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PurR DNA-binding transcriptional repressor

Synonyms: PurR-Hypoxanthine, PurR-Guanine, PurR


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
PurR Non-Functional   Apo [BPP], [GEA], [IPI] [1], [2], [3]
PurR-Guanine Functional Allosteric Holo [BPP], [GEA], [IPI] [1], [2], [3]
PurR-Hypoxanthine Functional Allosteric Holo [BPP], [GEA], [IPI] [1], [2], [3]
Evolutionary Family: GalR/LacI
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: purR
  Genome position: 1737844-1738869
  Length: 1026 bp / 341 aa
Operon name: purR
TU(s) encoding the TF:
Transcription unit        Promoter
purR
purRp


Regulon       
Regulated gene(s) carA, carB, codA, codB, cvpA, gcvH, gcvP, gcvT, glnB, glyA, guaA, guaB, hflD, prs, purA, purB, purC, purD, purE, purF, purH, purK, purL, purM, purN, purR, pyrC, pyrD, speA, speB, ubiX
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
purine biosynthesis (14)
nucleotide and nucleoside conversions (7)
pyrimidine biosynthesis (5)
amino acids (5)
formyl-THF biosynthesis (5)
Read more >
Regulated operon(s) carAB, codBA, cvpA-purF-ubiX, gcvTHP, glrR-glnB, glyA, guaBA, hflD-purB, lolB-ispE-prs, purA, purC, purEK, purHD, purL, purMN, purR, pyrC, pyrD, speAB
First gene in the operon(s) carA, codB, cvpA, gcvT, glnB, glnB, glyA, guaB, hflD, prs, purA, purC, purE, purH, purL, purM, purR, pyrC, pyrD, speA
Simple and complex regulons CRP,DnaA,Fis,PurR
CRP,FNR,GcvA,Lrp,PurR
FNR,PurR
Fis,IHF,PepA,PurR,RutR
Fis,PurR
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[PurR,-](20)


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
  PurR-Hypoxanthine repressor carAp1 Sigma70 -128.5 -228.5 carA, carB
tcttcttgctGCGCAAGCGTTTTCCAgaacaggtta
 29415 29430 [AIBSCS], [BPP], [GEA] [4], [5], [6]
  PurR-Hypoxanthine repressor codBp Sigma70 -36.5 -74.5 codB, codA
atatttccccACGAAAACGATTGCTTtttatcttca
 354840 354855 [AIBSCS], [GEA], [HIBSCS] [4], [7], [8]
  PurR-Hypoxanthine repressor cvpAp1 Sigma70 -28.5 -65.5 cvpA, purF, ubiX
aggaaatcccTACGCAAACGTTTTCTttttctgtta
 2430821 2430836 [BCE], [BPP], [GEA], [HIBSCS], [SM] [4], [9], [10], [11], [12]
  PurR-Hypoxanthine repressor gcvTp Sigma70 7.5 -98.5 gcvT, gcvH, gcvP
gttcaggcaaAAGAGAACGATTGCGTtggggaccgg
 3050758 3050773 [AIBSCS], [GEA], [HIBSCS] [4], [13]
  PurR-Hypoxanthine repressor glnBp1 Sigma70 -42.5 -75.5 glnB
cacgagctggATGCAAACGATTTCAAggaatgaatt
 2687476 2687491 [BCE], [GEA], [HIBSCS] [14]
  PurR-Hypoxanthine repressor glnBp2 Sigma70 20.5 -75.5 glnB
cacgagctggATGCAAACGATTTCAAggaatgaatt
 2687476 2687491 [BCE], [GEA], [HIBSCS] [14]
  PurR-Hypoxanthine repressor glyAp Sigma70 -59.5 -126.5 glyA
cgtagcctgaAGGTAATCGTTTGCGTaaattccttt
 2685626 2685641 [AIBSCS], [BPP], [GEA], [HIBSCS], [SM] [4], [15], [16], [17]
  PurR-Hypoxanthine repressor guaBp Sigma70 -24.5 -61.5 guaB, guaA
aaaggggtagATGCAATCGGTTACGCtctgtataat
 2634124 2634139 [AIBSCS], [BCE], [GEA] [4], [10]
  PurR-Hypoxanthine repressor hflDp Sigma70 892.5 836.5 hflD, purB
tttgctgccgACGCAATCGGTTACCTtgatgcaatc
 1191787 1191802 [AIBSCS], [BPP], [GEA], [HIBSCS] [4], [18]
  PurR-Hypoxanthine repressor prsp Sigma70 -48.5 -350.5 prs
aggttatcgcAAGAAAACGTTTTCGCgaggttgatg
 1262218 1262233 [BCE], [GEA], [HIBSCS] [14]
  PurR-Hypoxanthine repressor purAp Sigma70 -90.5 -113.5 purA
ctacatgttgAGGAAAACGATTGGCTgaacaaaaaa
 4404566 4404581 [BPP], [GEA], [HIBSCS] [4], [19]
  PurR-Hypoxanthine repressor purAp Sigma70 9.5 -14.5 purA
atccatttttAAGCAAACGGTGATTTtgaaaaatgg
 4404665 4404680 [BPP], [GEA], [HIBSCS] [4], [19]
  PurR-Hypoxanthine repressor purCp Sigma70 2.5 -161.5 purC
ctgatatgatACGCAAACGTGTGCGTctgcaggaaa
 2597772 2597787 [AIBSCS], [BPP], [GEA], [HIBSCS] [4], [9]
  PurR-Hypoxanthine repressor purEp Sigma70 -37.5 -79.5 purE, purK
tttcacagccACGCAACCGTTTTCCTtgctctcttt
 553172 553187 [AIBSCS], [BCE], [GEA], [HIBSCS] [4], [9], [10], [20]
  PurR-Hypoxanthine repressor purHp Sigma70 -20.5 -115.5 purH, purD
cgcgagcgttGCGCAAACGTTTTCGTtacaatgcgg
 4207640 4207655 [AIBSCS], [BPP], [GEA], [HIBSCS] [4], [9]
  PurR-Hypoxanthine repressor purLp Sigma70 -38.5 -84.5 purL
ttttatttccACGCAAACGGTTTCGTcagcgcatca
 2695620 2695635 [AIBSCS], [BCE], [GEA], [HIBSCS] [4], [9], [10]
  PurR-Hypoxanthine repressor purMp Sigma70 -27.5 -71.5 purM, purN
taaagcagtcTCGCAAACGTTTGCTTtccctgttag
 2621118 2621133 [AIBSCS], [GEA], [HIBSCS], [SM] [4], [10], [21], [22]
  PurR-Hypoxanthine repressor purRp Sigma70 103.5 -52.5 purR
aggtgtgtaaAGGCAAACGTTTACCTtgcgattttg
 1737784 1737799 [BCE], [BPP], [GEA], [HIBSCS], [SM] [4], [10], [23]
  PurR-Hypoxanthine repressor purRp Sigma70 191.5 35.5 purR
gtagcgaaacGAGCAAACGTTTCCACtacaactgtg
 1737872 1737887 [BCE], [BPP], [GEA], [HIBSCS], [SM] [10], [23]
  PurR-Hypoxanthine repressor pyrCp Sigma70 -23.5 -59.5 pyrC
tttcgtgcaaAGGAAAACGTTTCCGCttatcctttg
 1122659 1122674 [BPP], [GEA], [HIBSCS], [SM] [24], [25], [26]
  PurR-Hypoxanthine repressor pyrDp Sigma70 -58.5 -94.5 pyrD
gaaacaggttCGGAAAACGTTTGCGTtttttttgcc
 1004666 1004681 [AIBSCS], [BCE], [GEA], [HIBSCS] [4], [26]
  PurR-Hypoxanthine repressor speAp Sigma70 11.5 -126.5 speA, speB
tgttatgaaaAAGAAACCGGTTGCGCagttggagcg
 3086030 3086045 [BCE], [GEA], [HIBSCS] [14]


