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Escherichia coli K-12 substr. MG1655 Polypeptide: KdpE transcriptional activator



Gene: kdpE Accession Numbers: EG10517 (EcoCyc), b0694, ECK0682

Synonyms: KdpE response regulator

Regulation Summary Diagram: ?

Alternative forms of KdpE transcriptional activator: KdpE-Phosphorylated

Summary:
KdpE is a transcriptional regulator involved in the regulation of genes involved in a high-affinity potassium (K+) uptake system [Ballal07, Jung02, Altendorf94]. The genes of this system and their regulators are widely distributed among the gram-negative and gram-positive bacteria and archaea [Ballal07]. 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 [Walderhaug92]. 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 [Polarek92]. It has been suggested that sometimes the genes of the two operons are transcribed in only one transcript [Polarek92]. In some species the arrangement of these genes in the genome is different than in Escherichia coli [Ballal07].

KdpD exhibits both kinase and phosphatase activities towards KdpE [Jung97, Brandon00, Jung98]. Under K+-limiting conditions or under osmotic stress imposed by a salt, autophosphorylation of KdpD at His-673 is stimulated [Ballal07, Jung00, Voelkner93]. Subsequently, the phosphate group is transferred from KdpD to Asp-52 of KdpE [Nakashima93, Nakashima92, Jung97], leading to the dimerization and activation of KdpE [ToroRoman05]. At high concentrations of K+, the kinase activity of KdpD is inhibited [Jung00].

Under salt stress, the universal stress protein UspC binds to KdpD and stabilizes the KdpD-KdpE-DNA complex; therefore, this system can be activated even though K+ accumulates under this environmental condition [Heermann09]. 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 [Luttmann09].

KdpE is a member of the OmpR/PhoB subfamily of response regulators [Walderhaug92, Epstein90] and binds a 23-bp recognition sequence [Sugiura92]. The crystal structure of KdpE with and without bound beryllium fluoride has been solved [ToroRoman05].

Overproduction of KdpE causes a drug resistance phenotype [Hirakawa03a].

Citations: [Pao95, Parkinson92, Stock90, Parkinson93]

Locations: cytosol

Map Position: [720,279 <- 720,956] (15.52 centisomes)
Length: 678 bp / 225 aa

Molecular Weight of Polypeptide: 25.362 kD (from nucleotide sequence)

pI: 6.24, 6.38

Unification Links: ASAP:ABE-0002366 , CGSC:31571 , DIP:DIP-10063N , EchoBASE:EB0512 , EcoGene:EG10517 , EcoliWiki:b0694 , ModBase:P21866 , OU-Microarray:b0694 , PortEco:kdpE , PR:PRO_000023053 , Protein Model Portal:P21866 , RegulonDB:EG10517 , SMR:P21866 , String:511145.b0694 , Swiss-Model:P21866 , UniProt:P21866

Relationship Links: InterPro:IN-FAMILY:IPR001789 , InterPro:IN-FAMILY:IPR001867 , InterPro:IN-FAMILY:IPR011006 , InterPro:IN-FAMILY:IPR011991 , PDB:Structure:1ZH2 , PDB:Structure:1ZH4 , PDB:Structure:3ZQ7 , Pfam:IN-FAMILY:PF00072 , Pfam:IN-FAMILY:PF00486 , Prosite:IN-FAMILY:PS50110 , Smart:IN-FAMILY:SM00448 , Smart:IN-FAMILY:SM00862

In Paralogous Gene Group: 121 (40 members) , 182 (3 members)

Reactions known to consume the compound:

KdpDE Two-Component Signal Transduction System, potassium-dependent :
KdpD sensory histidine kinase - phosphorylated[inner membrane] + KdpE → KdpE-Pasp + KdpD[inner membrane]

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0001121 - transcription from bacterial-type RNA polymerase promoter Inferred from experiment [Sugiura92]
GO:0006355 - regulation of transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01, Polarek92]
GO:0000160 - phosphorelay signal transduction system Inferred by computational analysis [UniProtGOA11a, GOA01]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0000986 - bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding Inferred from experiment [Sugiura92]
GO:0001131 - bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity Inferred from experiment [Sugiura92]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Luttmann09, Gao08]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level complex regulation two component regulatory systems (external signal)

DNA binding site length: 12 base-pairs

Symmetry: Inverted Repeat

Essentiality data for kdpE knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Sequence Features

Feature Class Location Citations Comment State
Conserved-Region 1 -> 116
[UniProt09]
UniProt: Response regulatory;
 
4-aspartylphosphate-Modification 52
[UniProt11a]
UniProt: 4-aspartylphosphate; Non-Experimental Qualifier: by similarity.
Unmodified
Sequence-Conflict 160 -> 176
[Walderhaug92, UniProt10]
Alternate sequence: LAVLLNNAGKVLTQRQL → AGRCSTMPEKYSPSGPV; UniProt: (in Ref. 1; AAA24042);
 


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0694 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10517; confirmed by SwissProt match.


References

Altendorf94: 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. PMID: 7855422

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Ballal07: Ballal A, Basu B, Apte SK (2007). "The Kdp-ATPase system and its regulation." J Biosci 32(3);559-68. PMID: 17536175

Brandon00: 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. PMID: 11123681

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Epstein90: 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. PMID: 1970651

Gao08: Gao R, Tao Y, Stock AM (2008). "System-level mapping of Escherichia coli response regulator dimerization with FRET hybrids." Mol Microbiol 69(6);1358-72. PMID: 18631241

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Heermann09: 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. PMID: 19101563

Hirakawa03a: 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. PMID: 12618449

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Jung00: 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. PMID: 11016946

Jung02: 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. PMID: 11931551

Jung97: 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. PMID: 9099740

Jung98: 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. PMID: 9651326

Luttmann09: 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. PMID: 19400808

Nakashima92: 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 1992;6(13);1777-84. PMID: 1630317

Nakashima93: 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 1993;7(1);109-16. PMID: 8437514

Pao95: Pao GM, Saier MH (1995). "Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution." J Mol Evol 1995;40(2);136-54. PMID: 7699720

Parkinson92: Parkinson JS, Kofoid EC (1992). "Communication modules in bacterial signaling proteins." Annu Rev Genet 1992;26;71-112. PMID: 1482126

Parkinson93: Parkinson JS (1993). "Signal transduction schemes of bacteria." Cell 1993;73(5);857-71. PMID: 8098993

Polarek92: 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 1992;174(7);2145-51. PMID: 1532387

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Stock90: Stock JB, Stock AM, Mottonen JM (1990). "Signal transduction in bacteria." Nature 1990;344(6265);395-400. PMID: 2157156

Sugiura92: 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 1992;6(13);1769-76. PMID: 1630316

ToroRoman05: 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. PMID: 16322582

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Voelkner93: 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 1993;217(3);1019-26. PMID: 8223625

Walderhaug92: 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 1992;174(7);2152-9. PMID: 1532388


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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