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KdpE DNA-binding transcriptional activator

Synonyms: KdpE-Phosphorylated, KdpE
Summary:
KdpE is a transcriptional regulator involved in the regulation of genes involved in a high-affinity potassium (K+) uptake system [5, 6, 7] The genes of this system and their regulators are widely distributed among the gram-negative and gram-positive bacteria and archaea [5] KdpE activates expression of the kdpFABC operon encoding the P-type ATPase KdpFABC, a high-affinity potassium transport system.
KdpE belongs to the two-component system KdpD/KdpE [8] The operon containing both genes, kdpE, encoding the response regulator, and kdpD, encoding the sensor kinase, is located next to and in the same direction as an operon (kdpFABC) regulated by KdpE [9] It has been suggested that sometimes the genes of the two operons are transcribed in only one transcript [9] In some species the arrangement of these genes in the genome is different than in Escherichia coli [5]
KdpD exhibits both kinase and phosphatase activities towards KdpE [10, 11, 12] Under K+-limiting conditions or under osmotic stress imposed by a salt, autophosphorylation of KdpD at His-673 is stimulated [5, 13, 14] Subsequently, the phosphate group is transferred from KdpD to Asp-52 of KdpE [10, 15, 16] leading to the dimerization and activation of KdpE [17] At high concentrations of K+, the kinase activity of KdpD is inhibited [13]
Under salt stress, the universal stress protein UspC binds to KdpE and stabilizes the KdpD-KdpE-DNA complex; therefore, this system can be activated even though K+ accumulates under this environmental condition [1] In addition, expression of the kdpFABC operon is regulated by the phosphoryl group transfer chain Ntr-PTS: dephosphorylated enzyme IIANtr binds to KdpD, and this interaction strongly stimulates KdpD kinase activity [18]
KdpE is a member of the OmpR/PhoB subfamily of response regulators [8, 19]and binds a 23-bp recognition sequence [4] The crystal structure of KdpE with and without bound beryllium fluoride has been solved [17]
Overproduction of KdpE causes a drug resistance phenotype [20]
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
KdpE Non-Functional   Apo [BPP], [IEP], [IPI] [1], [2]
KdpE-Phosphorylated Functional Covalent Holo [BPP], [IEP], [IPI] [1], [2]
Evolutionary Family: OmpR
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: kdpE
  Genome position: 721056-721733
  Length: 678 bp / 225 aa
Operon name: kdpDE
TU(s) encoding the TF:
Transcription unit        Promoter
kdpDE
null


Regulon       
Regulated gene(s) kdpA, kdpB, kdpC, kdpF
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
The P-type ATPase (P-ATPase) Superfamily (4)
membrane (3)
Regulated operon(s) kdpFABC
First gene in the operon(s) kdpF
Simple and complex regulons KdpE
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[KdpE,+](1)


Transcription factor binding sites (TFBSs) arrangements       

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  KdpE-Phosphorylated activator kdpFp Sigma70 -63.0 -91.0 kdpF, kdpA, kdpB, kdpC
ttttgccattTTTATACTTTTTTTACAccccgcccgc
728904 728920 [BPP], [GEA], [HIBSCS], [SM] [3], [4]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [BPP] Binding of purified proteins

 [IEP] Inferred from expression pattern

 [IPI] Inferred from physical interaction

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation



Reference(s)    

 [1] Heermann R., Weber A., Mayer B., Ott M., Hauser E., Gabriel G., Pirch T., Jung K., 2009, The universal stress protein UspC scaffolds the KdpD/KdpE signaling cascade of Escherichia coli under salt stress., J Mol Biol. 386(1):134-48

 [2] Yamamoto K., Hirao K., Oshima T., Aiba H., Utsumi R., Ishihama A., 2005, Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli., J Biol Chem. 280(2):1448-56

 [3] Narayanan A., Paul LN., Tomar S., Patil DN., Kumar P., Yernool DA., 2012, Structure-function studies of DNA binding domain of response regulator KdpE reveals equal affinity interactions at DNA half-sites., PLoS One. 7(1):e30102

