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PrpR DNA-binding transcriptional dual regulator

Synonyms: PrpR-2-methylcitrate, PrpR
The Propionate Regulator, PrpR, is a transcription factor that controls expression of genes involved in catabolism of propionate [2] It is negatively autoregulated, sensitive to catabolite control, and coordinately activates transcription of a divergent operon related to propionate catabolism [2] Synthesis of this operon is induced when E. coli is grown in the absence of glucose or glycerol.
PrpR belongs to the NtrC family of activators, which interact directly with the RpoN RNA polymerase [3] PrpR is a σ54-dependent activator and belongs to the AAA+ superfamily of mechano-chemical ATPases. It consists of three domains, an amino-terminal domain involved in effector recognition, a catalytic domain, and a carboxy-terminal DNA-binding domain [1] This regulator binds to a palindromic sequence (5'-GTTTCAT-10n-ATGAAAC-3') that overlaps prpRp [2]
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
PrpR Functional   Apo [BPP], [GEA], [IDA], [SM] [1]
PrpR-2-methylcitrate Functional Allosteric Holo [BPP], [GEA], [IDA], [SM] [1]
Evolutionary Family: EBP
Connectivity class: Local Regulator
Gene name: prpR
  Genome position: 346857-348443
  Length: 1587 bp / 528 aa
Operon name: prpR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) prpB, prpC, prpD, prpE, prpR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
fatty acids (5)
carbon compounds (3)
Transcription related (1)
activator (1)
repressor (1)
Regulated operon(s) prpBCDE, prpR
First gene in the operon(s) prpB, prpR
Simple and complex regulons AscG,CRP,PhoB,PrpR
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
  PrpR-2-methylcitrate activator prpBp Sigma54 -147.5 -183.5 prpB, prpC, prpD, prpE
348487 348510 [GEA], [HIBSCS] [2]
  PrpR-2-methylcitrate activator prpBp Sigma54 -113.5 -149.5 prpB, prpC, prpD, prpE
348521 348544 [HIBSCS] [2]
  PrpR-2-methylcitrate repressor prpRp Sigma70 -61.5 -89.5 prpR
348521 348544 [HIBSCS] [2]
  PrpR-2-methylcitrate repressor prpRp Sigma70 -27.5 -55.5 prpR
348487 348510 [GEA], [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

 [IDA] Inferred from direct assay

 [SM] Site mutation

 [HIBSCS] Human inference based on similarity to consensus sequences


 [1] Palacios S., Escalante-Semerena JC., 2004, 2-Methylcitrate-dependent activation of the propionate catabolic operon (prpBCDE) of Salmonella enterica by the PrpR protein., Microbiology. 150(Pt 11):3877-87

 [2] Lee SK., Newman JD., Keasling JD., 2005, Catabolite repression of the propionate catabolic genes in Escherichia coli and Salmonella enterica: evidence for involvement of the cyclic AMP receptor protein., J Bacteriol. 187(8):2793-800

 [3] Merrick MJ., 1993, In a class of its own--the RNA polymerase sigma factor sigma 54 (sigma N)., Mol Microbiol. 10(5):903-9