Transcription Factor

						

			
Accessions: ECK120005141 (RegulonDB 7.5)

			
Names: OmpR
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: Transcription related; two component regulatory systems (external signal); repressor; activator; operon; cytoplasm; intracellular signal transduction; intracellular; regulation of transcription, DNA-dependent; DNA binding; two-component signal transduction system (phosphorelay); two-component response regulator activity; transcription, DNA-dependent; transcription activator activity; transcription repressor activity
Length: 240
Pfam Domains:     7-116 Response regulator receiver domain
  157-232 Transcriptional regulatory protein, C terminal
Sequence: 
(in bold interface residues)		   1 MQENYKILVVDDDMRLRALLERYLTEQGFQVRSVANAEQMDRLLTRESFHLMVLDLMLPG   60
  61 EDGLSICRRLRSQSNPMPIIMVTAKGEEVDRIVGLEIGADDYIPKPFNPRELLARIRAVL  120
 121 RRQANELPGAPSQEEAVIAFGKFKLNLGTREMFREDEPMPLTSGEFAVLKALVSHPREPL  180
 181 SRDKLMNLARGREYSAMERSIDVQISRLRRMVEEDPAHPRYIQTVWGLGYVFVPDGSKA*  240
Interface Residues: 88, 95, 100, 198, 199, 200, 202, 203, 204, 206, 207, 226
3D-footprint Homologues: 3l4j_A, 8jo2_H, 5x5l_H, 8hih_Q, 4kfc_B, 6lxn_A, 8hml_B, 4nhj_A, 7e1b_B, 2z33_A, 5ed4_A, 8b4b_W
Binding Motifs: OmpR wAhaTGwWACmAArwdTww
Binding Sites: ECK120011581
ECK120011786
ECK120011788
ECK120011790
ECK120012832
ECK120012834
ECK120012836
ECK120012844
ECK120013323
ECK120013325
ECK120013327
ECK120013329
ECK120013346
ECK120013472
ECK120013474
ECK120013826
ECK120020632
ECK120023297
ECK120023298
ECK120034997
			
Publications: Shin S., Park C. Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR. J Bacteriol. 177(16):4696-702 (1995). [Pubmed]


Batchelor E., Goulian M. Imaging OmpR localization in Escherichia coli. Mol Microbiol. 59(6):1767-78 (2006). [Pubmed]


Yoshida T., Cai S., Inouye M. Interaction of EnvZ, a sensory histidine kinase, with phosphorylated OmpR, the cognate response regulator. Mol Microbiol. 46(5):1283-94 (2002). [Pubmed]


Forst S., Delgado J., Inouye M. Phosphorylation of OmpR by the osmosensor EnvZ modulates expression of the ompF and ompC genes in Escherichia coli. Proc Natl Acad Sci U S A. 86(16):6052-6 (1989). [Pubmed]


Egger LA., Inouye M. Purification and characterization of the periplasmic domain of EnvZ osmosensor in Escherichia coli. Biochem Biophys Res Commun. 231(1):68-72 (1997). [Pubmed]


Khorchid A., Inouye M., Ikura M. Structural characterization of Escherichia coli sensor histidine kinase EnvZ: the periplasmic C-terminal core domain is critical for homodimerization. Biochem J. 385(Pt 1):255-64 (2005). [Pubmed]


Nakashima K., Kanamaru K., Aiba H., Mizuno T. Osmoregulatory expression of the porin genes in Escherichia coli: evidence for signal titration in the signal transduction through EnvZ-OmpR phosphotransfer. FEMS Microbiol Lett. 66(1):43-7 (1991). [Pubmed]


Qin L., Dutta R., Kurokawa H., Ikura M., Inouye M. A monomeric histidine kinase derived from EnvZ, an Escherichia coli osmosensor. Mol Microbiol. 36(1):24-32 (2000). [Pubmed]


Kenney LJ. Structure/function relationships in OmpR and other winged-helix transcription factors. Curr Opin Microbiol. 5(2):135-41 (2002). [Pubmed]


Qin L., Yoshida T., Inouye M. The critical role of DNA in the equilibrium between OmpR and phosphorylated OmpR mediated by EnvZ in Escherichia coli. Proc Natl Acad Sci U S A. 98(3):908-13 (2001). [Pubmed]


Garrett S., Taylor RK., Silhavy TJ., Berman ML. Isolation and characterization of delta ompB strains of Escherichia coli by a general method based on gene fusions. J Bacteriol. 162(2):840-4 (1985). [Pubmed]


Nara F., Matsuyama S., Mizuno T., Mizushima S. Molecular analysis of mutant ompR genes exhibiting different phenotypes as to osmoregulation of the ompF and ompC genes of Escherichia coli. Mol Gen Genet. 202(2):194-9 (1986). [Pubmed]


