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NrdR DNA-binding transcriptional repressor

Synonyms: NrdR-Zn2+, NrdR-dATP, NrdR-ATP


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
NrdR-ATP Functional Allosteric Holo [AIFS], [BPP], [IMP] [1]
NrdR-Zn2+ Functional Allosteric Holo [AIFS], [BPP], [IMP] [1]
NrdR-dATP Functional Allosteric Holo [AIFS], [BPP], [IMP] [1]
Evolutionary Family: NrdR
Connectivity class: Local Regulator
Gene name: nrdR
  Genome position: 433002-433451
  Length: 450 bp / 149 aa
Operon name: nrdR-ribDE-nusB-thiL-pgpA
TU(s) encoding the TF:
Transcription unit        Promoter
nrdR-ribDE-nusB-thiL-pgpA
nrdRp


Regulon       
Regulated gene(s) nrdA, nrdB, nrdD, nrdE, nrdF, nrdG, nrdH, nrdI, yfaE
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
nucleotide and nucleoside conversions (5)
posttranslational modification (3)
2'-deoxyribonucleotide metabolism (1)
inhibition / activation of enzymes (1)
thioredoxin, glutaredoxin (1)
Regulated operon(s) nrdAB-yfaE, nrdDG, nrdHIEF
First gene in the operon(s) nrdA, nrdD, nrdH
Simple and complex regulons ArgP,CRP,DnaA,Fis,H-NS,NrdR
FNR,H-NS,NrdR
Fur,IscR,NrdR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[NrdR,-](3)


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
  NrdR-Zn2+ repressor nrdAp Sigma70 -7.5 -117.5 nrdA, nrdB, yfaE
agggtcatttTCACACTATCTTGCAGtgaatcccaa
2344740 2344755 [BPP], [GEA], [HIBSCS], [SM] [1]
  NrdR-Zn2+ repressor nrdAp Sigma70 25.5 -85.5 nrdA, nrdB, yfaE
ccaaacatacCCCCTATATATAGTGTtctaagcagc
2344772 2344787 [BPP], [GEA], [HIBSCS], [SM] [1]
  NrdR-Zn2+ repressor nrdDp Sigma70 -22.5 -200.5 nrdD, nrdG
ttgatgcaaaGCACTATATATAGACTttaaaatgcg
4462853 4462868 [BPP], [GEA], [HIBSCS] [1]
  NrdR-Zn2+ repressor nrdDp Sigma70 9.5 -169.5 nrdD, nrdG
atgcgtcccaACCCAATATGTTGTATtaatcgacta
4462822 4462837 [BPP], [GEA], [HIBSCS] [1]
  NrdR-Zn2+ repressor nrdHp Sigma70 -45.5 -112.5 nrdH, nrdI, nrdE, nrdF
cgaccactatTTGCTATATATTGTGTggttgaatct
2800603 2800618 [BPP], [GEA], [HIBSCS] [1]
  NrdR-Zn2+ repressor nrdHp Sigma70 -14.5 -81.5 nrdH, nrdI, nrdE, nrdF
aatcttttttCAACTACATCTAGTATctctgtatca
2800634 2800649 [BPP], [GEA], [HIBSCS] [1]


Alignment and PSSM for NrdR TFBSs    

Aligned TFBS of NrdR   
  Sequence
 

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

 [AIFS] Automated inference of function from sequence

 [BPP] Binding of purified proteins

 [IMP] Inferred from mutant phenotype

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation



Reference(s)    

 [1] Torrents E., Grinberg I., Gorovitz-Harris B., Lundstrom H., Borovok I., Aharonowitz Y., Sjoberg BM., Cohen G., 2007, NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes., J Bacteriol. 189(14):5012-21



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