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ZntR DNA-binding transcriptional activator

Synonyms: ZntR-Zn2+, ZntR-Cd2+, ZntR-Hg, ZntR
ZntR, zinc transport regulator, regulates a gene involved in the Zn(II), Cd(II), and Pb(II) transport systems [2]
In the presence of any of these ions, ZntR activates transcription of zntA by a DNA distortion mechanism that makes the promoter a better substrate for RNA polymerase [2, 3] The interaction of ZntR with Zn(II) has been characterized [3] but its interaction with other ions has not been described. An inverted repeat sequence of 22 bp, located in the spacer between the -10 and the -35 boxes, has been identified as the ZntR dimer-binding site [2, 3]
The crystal structure of an N-terminally truncated fragment of ZntR bound to zinc was solved at a resolution of 19 Å [1] Each monomer of ZntR has three domains: a dimerization helix, a signal recognition site and a DNA-binding motif (helix-turn-helix) [1, 2] Two zinc ions are bound to each monomer [1]
ZntR belongs to the MerR family, and although most members of this family are transcribed divergently from the genes they regulate, zntR is distant on the genome from its regulated gene [2]
The ClpXP and Lon proteases degrade ZntR, but the regulator is protected against proteolysis when it is bound to zinc and DNA.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
ZntR Non-Functional   Apo [IPI] [1]
ZntR-Cd2+ Functional Allosteric Holo [IPI] [1]
ZntR-Hg Functional Allosteric Holo [IPI] [1]
ZntR-Zn2+ Functional Allosteric Holo [IPI] [1]
Evolutionary Family: MerR
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: zntR
  Genome position: 3438705-3439130
  Length: 426 bp / 141 aa
Operon name: yhdN-zntR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s) zntA
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
ATP proton motive force interconversion (1)
The P-type ATPase (P-ATPase) Superfamily (1)
detoxification (1)
membrane (1)
Regulated operon(s) zntA
First gene in the operon(s) zntA
Simple and complex regulons ZntR
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
  ZntR-Zn2+ activator zntAp Sigma70 -24.5 -53.5 zntA
3606387 3606408 [BPP], [SM] [2], [3]

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


 [IPI] Inferred from physical interaction

 [BPP] Binding of purified proteins

 [SM] Site mutation


 [1] Changela A., Chen K., Xue Y., Holschen J., Outten CE., O'Halloran TV., Mondragon A., 2003, Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR., Science. 301(5638):1383-7

 [2] Brocklehurst KR., Hobman JL., Lawley B., Blank L., Marshall SJ., Brown NL., Morby AP., 1999, ZntR is a Zn(II)-responsive MerR-like transcriptional regulator of zntA in Escherichia coli., Mol Microbiol. 31(3):893-902

 [3] Outten CE., Outten FW., O'Halloran TV., 1999, DNA distortion mechanism for transcriptional activation by ZntR, a Zn(II)-responsive MerR homologue in Escherichia coli., J Biol Chem. 274(53):37517-24

 [4] Pruteanu M., Neher SB., Baker TA., 2007, Ligand-controlled proteolysis of the Escherichia coli transcriptional regulator ZntR., J Bacteriol. 189(8):3017-25