Alignment and PSSM for PurR TFBSs    

Aligned TFBS of PurR   
  Sequence
  GCGCAAGCGTTTTCCA
  AAGCAATCGTTTTCGT
  ACGCAACCGTTTTCCT
  ACGCAAACGTTTTCCG
  GCGGAAACGTTTTCCT
  ACGCAATCGGTTACCT
  GCGAAAACGTTTTCTT
  AGGCAAACGTTTACCT
  GTGGAAACGTTTGCTC
  ACGCAAACGTTTTCTT
  ACGCAAACGTGTGCGT
  TCGCAAACGTTTGCTT
  ATGCAATCGGTTACGC
  ACGCAAACGATTACCT
  ATGCAAACGATTTCAA
  ACGCAAACGGTTTCGT
  ACGCAATCGTTCTCTT
  GCGCAACCGGTTTCTT
  GCGCAAACGTTTTCGT
  AGCCAATCGTTTTCCT
  AAGCAAACGGTGATTT

Position weight matrix (PWM).    
A	14	2	0	1	21	21	13	0	0	2	0	0	5	0	1	2
C	0	14	1	18	0	0	2	21	0	0	0	1	0	20	8	2
G	6	2	20	2	0	0	1	0	21	5	1	1	3	0	5	1
T	1	3	0	0	0	0	5	0	0	14	20	19	13	1	7	16

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

 [IPI] Inferred from physical interaction

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [HIBSCS] Human inference based on similarity to consensus sequences

 [BCE] Binding of cellular extracts

 [SM] Site mutation


Reference(s)    

 [1] Choi KY., Zalkin H., 1992, Structural characterization and corepressor binding of the Escherichia coli purine repressor., J Bacteriol. 174(19):6207-14

 [2] Meng LM., Nygaard P., 1990, Identification of hypoxanthine and guanine as the co-repressors for the purine regulon genes of Escherichia coli., Mol Microbiol. 4(12):2187-92

 [3] Rolfes RJ., Zalkin H., 1990, Purification of the Escherichia coli purine regulon repressor and identification of corepressors., J Bacteriol. 172(10):5637-42

