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Escherichia coli K-12 substr. MG1655 Protein: KdpD sensory histidine kinase / protein phosphatase



Gene: kdpD Accession Numbers: EG10516 (EcoCyc), b0695, ECK0683

Synonyms: kac

Regulation Summary Diagram: ?

Subunit composition of KdpD sensory histidine kinase / protein phosphatase = [KdpD]2

Alternative forms of KdpD sensory histidine kinase / protein phosphatase: KdpD sensory histidine kinase - phosphorylated (summary available)

Summary:
KdpD is the sensor member of the KdpDE two-component system which responds to changes in internal and/or external potassium ion (K+) concentration and regulates transcription of the kdpFABC operon encoding a K+ transporting ATPase.

Defining the primary stimulus perceived by KdpD has proven contentious. Once suggested to be a sensor for changes in turgor pressure, KdpD appears to actually track changes in K+ concentration [Laimins81, Asha93, Hamann08]. Apparent induction of KdpD function via osmolytes is reconciled with this idea by the fact that internal K+ levels rise in response to osmotic shocks [Puppe96, Nakashima93]. Autophosphorylation activity of KdpD and increased transcription of the kdpFABC operon is stimulated by osmotic shock and inhibited by increased abundance of K+ [Nakashima93, Puppe96, Jung00, Jung01]. Extracellular K+ concentration is sensed by KpdD. A decline in extracellular K+ concentration stimulates expression of the kdpFABC operon [Laermann13].

kdpD was first identified as essential for K+ uptake [Burmeister69].

KdpD is the sensor member of a sensor-effector pair with KdpE [Walderhaug92, Rhoads78a]. Membrane-inserted KdpD autophosphorylates as well as carrying out the phosphorylation and dephosphorylation of KdpE, with phosphorylation increasing in response to higher levels of K+ and Na+ [Nakashima92, Nakashima93, Voelkner93, Jung97]. Reduction in net phosphatase activity and a concomitant increase in phosphorylated KdpE leads to upregulation of kdpFABC transcription [Brandon00]. The phosphatase activity of KdpD requires ATP binding, but not hydrolysis [Jung98]. KdpD activity generally depends on negatively charged membrane phospholipids [Stallkamp99].

KdpD is a transmembrane protein that is catalytically active as a dimer [Heermann98]. KdpD has cytoplasmic amino- and carboxy-terminal regions joined by a transmembrane domain with four transmembrane spans [Zimmann95]. The transmembrane portion of KdpD has been alternately reported to be essential or dispensible for normal protein function [Puppe96, Heermann03]. Sensing and phosphorylation activity have been reported to reside predominantly in the soluble carboxy-terminal domain, with control of the phosphatase/kinase equilibrium provided by arginines within the transmembrane domain [Rothenbucher06, Jung98a]. The amino-terminal domain of KdpD binds ATP and may be required for phosphatase activity [Heermann00, Jung98]. Mutational analysis of the transmembrane domain demonstrates that osmosensing and K+ sensing are separable functions [Stallkamp02]. Additional mutational analyses show that both osmosensing and K+ sensing appear to occur largely in the carboxy-terminal portion of the fourth transmembrane-spanning helix [Zimmann07]. KdpD has also been analyzed by replacing key cysteines [Jung98b].

Binding of the UspC universal stress protein to KdpD enhances the KdpD/KdpE phosphorylation cascade in vitro at K+ concentrations that would otherwise block phosphorylation. This may explain how the Kdp two component system can be activated under conditions of salt stress where K+ levels rise far above the normal range. The UspC protein interacts with a usp domain in the N-terminal region of KdpN and stable complexes of UspC/KdpD/phosphorylated KdpE/DNA have been observed in vitro. In vivo, uspC null mutants show down regulation of KdpFABC production under conditions of salt stress [Heermann09, Heermann09a].

Dephosphorylated PtsN binds to KpdD and activates the KpdDE phosphorelay resulting in increased expression of the high affinity K+ transporter [Luttmann09].

