RegulonDB RegulonDB 10.8:Regulon Page

NrdR DNA-binding transcriptional repressor

Synonyms: NrdR-dATP, NrdR-ATP, NrdR, NrdR-Zn2+
NrdR is a zinc-finger/ATP cone transcriptional regulatory protein that regulates the expression of several operons that encode ribonucleotide reductases (RNRs), according to the abundance of deoxyribonucleoside triphosphates (dNTPs) generated from ribonucleotides []. NrdR has an N-terminal zinc-finger-like DNA-binding domain and a C-terminal ATP cone domain. The ATP cone domain is similar to the allosteric domain found in some RNRs [1] NrdR is bound by approximately equal amounts of ATP and dATP in vivo [] Triphosphates bind preferentially to NrdR compared to nucleoside monophosphates and triphosphates [] NrdR is directly regulated by ATP, rather than ATP serving as the cofactor to facilitate dATP binding [] The apo and holo forms of NrdR are capable of binding to DNA; furthermore, this binding capability is enhanced by high concentrations of zinc [] In Streptomyces coelicolor, it was shown that NrdR is an oligomeric protein that binds zinc, ATP, dATP, and the previously hypothesized NrdR box [].
Read more >

Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
NrdR Non-Functional   Apo nd nd
NrdR-ATP Functional Allosteric Holo [AIFS], [BPP], [IMP] [1]
NrdR-Zn2+ Functional Allosteric Holo [AIFS], [APPHINH], [BPP], [HIFS], [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

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 (4)
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
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
  NrdR-Zn2+ repressor nrdAp Sigma70 -7.5 -117.5 nrdA, nrdB, yfaE
2344740 2344755 [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [1]
  NrdR-Zn2+ repressor nrdAp Sigma70 25.5 -85.5 nrdA, nrdB, yfaE
2344772 2344787 [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [1]
  NrdR-Zn2+ repressor nrdDp Sigma70 -22.5 -200.5 nrdD, nrdG
4462853 4462868 [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1]
  NrdR-Zn2+ repressor nrdDp Sigma70 9.5 -169.5 nrdD, nrdG
4462822 4462837 [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1]
  NrdR-Zn2+ repressor nrdHp Sigma70 -45.5 -112.5 nrdH, nrdI, nrdE, nrdF
2800603 2800618 [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1]
  NrdR-Zn2+ repressor nrdHp Sigma70 -14.5 -81.5 nrdH, nrdI, nrdE, nrdF
2800634 2800649 [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [1]

Alignment and PSSM for NrdR TFBSs    

Aligned TFBS of NrdR   

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

;	consensus.strict             	taaatgCtAtATataGtGt
;	consensus.strict.rc          	ACACTATATATAGCATTTA
;	consensus.IUPAC              	taamtrCwAkATatwGtGt
;	consensus.IUPAC.rc           	ACACWATATMTWGYAKTTA
;	consensus.regexp             	taa[ac]t[ag]C[at]A[gt]ATat[at]GtGt
;	consensus.regexp.rc          	ACAC[AT]ATAT[AC]T[AT]G[CT]A[GT]TTA

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


 [AIFS] Automated inference of function from sequence

 [BPP] Binding of purified proteins

 [IMP] Inferred from mutant phenotype

 [APPHINH] Assay of protein purified to homogeneity from its native host

 [HIFS] Human inference of function from sequence

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

 [CV(GEA)] cross validation(GEA)

 [CV(GEA/SM)] cross validation(GEA/SM)

 [CV(SM)] cross validation(SM)

 [GEA] Gene expression analysis

 [SM] Site mutation


 [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