Transcription Factor
| Accessions: | ECK120004960 (RegulonDB 7.5) |
| Names: | IclR, IclR transcriptional repressor |
| Organisms: | ECK12 |
| Libraries: | RegulonDB 7.5 1 1 Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muniz-Rascado L, Garcia-Sotelo JS, Weiss V, Solano-Lira H, Martinez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernandez S, Alquicira-Hernandez K, Lopez-Fuentes A, Porron-Sotelo L, Huerta AM, Bonavides-Martinez C, Balderas-Martinez YI, Pannier L, Olvera M, Labastida A, Jimenez-Jacinto V, Vega-Alvarado L, Del Moral-Chavez V, Hernandez-Alvarez A, Morett E, Collado-Vides J. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 2013 Jan 1;41(D1):D203-D213. [Pubmed] |
| Notes: | The transcription factor IclR, for Isocitrate lyase Regulator, is negatively autoregulated Gui L,1996and it regulates the expression of the glyoxylate bypass operon Peskov K,2008; Resnik E,1996; Galinier A,1991; Cortay JC,1989; Maloy SR,1982; Cortay JC,1991 Transcription of this operon is induced when E. coli is grown during acetate accumulation in the exponential phase; Glyoxylate and pyruvate have been identified as effectors of IclR and show antagonistic effects; While glyoxylate favors the inactive dimeric state of IclR, pyruvate increases the binding of IclR to the aceBp promoter by stabilizing the active tetrameric form of the protein Lorca GL,2007On other hand, the genes of the aceBAK operon are expressed to varied degrees due to two facts: first, they are differentially regulated at the translational level, and second, there is a putative premature transcriptional termination in the region preceding the aceK gene Cozzone AJ,2005 IclR represses aceBAK transcription through two mechanisms Yamamoto K,2003 (1) binding to the proximal site, overlapping the -35 promoter box, and preventing RNA polymerase binding Pan B,1996; Negre D,1992; Cortay JC,1991 and (2) binding to the distal site after the RNA polymerase has bound to the promoter and formed the open complex, avoiding the polymerase escape of the promoter through its interaction with the α-subunits; Perhaps the IclR binding at both sites forms an intermolecular bridge that leads to a DNA loop structure and thus enhances the aceBAK repression Yamamoto K,2003This regulator belongs to the IclR family of repressors; IclR is composed of two domains: the amino-terminal domain, which contains the DNA-binding region, and the carboxy-terminal domain, which is responsible for inducer binding Negre D,1992; Sunnarborg A,1990; Lorca GL,2007; Donald LJ,1996; Negre D,1991The crystal structure of the C-terminal domain of IclR (2.3Å) has been solved Lorca GL,2007An iclR mutation affects the carbon flow in the metabolism Lin H,2005; Sanchez AM, 2005 Under glucose-abundant conditions, a double mutant of IclR and ArcA causes an increase in biomass yield (47%) and reduction of acetate (70%) and CO2 (16%) production; Under glucose-limited conditions, this double mutant exhibits an increase of biomass of only 13% Waegeman H,2011.; glyoxylate bypass; repressor; Transcription related; operon; transcription, DNA-dependent; regulation of transcription, DNA-dependent; DNA binding; glyoxylate cycle; cytoplasm |
| Length: | 275 |
| Pfam Domains: | 26-77 IclR helix-turn-helix domain 145-267 Bacterial transcriptional regulator |
| Sequence: (in bold interface residues) | 1 MVAPIPAKRGRKPAVATAPATGQVQSLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTT 60 61 HRLLTTMQQQGFVRQVGELGHWAIGAHAFMVGSSFLQSRNLLAIVHPILRNLMEESGETV 120 121 NMAVLDQSDHEAIIIDQVQCTHLMRMSAPIGGKLPMHASGAGKAFLAQLSEEQVTKLLHR 180 181 KGLHAYTHATLVSPVHLKEDLAQTRKRGYSFDDEEHALGLRCLAACIFDEHREPFAAISI 240 241 SGPISRITDDRVTEFGAMVIKAAKEVTLAYGGMR* |
| Interface Residues: | 46, 57, 58, 59, 61, 62, 66 |
| 3D-footprint Homologues: | 2xro_E, 4wcg_A |
| Binding Motifs: | IclR TTTtcAT |
| Binding Sites: | ECK120012593 ECK120016618 ECK120016620 ECK120016622 ECK120016624 ECK120016626 ECK120016628 ECK120016630 |
