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MntR DNA-binding transcriptional dual regulator

Synonyms: MntR-Cd2+, MntR-Mn2+, MntR
Summary:
MntR, Mn2+ transport regulator , the primary sensor and transducer of manganese abundance, is a dual regulator that senses manganese and negatively or positively controls the transcription of different genes involved in manganese homeostasis [1, 3]
This protein belongs to the DtxR family. The members of this family have three domains: an N-terminal domain with a helix-turn-helix motif, which binds to DNA; a central domain for dimerization and metal ion binding; and a C-terminal alpha-spectrin SH3-like domain. However, MntR lacks the SH3-like domain [1]
The 3D structure of apo-MntR has been solved. The protein dimerizes via its C-terminal domain. The N-terminal and C-terminal domains are connected by a long α-helical linker [2] The N-terminal domain is expected to bind two manganese ions per monomer, in analogy to BsMntR from B. subtilis, which has been crystallized with and without bound manganese [6, 7] All residues involved in manganese binding in BsMntR ar conserved in MntR [2]
MntR does not seem to be autoregulated [1]
Many iron acquisition genes are derepressed in the mntR mutant [3] Read more >


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
MntR Non-Functional   Apo [BPP], [GEA], [IEP], [IPI] [1], [2], [3]
MntR-Cd2+ Functional Allosteric Holo [BPP], [GEA], [IEP], [IPI] [1], [2], [3]
MntR-Mn2+ Functional Allosteric Holo [BPP], [GEA], [IEP], [IPI] [1], [2], [3]
Evolutionary Family: DtxR
Connectivity class: Local Regulator
Gene name: mntR
  Genome position: 853183-853650
  Length: 468 bp / 155 aa
Operon name: mntR-ybiR
TU(s) encoding the TF:
Transcription unit        Promoter
mntR-ybiR
mntRp


Regulon       
Regulated gene(s) dps, mntH, mntP, mntS, rybA
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (2)
incorporation of metal ions (1)
nucleoproteins, basic proteins (1)
starvation (1)
Porters (Uni-, Sym- and Antiporters) (1)
Read more >
Regulated operon(s) dps, mntH, mntP, rybA-mntS
First gene in the operon(s) dps, mntH, mntP, mntS
Simple and complex regulons Fis,H-NS,IHF,MntR,OxyR
Fur,MntR
Fur,MntR,OxyR
MntR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[MntR,-](3)
[MntR,+](1)


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
  MntR-Mn2+ repressor dpsp Sigma70 -17.5 -56.5 dps
gaatagcggaACACATAGCCGGTGCTATACTTaatctcgtta
848957 848978 [GEA], [HIBSCS] [4]
  MntR-Mn2+ repressor mntHp Sigma70 5.5 -23.5 mntH
gcatagcatgAAACATAGCAAAGGCTATGTTTtagaggcaca
2512719 2512740 [AIBSCS], [BPP], [GEA] [1], [5]
  MntR-Mn2+ activator mntPp Sigma70 -183.5 -412.5 mntP
aataagttatGAATTTAGCCAAAGCTATGTTTagtgtatttt
1905265 1905286 [GEA], [HIBSCS] [3]
  MntR-Mn2+ activator mntPp Sigma70 -143.5 -372.5 mntP
tttaataatcAGACATAGCTTAGGCTATATTAcctcttccct
1905305 1905326 [GEA], [HIBSCS] [3]
  MntR-Mn2+ repressor rybAp Sigma70 -19.5 -86.5 mntS, rybA
aaaaaattaaCGTTTTAGCAATAGCTATATAAtatagcctgt
853073 853094 [GEA], [HIBSCS] [3]
  MntR-Mn2+ repressor rybAp Sigma70 -0.5 -67.5 mntS, rybA
aatagctataTAATATAGCCTGTGCTATATCTgtatgtaatg
853054 853075 [GEA], [HIBSCS] [3]


Alignment and PSSM for MntR TFBSs    

Aligned TFBS of MntR   
  Sequence
 

Position weight matrix (PWM).   
A	4	4	0	4	0	6	0	0	4	3	4	3	0	0	0	6	0	2	0	1	2
C	0	0	1	0	0	0	0	6	2	2	1	0	0	6	0	0	0	0	0	1	0
G	2	1	0	0	0	0	6	0	0	0	0	3	6	0	0	0	0	4	0	1	0
T	0	1	5	2	6	0	0	0	0	1	1	0	0	0	6	0	6	0	6	3	4

PWM logo   


 


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


Evidence    

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IEP] Inferred from expression pattern

 [IPI] Inferred from physical interaction

 [HIBSCS] Human inference based on similarity to consensus sequences

 [AIBSCS] Automated inference based on similarity to consensus sequences



Reference(s)    

 [1] Patzer SI., Hantke K., 2001, Dual repression by Fe(2+)-Fur and Mn(2+)-MntR of the mntH gene, encoding an NRAMP-like Mn(2+) transporter in Escherichia coli., J Bacteriol. 183(16):4806-13

 [2] Tanaka T., Shinkai A., Bessho Y., Kumarevel T., Yokoyama S., 2009, Crystal structure of the manganese transport regulatory protein from Escherichia coli., Proteins. 77(3):741-6

 [3] Waters LS., Sandoval M., Storz G., 2011, The Escherichia coli MntR miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis., J Bacteriol. 193(21):5887-97

 [4] Yamamoto K., Ishihama A., Busby SJ., Grainger DC., 2011, The Escherichia coli K-12 MntR Miniregulon Includes dps, Which Encodes the Major Stationary-Phase DNA-Binding Protein., J Bacteriol. 193(6):1477-80

 [5] Kehres DG., Janakiraman A., Slauch JM., Maguire ME., 2002, Regulation of Salmonella enterica serovar Typhimurium mntH transcription by H(2)O(2), Fe(2+), and Mn(2+)., J Bacteriol. 184(12):3151-8

 [6] Glasfeld A., Guedon E., Helmann JD., Brennan RG., 2003, Structure of the manganese-bound manganese transport regulator of Bacillus subtilis., Nat Struct Biol. 10(8):652-7

 [7] DeWitt MA., Kliegman JI., Helmann JD., Brennan RG., Farrens DL., Glasfeld A., 2007, The conformations of the manganese transport regulator of Bacillus subtilis in its metal-free state., J Mol Biol. 365(5):1257-65



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