 [4] Sugiura A., Nakashima K., Tanaka K., Mizuno T., 1992, Clarification of the structural and functional features of the osmoregulated kdp operon of Escherichia coli., Mol Microbiol. 6(13):1769-76

 [5] Ballal A., Basu B., Apte SK., 2007, The Kdp-ATPase system and its regulation., J Biosci. 32(3):559-68

 [6] Jung K., Altendorf K., 2002, Towards an understanding of the molecular mechanisms of stimulus perception and signal transduction by the KdpD/KdpE system of Escherichia coli., J Mol Microbiol Biotechnol. 4(3):223-8

 [7] Altendorf K., Voelkner P., Puppe W., 1994, The sensor kinase KdpD and the response regulator KdpE control expression of the kdpFABC operon in Escherichia coli., Res Microbiol. 145(5-6):374-81

 [8] Walderhaug MO., Polarek JW., Voelkner P., Daniel JM., Hesse JE., Altendorf K., Epstein W., 1992, KdpD and KdpE, proteins that control expression of the kdpABC operon, are members of the two-component sensor-effector class of regulators., J Bacteriol. 174(7):2152-9

 [9] Polarek JW., Williams G., Epstein W., 1992, The products of the kdpDE operon are required for expression of the Kdp ATPase of Escherichia coli., J Bacteriol. 174(7):2145-51

 [10] Jung K., Tjaden B., Altendorf K., 1997, Purification, reconstitution, and characterization of KdpD, the turgor sensor of Escherichia coli., J Biol Chem. 272(16):10847-52

 [11] Brandon L., Dorus S., Epstein W., Altendorf K., Jung K., 2000, Modulation of KdpD phosphatase implicated in the physiological expression of the kdp ATPase of Escherichia coli., Mol Microbiol. 38(5):1086-92

 [12] Jung K., Altendorf K., 1998, Truncation of amino acids 12-128 causes deregulation of the phosphatase activity of the sensor kinase KdpD of Escherichia coli., J Biol Chem. 273(28):17406-10

 [13] Jung K., Veen M., Altendorf K., 2000, K+ and ionic strength directly influence the autophosphorylation activity of the putative turgor sensor KdpD of Escherichia coli., J Biol Chem. 275(51):40142-7

 [14] Voelkner P., Puppe W., Altendorf K., 1993, Characterization of the KdpD protein, the sensor kinase of the K(+)-translocating Kdp system of Escherichia coli., Eur J Biochem. 217(3):1019-26

 [15] Nakashima K., Sugiura A., Kanamaru K., Mizuno T., 1993, Signal transduction between the two regulatory components involved in the regulation of the kdpABC operon in Escherichia coli: phosphorylation-dependent functioning of the positive regulator, KdpE., Mol Microbiol. 7(1):109-16

 [16] Nakashima K., Sugiura A., Momoi H., Mizuno T., 1992, Phosphotransfer signal transduction between two regulatory factors involved in the osmoregulated kdp operon in Escherichia coli., Mol Microbiol. 6(13):1777-84

 [17] Toro-Roman A., Wu T., Stock AM., 2005, A common dimerization interface in bacterial response regulators KdpE and TorR., Protein Sci. 14(12):3077-88

 [18] Luttmann D., Heermann R., Zimmer B., Hillmann A., Rampp IS., Jung K., Gorke B., 2009, Stimulation of the potassium sensor KdpD kinase activity by interaction with the phosphotransferase protein IIA(Ntr) in Escherichia coli., Mol Microbiol. 72(4):978-94

 [19] Epstein W., Walderhaug MO., Polarek JW., Hesse JE., Dorus E., Daniel JM., 1990, The bacterial Kdp K(+)-ATPase and its relation to other transport ATPases, such as the Na+/K(+)- and Ca2(+)-ATPases in higher organisms., Philos Trans R Soc Lond B Biol Sci. 326(1236):479-86: discussion 486-7

 [20] Hirakawa H., Nishino K., Hirata T., Yamaguchi A., 2003, 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



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