RegulonDB RegulonDB 10.10: Gene Form
   

iclR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

metH arpA iclR aceK MetR FadR IclR Fur TSS_4839 TSS_4839 metHp metHp iclRp iclRp metHp2 metHp2 arpAp9 arpAp9 arpAp1 arpAp1 arpAp8 arpAp8

Gene      
Name: iclR    Texpresso search in the literature
Synonym(s): ECK4010, EG10491, b4018
Genome position(nucleotides): 4222804 <-- 4223628 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.18
External database links:  
ASAP:
 ABE-0013136
CGSC:
 614
ECHOBASE:
 EB0486
ECOLIHUB:
 iclR
OU-MICROARRAY:
 b4018
STRING:
 511145.b4018
COLOMBOS: iclR


Shine dalgarno      
Sequence: tacagaaaaaAGAGACtgtCAT


Product      
Name: DNA-binding transcriptional repressor IclR
Synonym(s): IclR
Sequence: Get amino acid sequence Fasta Format
Regulator Family: IclR
Cellular location: cytosol
Molecular weight: 29.739
Isoelectric point: 8.17
Motif(s):
 
Type Positions Sequence
145 -> 267 RMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHRKGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISISGPISRITDDRVTEFGAMVIKAAKEVT
146 -> 146 M
26 -> 76 SLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQV
46 -> 65 LTELAQQAGLPNSTTHRLLT
154 -> 154 L

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.2 - glyoxylate bypass
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0003700 - DNA-binding transcription factor activity
biological_process GO:0006097 - glyoxylate cycle
GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
Evidence: [APPH] Assay of protein purified to homogeneity
[HIFS] Human inference of function from sequence
[IFC] Inferred by functional complementation
[IPI] Inferred from physical interaction
Reference(s): [1] Blattner FR., et al., 1993
[2] Cortay JC., et al., 1991
[3] Galinier A., et al., 1991
[4] Gui L., et al., 1996
[5] Negre D., et al., 1992
[6] Negre D., et al., 1991
[7] Sunnarborg A., et al., 1990
[8] Yamamoto K., et al., 2003
External database links:  
DIP:
 DIP-10008N
ECOCYC:
 PD04099
ECOLIWIKI:
 b4018
INTERPRO:
 IPR029016
INTERPRO:
 IPR036390
INTERPRO:
 IPR036388
INTERPRO:
 IPR014757
INTERPRO:
 IPR005471
MINT:
 P16528
MODBASE:
 P16528
PDB:
 2O99
PDB:
 1TD5
PDB:
 2O9A
PFAM:
 PF09339
PFAM:
 PF01614
PRIDE:
 P16528
PRODB:
 PRO_000022991
PROSITE:
 PS51078
PROSITE:
 PS51077
REFSEQ:
 NP_418442
SMART:
 SM00346
SMR:
 P16528
UNIPROT:
 P16528


Operon      
Name: iclR         
Operon arrangement:
Transcription unit        Promoter
iclR


Transcriptional Regulation      
Display Regulation             
Activated by: FadR
Repressed by: IclR


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 arpAp8 4222513 reverse nd [ICWHO] [9]
  promoter arpAp1 4222629 reverse nd [ICWHO] [9]
  promoter arpAp9 4222691 reverse nd [ICWHO] [9]
  promoter TSS_4839 4223784 forward nd [RS-EPT-CBR] [10]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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


Reference(s)    

 [1] Blattner FR., Burland V., Plunkett G., Sofia HJ., Daniels DL., 1993, Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes., Nucleic Acids Res 21(23):5408-17

 [2] Cortay JC., Negre D., Galinier A., Duclos B., Perriere G., Cozzone AJ., 1991, Regulation of the acetate operon in Escherichia coli: purification and functional characterization of the IclR repressor., EMBO J 10(3):675-9

 [3] Galinier A., Bleicher F., Negre D., Perriere G., Duclos B., Cozzone AJ., Cortay JC., 1991, Primary structure of the intergenic region between aceK and iclR in the Escherichia coli chromosome., Gene 97(1):149-50

 [4] Gui L., Sunnarborg A., Pan B., LaPorte DC., 1996, Autoregulation of iclR, the gene encoding the repressor of the glyoxylate bypass operon., J Bacteriol 178(1):321-4

 [5] Negre D., Cortay JC., Galinier A., Sauve P., Cozzone AJ., 1992, Specific interactions between the IclR repressor of the acetate operon of Escherichia coli and its operator., J Mol Biol 228(1):23-9

 [6] Negre D., Cortay JC., Old IG., Galinier A., Richaud C., Saint Girons I., Cozzone AJ., 1991, Overproduction and characterization of the iclR gene product of Escherichia coli K-12 and comparison with that of Salmonella typhimurium LT2., Gene 97(1):29-37

 [7] Sunnarborg A., Klumpp D., Chung T., LaPorte DC., 1990, Regulation of the glyoxylate bypass operon: cloning and characterization of iclR., J Bacteriol 172(5):2642-9

 [8] Yamamoto K., Ishihama A., 2003, Two different modes of transcription repression of the Escherichia coli acetate operon by IclR., Mol Microbiol 47(1):183-94

 [9] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [10] 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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