RegulonDB RegulonDB 11.1: 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 aceEp2 aceEp2 aceEp1 aceEp1 TSS_239 TSS_239 TSS_238 TSS_238 pdhRp2 pdhRp2 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
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.82
External database links:  
ASAP:
 ABE-0000394
CGSC:
 30488
ECHOBASE:
 EB1080
ECOLIHUB:
 pdhR
OU-MICROARRAY:
 b0113
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 Comment
9 -> 77 PKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFVQSS UniProt: HTH gntR-type.
12 -> 74 SDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFV
37 -> 56 ERELAKQFDVSRPSLREAIQ UniProt: H-T-H motif.
99 -> 226 DLLETRHALEGIAAYYAALRSTDEDKERIRELHHAIELAQQSGDLDAESNAVLQYQIAVTEAAHNVVLLHLLRCMEPMLAQNVRQNFELLYSRREMLPLVSSHRTRIFEAIMAGKPEEAREASHRHLA
118 -> 118 R UniProt: In ACEC816; constitutively activated..

 
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: [COMP-HINF-FN-FROM-SEQ] Human inference of function from sequence
[EXP-IDA-PART-PURIFIED-PROTEIN] Assay of partially-purified protein
[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
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:  
ALPHAFOLD:
 P0ACL9
ECOCYC:
 EG11088-MONOMER
ECOLIWIKI:
 b0113
INTERPRO:
 IPR036388
INTERPRO:
 IPR036390
INTERPRO:
 IPR011711
INTERPRO:
 IPR008920
INTERPRO:
 IPR000524
MODBASE:
 P0ACL9
PDB:
 5KVR
PDB:
 5TPM
PFAM:
 PF07729
PFAM:
 PF00392
PRIDE:
 P0ACL9
PRINTS:
 PR00035
PRODB:
 PRO_000023501
PROSITE:
 PS50949
REFSEQ:
 NP_414655
SMART:
 SM00345
SMART:
 SM00895
SMR:
 P0ACL9
UNIPROT:
 P0ACL9


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


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


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 nd [RS-EPT-CBR] [6]
  promoter TSS_235 120955 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_236 (cluster) 121676 reverse nd [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 nd [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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