 [4] Cho BK., Federowicz SA., Embree M., Park YS., Kim D., Palsson BO., 2011, The PurR regulon in Escherichia coli K-12 MG1655., Nucleic Acids Res. 39(15):6456-64

 [5] Devroede N., Huysveld N., Charlier D., 2006, Mutational analysis of intervening sequences connecting the binding sites for integration host factor, PepA, PurR, and RNA polymerase in the control region of the Escherichia coli carAB operon, encoding carbamoylphosphate synthase., J Bacteriol. 188(9):3236-45

 [6] Devroede N., Thia-Toong TL., Gigot D., Maes D., Charlier D., 2004, Purine and pyrimidine-specific repression of the Escherichia coli carAB operon are functionally and structurally coupled., J Mol Biol. 336(1):25-42

 [7] Danielsen S., Kilstrup M., Barilla K., Jochimsen B., Neuhard J., 1992, Characterization of the Escherichia coli codBA operon encoding cytosine permease and cytosine deaminase., Mol Microbiol. 6(10):1335-44

 [8] Kilstrup M., Meng LM., Neuhard J., Nygaard P., 1989, Genetic evidence for a repressor of synthesis of cytosine deaminase and purine biosynthesis enzymes in Escherichia coli., J Bacteriol. 171(4):2124-7

 [9] He B., Shiau A., Choi KY., Zalkin H., Smith JM., 1990, Genes of the Escherichia coli pur regulon are negatively controlled by a repressor-operator interaction., J Bacteriol. 172(8):4555-62

 [10] Meng LM., Kilstrup M., Nygaard P., 1990, Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli., Eur J Biochem. 187(2):373-9

 [11] Rolfes RJ., Zalkin H., 1988, Regulation of Escherichia coli purF. Mutations that define the promoter, operator, and purine repressor gene., J Biol Chem. 263(36):19649-52

 [12] Rolfes RJ., Zalkin H., 1988, Escherichia coli gene purR encoding a repressor protein for purine nucleotide synthesis. Cloning, nucleotide sequence, and interaction with the purF operator., J Biol Chem. 263(36):19653-61

 [13] Wilson RL., Urbanowski ML., Stauffer GV., 1995, DNA binding sites of the LysR-type regulator GcvA in the gcv and gcvA control regions of Escherichia coli., J Bacteriol. 177(17):4940-6

 [14] He B., Choi KY., Zalkin H., 1993, Regulation of Escherichia coli glnB, prsA, and speA by the purine repressor., J Bacteriol. 175(11):3598-606

 [15] Lorenz E., Stauffer GV., 1995, Characterization of the MetR binding sites for the glyA gene of Escherichia coli., J Bacteriol. 177(14):4113-20

 [16] Lorenz E., Stauffer GV., 1996, RNA polymerase, PurR and MetR interactions at the glyA promoter of Escherichia coli., Microbiology. 142 ( Pt 7):1819-24

 [17] Steiert JG., Kubu C., Stauffer GV., 1992, The PurR binding site in the glyA promoter region of Escherichia coli., FEMS Microbiol Lett. 78(2-3):299-304

 [18] He B., Smith JM., Zalkin H., 1992, Escherichia coli purB gene: cloning, nucleotide sequence, and regulation by purR., J Bacteriol. 174(1):130-6

 [19] He B., Zalkin H., 1994, Regulation of Escherichia coli purA by purine repressor, one component of a dual control mechanism., J Bacteriol. 176(4):1009-13

 [20] Watanabe W., Sampei G., Aiba A., Mizobuchi K., 1989, Identification and sequence analysis of Escherichia coli purE and purK genes encoding 5'-phosphoribosyl-5-amino-4-imidazole carboxylase for de novo purine biosynthesis., J Bacteriol. 171(1):198-204

 [21] Liu IF., Aedo S., Tse-Dinh YC., 2011, Resistance to topoisomerase cleavage complex induced lethality in Escherichia coli via titration of transcription regulators PurR and FNR., BMC Microbiol. 11:261

 [22] Smith JM., Daum HA., 1986, Nucleotide sequence of the purM gene encoding 5'-phosphoribosyl-5-aminoimidazole synthetase of Escherichia coli K12., J Biol Chem. 261(23):10632-6

 [23] Rolfes RJ., Zalkin H., 1990, Autoregulation of Escherichia coli purR requires two control sites downstream of the promoter., J Bacteriol. 172(10):5758-66

 [24] Choi KY., Zalkin H., 1990, Regulation of Escherichia coli pyrC by the purine regulon repressor protein., J Bacteriol. 172(6):3201-7

 [25] Wilson HR., Chan PT., Turnbough CL., 1987, Nucleotide sequence and expression of the pyrC gene of Escherichia coli K-12., J Bacteriol. 169(7):3051-8

 [26] Wilson HR., Turnbough CL., 1990, Role of the purine repressor in the regulation of pyrimidine gene expression in Escherichia coli K-12., J Bacteriol. 172(6):3208-13


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