RegulonDB RegulonDB 10.9:Regulon Page

AllR DNA-binding transcriptional repressor

Synonyms: AllR-allantoin, AllR-glyox, AllR
AllR (for "allantoin repressor") regulates several genes involved in the anaerobic utilization of allantoin as a nitrogen source [1, 3] At very low concentrations of glyoxylate, AllR represses transcription from allAp, allSp, and gclp. A highly conserved region featuring an almost perfect palindromic sequence has been identified in gclp and in the intergenic region between the divergent promoters allAp and allSp. It has been proven that AllR binds to this region, and it has been proposed that it may interfere with RNA polymerase by steric hindrance or contact inhibition, thus repressing transcription. In the presence of glyoxylate (the coeffector molecule of this regulator), DNA binding by AllR is inhibited and transcription of the allantoin regulon is derepressed [1] AllR belongs to the IclR family. Members of this family of regulators feature a conserved domain architecture, with a DNA-binding motif in the N-terminal domain and a ligand-binding motif in the C-terminal domain. This regulator adopts a tetrameric conformation [1] The allR gene is expressed under both aerobic and anaerobic conditions, and it is autoregulated [] Read more >

Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
AllR Functional   Apo [BPP], [GEA] [1]
AllR-allantoin Functional   Holo nd nd
AllR-glyox Non-Functional Allosteric Holo [BPP], [GEA] [1]
Evolutionary Family: IclR
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: allR
  Genome position: 533011-533826
  Length: 816 bp / 271 aa
Operon name: allR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) allA, allB, allS, gcl, glxK, glxR, hyi, ybbW, ybbY
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
glyoxylate degradation (3)
allantoin assimilation (2)
nitrogen metabolism (2)
glycolate metabolism (2)
carbon compounds (2)
Read more >
Regulated operon(s) allA, allS, gcl-hyi-glxR-ybbW-allB-ybbY-glxK
First gene in the operon(s) allA, allS, gcl
Simple and complex regulons AllR
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
  AllR-allantoin repressor allAp nd -53.0 -114.0 allA
532329 532345 [BCE], [BPP], [GEA], [SM] [1], [2]
  AllR-allantoin repressor allSp nd -37.0 -116.0 allS
532329 532345 [BCE], [BPP], [GEA], [SM] [1], [2]
  AllR-allantoin repressor gclp Sigma70 -20.0 -29.0 gcl, hyi, glxR, ybbW, allB, ybbY, glxK
533879 533895 [BCE], [BPP], [GEA], [SM] [1], [2]

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