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PuuR DNA-binding transcriptional repressor

Synonyms: PuuR, PuuR-putrescine
PuuR is a transcription repressor that regulates transcription of several genes and operons involved in putrescine utilization and transport [1, 5] Transcription of puuA was induced in a puuR deletion mutant [3]. This regulator is comprised of two domains: the carboxy-terminal domain, which is similar to cupin superfamily proteins, and the amino-terminal domain, which has high similarity to regulators of the HTH-XRE family [5] Nemoto et al. showed that this regulator binds to four target sites in the divergent region located between the operons puuA and puuDR. Its regulator represses transcription by overlapping the promoters puuAp and puuDp, and the binding targets for PuuR consist of 15 nucleotides, with the following recognition sequence: AAAATATAATGAACA [5] The transcription of the puu genes occurs when putrescine interacts with PuuR; this effect changes the conformation of PuuR, and its regulator dissociates from the binding sites.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
PuuR Functional   Apo [AIFS], [IMP] [1], [2]
PuuR-putrescine Non-Functional   Holo nd nd
Evolutionary Family: HTH_3
Connectivity class: Local Regulator
Gene name: puuR
  Genome position: 1361911-1362468
  Length: 558 bp / 185 aa
Operon name: puuDRCBE
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) puuA, puuB, puuC, puuD, puuE, puuP, puuR, ymjE
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
amines (5)
Porters (Uni-, Sym- and Antiporters) (1)
membrane (1)
transcriptional level (1)
Regulated operon(s) puuA-ymjE-puuP, puuDRCBE
First gene in the operon(s) puuA, puuD
Simple and complex regulons ArcA,CRP,PuuR
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
  PuuR repressor puuAp Sigma38 -161.5 -221.5 puuA, ymjE, puuP
1361120 1361139 [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA], [IC] [3], [4], [5]
  PuuR repressor puuAp Sigma38 -126.5 -186.5 puuA, ymjE, puuP
1361085 1361104 [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [IC], [SM] [3], [4], [5]
  PuuR repressor puuAp Sigma38 -84.5 -144.5 puuA, ymjE, puuP
1361043 1361062 [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA], [IC] [3], [4], [5]
  PuuR repressor puuAp Sigma38 11.5 -49.5 puuA, ymjE, puuP
1360948 1360967 [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA], [IC] [3], [4], [5]
  PuuR repressor puuDp Sigma38 -94.5 -162.5 puuD, puuR, puuC, puuB, puuE
1360948 1360967 [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA], [IC] [3], [4], [5]
  PuuR repressor puuDp Sigma38 1.5 -67.5 puuD, puuR, puuC, puuB, puuE
1361043 1361062 [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA], [IC] [3], [4], [5]
  PuuR repressor puuDp Sigma38 43.5 -25.5 puuD, puuR, puuC, puuB, puuE
1361085 1361104 [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [IC], [SM] [3], [4], [5]
  PuuR repressor puuDp Sigma38 78.5 10.5 puuD, puuR, puuC, puuB, puuE
1361120 1361139 [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA], [IC] [3], [4], [5]

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