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MurR DNA-binding transcriptional dual regulator

Synonyms: MurR-N-acetyl-D-muramate 6-phosphate, MurR
Summary:
MurR "N-acetyl muramic acid repressor," represses genes involved in the catabolism of cell wall sugars [1] It represses transcription from the murQ promoter and also interferes with its own transcription. murR and murQ are unique and now well-known genes that are regulated by MurR. They are divergently orientated and expressed from nonoverlapping face-to-face (convergent) promoters, and their transcripts are complementary at their 5' ends [1] MurR is a member of the RpiR/AlsR family of transcriptional regulators, whose members contain two domains, a highly conserved N-terminal HTH domain and a C-terminal SIS (sugar phosphate isomerase/sugar phosphate-binding) domain [1, 3] It forms a stable multimer (most likely a tetramer) and binds to two adjacent inverted repeats within the murR/murQ operator region, preventing recruitment of RNA polymerase. MurNAc-6-P is the effector of MurR. MurR carries a so-called SIS domain in its C terminal which is involved in MurNAc-6-P binding.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
MurR Functional   Apo [BPP], [GEA], [IPI] [1]
MurR-N-acetyl-D-muramate 6-phosphate Non-Functional Allosteric Holo [BPP], [GEA], [IPI] [1]
Evolutionary Family: RpiR
Connectivity class: Local Regulator
Gene name: murR
  Genome position: 2544752-2545609
  Length: 858 bp / 285 aa
Operon name: murR
TU(s) encoding the TF:
Transcription unit        Promoter
murR
murRp
murR
murRp2


Regulon       
Regulated gene(s) murP, murQ, murR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (1)
Phosphotransferase Systems (PEP-dependent PTS) (1)
murein turnover, recycling (1)
Transcription related (1)
transcriptional level (1)
Regulated operon(s) murQP-yfeW, murR
First gene in the operon(s) murQ, murR
Simple and complex regulons CRP,MurR
MurR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[MurR,+](2)
[MurR,-](5)


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
  MurR repressor murQp Sigma38 -44.0 -84.0 murQ, murP
ctgcgagtgtAGACTCAATGATTCCTttaagcctgt
 2545682 2545697 [GEA], [BPP], [ICWHO] [1]
  MurR repressor murQp Sigma38 -12.0 -52.0 murQ, murP
ctgtcaattcGGGATATATGATTCCAtacatctgca
 2545714 2545729 [GEA], [BPP], [ICWHO] [1]
  MurR repressor murQp1 Sigma70 -44.0 -84.0 murQ, murP
ctgcgagtgtAGACTCAATGATTCCTttaagcctgt
 2545682 2545697 [GEA], [BPP], [ICWHO] [1]
  MurR repressor murQp1 Sigma70 -12.0 -52.0 murQ, murP
ctgtcaattcGGGATATATGATTCCAtacatctgca
 2545714 2545729 [GEA], [BPP], [ICWHO] [1]
  MurR repressor murQp2 Sigma70 -52.0 -84.0 murQ, murP
ctgcgagtgtAGACTCAATGATTCCTttaagcctgt
 2545682 2545697 [BPP], [GEA], [ICWHO], [BPP], [ICWHO] [1]
  MurR repressor murQp2 Sigma70 -20.0 -52.0 murQ, murP
ctgtcaattcGGGATATATGATTCCAtacatctgca
 2545714 2545729 [BPP], [GEA], [BPP], [ICWHO] [1]
  MurR activator murRp Sigma70 -125.0 -309.0 murR
taacatcgatCGCCGCGGCGATATCcggcagtacg
 2545911 2545925 [GEA], [APIORCISFBSCS] [2]
  MurR repressor murRp Sigma70 -125.0 -309.0 murR
taacatcgatCGCCGCGGCGATATCcggcagtacg
 2545911 2545925 [GEA], [APIORCISFBSCS] [2]
  MurR activator murRp2 Sigma38 -125.0 -309.0 murR
taacatcgatCGCCGCGGCGATATCcggcagtacg
 2545911 2545925 [GEA], [APIORCISFBSCS] [2]
  MurR repressor murRp2 Sigma38 -125.0 -309.0 murR
taacatcgatCGCCGCGGCGATATCcggcagtacg
 2545911 2545925 [GEA], [APIORCISFBSCS] [2]


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


Evidence    

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IPI] Inferred from physical interaction

 [ICWHO] Inferred computationally without human oversight

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


Reference(s)    

 [1] Jaeger T., Mayer C., 2008, The transcriptional factors MurR and catabolite activator protein regulate N-acetylmuramic acid catabolism in Escherichia coli., J Bacteriol 190(20):6598-608

 [2] Ishii D., Ishihama A., Yamamoto K., 2009, Two modes of autoregulation of the murR repressor in Escherichia coli., Biosci Biotechnol Biochem 73(11):2528-30

 [3] Bateman A, 1999, The SIS domain: a phosphosugar-binding domain., Trends Biochem Sci, 24(3):94 10.1016/s0968-0004(99)01357-2


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