Mizuno T., Mizushima S. Isolation and characterization of deletion mutants of ompR and envZ, regulatory genes for expression of the outer membrane proteins OmpC and OmpF in Escherichia coli. J Biochem (Tokyo). 101(2):387-96 (1987). [Pubmed]


Csonka LN., Hanson AD. Prokaryotic osmoregulation: genetics and physiology. Annu Rev Microbiol. 45:569-606 (1991). [Pubmed]


Maeda S., Takayanagi K., Nishimura Y., Maruyama T., Sato K., Mizuno T. Activation of the osmoregulated ompC gene by the OmpR protein in Escherichia coli: a study involving synthetic OmpR-binding sequences. J Biochem. 110(3):324-7 (1991). [Pubmed]


Huang KJ., Igo MM. Identification of the bases in the ompF regulatory region, which interact with the transcription factor OmpR. J Mol Biol. 262(5):615-28 (1996). [Pubmed]


Yoshida T., Qin L., Egger LA., Inouye M. Transcription regulation of ompF and ompC by a single transcription factor, OmpR. J Biol Chem. 281(25):17114-23 (2006). [Pubmed]


Prigent-Combaret C., Brombacher E., Vidal O., Ambert A., Lejeune P., Landini P., Dorel C. Complex regulatory network controls initial adhesion and biofilm formation in Escherichia coli via regulation of the csgD gene. J Bacteriol. 183(24):7213-23 (2001). [Pubmed]


Vidal O., Longin R., Prigent-Combaret C., Dorel C., Hooreman M., Lejeune P. Isolation of an Escherichia coli K-12 mutant strain able to form biofilms on inert surfaces: involvement of a new ompR allele that increases curli expression. J Bacteriol. 180(9):2442-9 (1998). [Pubmed]


Jubelin G., Vianney A., Beloin C., Ghigo JM., Lazzaroni JC., Lejeune P., Dorel C. CpxR/OmpR interplay regulates curli gene expression in response to osmolarity in Escherichia coli. J Bacteriol. 187(6):2038-49 (2005). [Pubmed]


Hirakawa H., Nishino K., Hirata T., Yamaguchi A. Comprehensive studies of drug resistance mediated by overexpression of response regulators of two-component signal transduction systems in Escherichia coli. J Bacteriol. 185(6):1851-6 (2003). [Pubmed]


Hirakawa H., Nishino K., Yamada J., Hirata T., Yamaguchi A. Beta-lactam resistance modulated by the overexpression of response regulators of two-component signal transduction systems in Escherichia coli. J Antimicrob Chemother. 52(4):576-82 (2003). [Pubmed]


Coyer J., Andersen J., Forst SA., Inouye M., Delihas N. micF RNA in ompB mutants of Escherichia coli: different pathways regulate micF RNA levels in response to osmolarity and temperature change. J Bacteriol. 172(8):4143-50 (1990). [Pubmed]


Yamamoto K., Nagura R., Tanabe H., Fujita N., Ishihama A., Utsumi R. Negative regulation of the bolA1p of Escherichia coli K-12 by the transcription factor OmpR for osmolarity response genes. FEMS Microbiol Lett. 186(2):257-62 (2000). [Pubmed]


Goh EB., Siino DF., Igo MM. The Escherichia coli tppB (ydgR) gene represents a new class of OmpR-regulated genes. J Bacteriol. 186(12):4019-24 (2004). [Pubmed]


Guillier M., Gottesman S. The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator. Nucleic Acids Res. 36(21):6781-94 (2008). [Pubmed]


Brissette RE., Tsung K., Inouye M. Mutations in a central highly conserved non-DNA-binding region of OmpR, an Escherichia coli transcriptional activator, influence its DNA-binding ability. J Bacteriol. 174(15):4907-12 (1992). [Pubmed]


Kato N., Tsuzuki M., Aiba H., Mizuno T. Gene activation by the Escherichia coli positive regulator OmpR: a mutational study of the DNA-binding domain of OmpR. Mol Gen Genet. 248(4):399-406 (1995). [Pubmed]


Kenney LJ., Bauer MD., Silhavy TJ. Phosphorylation-dependent conformational changes in OmpR, an osmoregulatory DNA-binding protein of Escherichia coli. Proc Natl Acad Sci U S A. 92(19):8866-70 (1995). [Pubmed]


Kondo H., Nakagawa A., Nishihira J., Nishimura Y., Mizuno T., Tanaka I. Escherichia coli positive regulator OmpR has a large loop structure at the putative RNA polymerase interaction site. Nat Struct Biol. 4(1):28-31 (1997). [Pubmed]


Martinez-Hackert E., Stock AM. The DNA-binding domain of OmpR: crystal structures of a winged helix transcription factor. Structure. 5(1):109-24 (1997). [Pubmed]


