,RtcR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[RtcR,+](1)


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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  RtcR activator rtcBp Sigma54 nd nd rtcB, rtcA
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1]


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


Evidence    

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis


Reference(s)    

 [1] Genschik P., Drabikowski K., Filipowicz W., 1998, Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon., J Biol Chem 273(39):25516-26


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