RegulonDB RegulonDB 10.8: Gene Form
   

pdhR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

aceE aroP pdhR tp2 NsrR PdhR FNR CRP CRP CRP CRP CRP BtsR Cra BtsR CRP TyrR TyrR TSS_245 TSS_245 TSS_244 TSS_244 TSS_243 TSS_243 TSS_242 (cluster) TSS_242 (cluster) TSS_241 TSS_241 aceEp aceEp TSS_239 TSS_239 TSS_238 TSS_238 pdhRp pdhRp TSS_236 (cluster) TSS_236 (cluster) aroPp1 aroPp1 aroPp2 aroPp2 TSS_235 TSS_235 TSS_234 (cluster) TSS_234 (cluster) TSS_233 TSS_233

Gene      
Name: pdhR    Texpresso search in the literature
Synonym(s): ECK0112, EG11088, aceC, b0113, genA, yacB
Genome position(nucleotides): 122092 --> 122856 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.82
External database links:  
ASAP:
 ABE-0000394
CGSC:
 30488
ECHOBASE:
 EB1080
OU-MICROARRAY:
 b0113
PortEco:
 pdhR
STRING:
 511145.b0113
COLOMBOS: pdhR


Product      
Name: DNA-binding transcriptional dual regulator PdhR
Synonym(s): AceC, GenA, PdhR, YacB
Sequence: Get amino acid sequence Fasta Format
Regulator Family: GntR
Cellular location: cytosol
Molecular weight: 29.425
Isoelectric point: 6.427
Motif(s):
 
Type Positions Sequence
118 -> 118 R
9 -> 77 PKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFVQSS
99 -> 226 DLLETRHALEGIAAYYAALRSTDEDKERIRELHHAIELAQQSGDLDAESNAVLQYQIAVTEAAHNVVLLHLLRCMEPMLAQNVRQNFELLYSRREMLPLVSSHRTRIFEAIMAGKPEEAREASHRHLA
12 -> 74 SDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFV
37 -> 56 ERELAKQFDVSRPSLREAIQ

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.1 - glycolysis
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [APP] Assay of partially-purified protein
[APPH] Assay of protein purified to homogeneity
[GEA] Gene expression analysis
[HIFS] Human inference of function from sequence
Reference(s): [1] Haydon DJ., et al., 1991
[2] Haydon DJ., et al., 1993
[3] Ogasawara H., et al., 2007
[4] Quail MA., et al., 1995
[5] Quail MA., et al., 1994
External database links:  
ECOCYC:
 EG11088-MONOMER
ECOLIWIKI:
 b0113
INTERPRO:
 IPR008920
INTERPRO:
 IPR000524
INTERPRO:
 IPR036388
INTERPRO:
 IPR036390
INTERPRO:
 IPR011711
MODBASE:
 P0ACL9
PDB:
 5TPM
PDB:
 5KVR
PFAM:
 PF00392
PFAM:
 PF07729
PRIDE:
 P0ACL9
PRINTS:
 PR00035
PRODB:
 PRO_000023501
PROSITE:
 PS50949
REFSEQ:
 NP_414655
SMART:
 SM00895
SMART:
 SM00345
SMR:
 P0ACL9
UNIPROT:
 P0ACL9


Operon      
Name: pdhR-aceEF-lpd         
Operon arrangement:
Transcription unit        Promoter
pdhR-aceEF-lpdA
aceEF
lpdA


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, FNR
Repressed by: FNR, Cra, BtsR, PdhR
Growth Conditions:

[1] 

C: Escherichia coli| L broth| pyruvate 40 mM| OD650 of 0.8
E: Escherichia coli| pdhR knockout mutant| L broth| pyruvate 40 mM| OD650 of 0.8

[2] 

C: Escherichia coli| L broth| OD650 of 0.8
E: Escherichia coli| pdhR knockout mutant; multicopy plasmid pGS613 (pdhR) mutant| L broth| OD650 of 0.8

[3] 

C: Escherichia coli| multicopy plasmid pGS623 (pdhR-lpd) mutant| L broth| OD650 of 0.2
E: Escherichia coli| multicopy plasmid pGS623 (pdhR-lpd) mutant| L broth| glucose 10 mM| OD650 of 0.2

[4] 

C: Escherichia coli| multicopy plasmid pGS623 (pdhR-lpd) mutant| L broth| OD650 of 0.2
E: Escherichia coli| multicopy plasmid pGS623 (pdhR-lpd) mutant| L broth| pyruvate 40 mM| OD650 of 0.2

[5] 

C: Escherichia coli| pdhR knockout mutant| minimal medium| glucose 11 mM| OD650 of 0.2
E: Escherichia coli| pdhR knockout mutant; multicopy plasmid pGS613 (pdhR) mutant| minimal medium| glucose 11 mM| OD650 of 0.2

[6] 

C: Escherichia coli| minimal medium| succinate 40 mM
E: Escherichia coli| minimal medium| pyruvate 40 mM

[7] 

C: Escherichia coli| pdhR knockout mutant; multicopy plasmid pGS613 (pdhR) mutant| L broth| OD650 of 0.8
E: Escherichia coli| pdhR knockout mutant; multicopy plasmid pGS613 (pdhR) mutant| L broth| pyruvate 40 mM| OD650 of 0.8

[8] 

C: Escherichia coli| pdhR knockout mutant| minimal medium| pyruvate 40 mM| OD650 of 0.2
E: Escherichia coli| pdhR knockout mutant; multicopy plasmid pGS613 (pdhR) mutant| minimal medium| pyruvate 40 mM| OD650 of 0.2


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_233 120916 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_234 (cluster) 120919 reverse For this promoter, there
Read more > 		[RS-EPT-CBR] [6]
  promoter TSS_235 120955 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_236 (cluster) 121676 reverse For this promoter, there
Read more > 		[RS-EPT-CBR] [6]
  promoter TSS_238 122852 forward nd [RS-EPT-CBR] [6]
  promoter TSS_239 122860 forward nd [RS-EPT-CBR] [6]
  promoter TSS_241 123388 forward nd [RS-EPT-CBR] [6]
  promoter TSS_242 (cluster) 123471 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [6]
  promoter TSS_243 124973 forward nd [RS-EPT-CBR] [6]
  promoter TSS_244 125226 forward nd [RS-EPT-CBR] [6]
  promoter TSS_245 125425 forward nd [RS-EPT-CBR] [6]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Haydon DJ., Guest JR., 1991, A new family of bacterial regulatory proteins., FEMS Microbiol Lett 63(2-3):291-5

 [2] Haydon DJ., Quail MA., Guest JR., 1993, A mutation causing constitutive synthesis of the pyruvate dehydrogenase complex in Escherichia coli is located within the pdhR gene., FEBS Lett 336(1):43-7

 [3] Ogasawara H., Ishida Y., Yamada K., Yamamoto K., Ishihama A., 2007, PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli., J Bacteriol 189(15):5534-41

 [4] Quail MA., Guest JR., 1995, Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli., Mol Microbiol 15(3):519-29

 [5] Quail MA., Haydon DJ., Guest JR., 1994, The pdhR-aceEF-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex., Mol Microbiol 12(1):95-104

 [6] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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