Head CG., Tardy A., Kenney LJ. Relative binding affinities of OmpR and OmpR-phosphate at the ompF and ompC regulatory sites. J Mol Biol. 281(5):857-70 (1998). [Pubmed]


Rhee JE., Sheng W., Morgan LK., Nolet R., Liao X., Kenney LJ. Amino acids important for DNA recognition by the response regulator OmpR. J Biol Chem. 283(13):8664-77 (2008). [Pubmed]


Rampersaud A., Harlocker SL., Inouye M. The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation. J Biol Chem. 269(17):12559-66 (1994). [Pubmed]


Harrison-McMonagle P., Denissova N., Martinez-Hackert E., Ebright RH., Stock AM. Orientation of OmpR monomers within an OmpR:DNA complex determined by DNA affinity cleaving. J Mol Biol. 285(2):555-66 (1999). [Pubmed]


Harlocker SL., Bergstrom L., Inouye M. Tandem binding of six OmpR proteins to the ompF upstream regulatory sequence of Escherichia coli. J Biol Chem. 270(45):26849-56 (1995). [Pubmed]


Mattison K., Oropeza R., Byers N., Kenney LJ. A phosphorylation site mutant of OmpR reveals different binding conformations at ompF and ompC. J Mol Biol. 315(4):497-511 (2002). [Pubmed]


Siryaporn A., Goulian M. Cross-talk suppression between the CpxA-CpxR and EnvZ-OmpR two-component systems in E. coli. Mol Microbiol. 70(2):494-506 (2008). [Pubmed]


Taylor RK., Hall MN., Enquist L., Silhavy TJ. Identification of OmpR: a positive regulatory protein controlling expression of the major outer membrane matrix porin proteins of Escherichia coli K-12. J Bacteriol. 147(1):255-8 (1981). [Pubmed]


Mizuno T., Wurtzel ET., Inouye M. Cloning of the regulatory genes (ompR and envZ) for the matrix proteins of the Escherichia coli outer membrane. J Bacteriol. 150(3):1462-6 (1982). [Pubmed]


Kojetin DJ., Sullivan DM., Thompson RJ., Cavanagh J. Classification of response regulators based on their surface properties. Methods Enzymol. 422:141-69 (2007). [Pubmed]


Mizuno T., Mizushima S. Signal transduction and gene regulation through the phosphorylation of two regulatory components: the molecular basis for the osmotic regulation of the porin genes. Mol Microbiol. 4(7):1077-82 (1990). [Pubmed]


Waukau J., Forst S. Molecular analysis of the signaling pathway between EnvZ and OmpR in Escherichia coli. J Bacteriol. 174(5):1522-7 (1992). [Pubmed]


Kanamaru K., Mizuno T. Signal transduction and osmoregulation in Escherichia coli: a novel mutant of the positive regulator, OmpR, that functions in a phosphorylation-independent manner. J Biochem. 111(4):425-30 (1992). [Pubmed]


Forst SA., Roberts DL. Signal transduction by the EnvZ-OmpR phosphotransfer system in bacteria. Res Microbiol. 145(5-6):363-73 (1994). [Pubmed]


Matsubara M., Mizuno T. EnvZ-independent phosphotransfer signaling pathway of the OmpR-mediated osmoregulatory expression of OmpC and OmpF in Escherichia coli. Biosci Biotechnol Biochem. 63(2):408-14 (1999). [Pubmed]


Matsubara M., Kitaoka SI., Takeda SI., Mizuno T. Tuning of the porin expression under anaerobic growth conditions by his-to-Asp cross-phosphorelay through both the EnvZ-osmosensor and ArcB-anaerosensor in Escherichia coli. Genes Cells. 5(7):555-69 (2000). [Pubmed]


Cai SJ., Inouye M. EnvZ-OmpR interaction and osmoregulation in Escherichia coli. J Biol Chem. 277(27):24155-61 (2002). [Pubmed]


Mattison K., Oropeza R., Kenney LJ. The linker region plays an important role in the interdomain communication of the response regulator OmpR. J Biol Chem. 277(36):32714-21 (2002). [Pubmed]


Yoshida T., Qin L., Inouye M. Formation of the stoichiometric complex of EnvZ, a histidine kinase, with its response regulator, OmpR. Mol Microbiol. 46(5):1273-82 (2002). [Pubmed]


Maris AE., Walthers D., Mattison K., Byers N., Kenney LJ. The response regulator OmpR oligomerizes via beta-sheets to form head-to-head dimers. J Mol Biol. 350(5):843-56 (2005). [Pubmed]
Related annotations: PaperBLAST

	
			


			

				

				
				
				
				

			

			

		

	
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