| Publications: | Waegeman H., Beauprez J., Moens H., Maertens J., De Mey M., Foulquie-Moreno MR., Heijnen JJ., Charlier D., Soetaert W. Effect of iclR and arcA knockouts on biomass formation and metabolic fluxes in Escherichia coli K12 and its implications on understanding the metabolism of Escherichia coli BL21 (DE3). BMC Microbiol. 11:70 (2011). [Pubmed] Cozzone AJ., El-Mansi M. Control of isocitrate dehydrogenase catalytic activity by protein phosphorylation in Escherichia coli. J Mol Microbiol Biotechnol. 9(3-4):132-46 (2005). [Pubmed] Negre D., Cortay JC., Galinier A., Sauve P., Cozzone AJ. Specific interactions between the IclR repressor of the acetate operon of Escherichia coli and its operator. J Mol Biol. 228(1):23-9 (1992). [Pubmed] Sunnarborg A., Klumpp D., Chung T., LaPorte DC. Regulation of the glyoxylate bypass operon: cloning and characterization of iclR. J Bacteriol. 172(5):2642-9 (1990). [Pubmed] Donald LJ., Chernushevich IV., Zhou J., Verentchikov A., Poppe-Schriemer N., Hosfield DJ., Westmore JB., Ens W., Duckworth HW., Standing KG. Preparation and properties of pure, full-length IclR protein of Escherichia coli. Use of time-of-flight mass spectrometry to investigate the problems encountered. Protein Sci. 5(8):1613-24 (1996). [Pubmed] Negre D., Cortay JC., Old IG., Galinier A., Richaud C., Saint Girons I., Cozzone AJ. 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 (1991). [Pubmed] Lin H., Bennett GN., San KY. Genetic reconstruction of the aerobic central metabolism in Escherichia coli for the absolute aerobic production of succinate. Biotechnol Bioeng. 89(2):148-56 (2005). [Pubmed] Sanchez AM., Bennett GN., San KY. Novel pathway engineering design of the anaerobic central metabolic pathway in Escherichia coli to increase succinate yield and productivity. Metab Eng. 7(3):229-39 (2005). [Pubmed] Gui L., Sunnarborg A., Pan B., LaPorte DC. Autoregulation of iclR, the gene encoding the repressor of the glyoxylate bypass operon. J Bacteriol. 178(1):321-4 (1996). [Pubmed] Peskov K., Goryanin I., Prank K., Tobin F., Demin O. Kinetic modeling of ace operon genetic regulation in Escherichia coli. J Bioinform Comput Biol. 6(5):933-59 (2008). [Pubmed] Resnik E., Pan B., Ramani N., Freundlich M., LaPorte DC. Integration host factor amplifies the induction of the aceBAK operon of Escherichia coli by relieving IclR repression. J Bacteriol. 178(9):2715-7 (1996). [Pubmed] Galinier A., Bleicher F., Negre D., Perriere G., Duclos B., Cozzone AJ., Cortay JC. Primary structure of the intergenic region between aceK and iclR in the Escherichia coli chromosome. Gene. 97(1):149-50 (1991). [Pubmed] Cortay JC., Bleicher F., Duclos B., Cenatiempo Y., Gautier C., Prato JL., Cozzone AJ. Utilization of acetate in Escherichia coli: structural organization and differential expression of the ace operon. Biochimie. 71(9-10):1043-1049 (1989). [Pubmed] Maloy SR., Nunn WD. Genetic regulation of the glyoxylate shunt in Escherichia coli K-12. J Bacteriol. 149(1):173-80 (1982). [Pubmed] Cortay JC., Negre D., Galinier A., Duclos B., Perriere G., Cozzone AJ. Regulation of the acetate operon in Escherichia coli: purification and functional characterization of the IclR repressor. EMBO J. 10(3):675-9 (1991). [Pubmed] Lorca GL., Ezersky A., Lunin VV., Walker JR., Altamentova S., Evdokimova E., Vedadi M., Bochkarev A., Savchenko A. Glyoxylate and pyruvate are antagonistic effectors of the Escherichia coli IclR transcriptional regulator. J Biol Chem. 282(22):16476-91 (2007). [Pubmed] Yamamoto K., Ishihama A. Two different modes of transcription repression of the Escherichia coli acetate operon by IclR. Mol Microbiol. 47(1):183-94 (2003). [Pubmed] Pan B., Unnikrishnan I., LaPorte DC. The binding site of the IclR repressor protein overlaps the promoter of aceBAK. J Bacteriol. 178(13):3982-4 (1996). [Pubmed] |
| Related annotations: | PaperBLAST |
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