Translocation of KdpD into the membrane is at least partially independent of the normal YidC/Sec translocation system [Facey03]. Membrane insertion of KdpD is dependent on signal recognition particle (SRP) with a short-region in the cytoplasmic domain serving as the SRP binding-domain [Maier08].

The kdpDE operon appears to undergo a substantial amount of "readthrough" transcription from the kdpFABC operon [Polarek92].

Locations: inner membrane

Map Position: [720,953 <- 723,637] (15.54 centisomes)
Length: 2685 bp / 894 aa

Molecular Weight of Polypeptide: 98.718 kD (from nucleotide sequence)

pI: 6.45

Unification Links: ASAP:ABE-0002368 , CGSC:585 , DIP:DIP-10062N , EchoBASE:EB0511 , EcoGene:EG10516 , EcoliWiki:b0695 , ModBase:P21865 , OU-Microarray:b0695 , PortEco:kdpD , PR:PRO_000023052 , Pride:P21865 , Protein Model Portal:P21865 , RegulonDB:EG10516 , SMR:P21865 , String:511145.b0695 , UniProt:P21865

Relationship Links: InterPro:IN-FAMILY:IPR003018 , InterPro:IN-FAMILY:IPR003594 , InterPro:IN-FAMILY:IPR003661 , InterPro:IN-FAMILY:IPR003852 , InterPro:IN-FAMILY:IPR004358 , InterPro:IN-FAMILY:IPR005467 , InterPro:IN-FAMILY:IPR006016 , InterPro:IN-FAMILY:IPR009082 , InterPro:IN-FAMILY:IPR014729 , InterPro:IN-FAMILY:IPR025201 , PDB:Structure:2KSF , Pfam:IN-FAMILY:PF00512 , Pfam:IN-FAMILY:PF00582 , Pfam:IN-FAMILY:PF02518 , Pfam:IN-FAMILY:PF02702 , Pfam:IN-FAMILY:PF13492 , Pfam:IN-FAMILY:PF13493 , Prints:IN-FAMILY:PR00344 , Prosite:IN-FAMILY:PS50109 , Smart:IN-FAMILY:SM00387 , Smart:IN-FAMILY:SM00388

In Paralogous Gene Group: 122 (29 members)

Reactions known to consume the compound:

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

Reactions known to produce 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:0007234 - osmosensory signaling via phosphorelay pathway Inferred from experiment [Nakashima93]
GO:0009593 - detection of chemical stimulus Inferred from experiment [Nakashima93]
GO:0023014 - signal transduction by phosphorylation Inferred by computational analysis Inferred from experiment [Nakashima93, GOA01a]
GO:0046777 - protein autophosphorylation Inferred from experiment [Voelkner93]
GO:0000160 - phosphorelay signal transduction system Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0006950 - response to stress Inferred by computational analysis [GOA01a]
GO:0007165 - signal transduction Inferred by computational analysis [GOA01a]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0018106 - peptidyl-histidine phosphorylation Inferred by computational analysis [GOA01, GOA01a]
Molecular Function: GO:0000155 - phosphorelay sensor kinase activity Inferred from experiment Inferred by computational analysis [GOA01a, Nakashima93]
GO:0004072 - aspartate kinase activity Inferred from experiment [Nakashima93]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Luttmann09]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0004673 - protein histidine kinase activity Inferred by computational analysis [GOA01, GOA01a]
GO:0004871 - signal transducer activity Inferred by computational analysis [GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016772 - transferase activity, transferring phosphorus-containing groups Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Zhang07, Daley05, Walderhaug92]
GO:0031235 - intrinsic component of the cytoplasmic side of the plasma membrane Inferred from experiment [Walderhaug92]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: cell structure membrane
information transfer protein related posttranslational modification
regulation type of regulation posttranscriptional covalent modification, demodification, maturation
regulation type of regulation transcriptional level complex regulation two component regulatory systems (external signal)

Essentiality data for kdpD 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]

Credits:
Last-Curated ? 06-Nov-2007 by Shearer A , SRI International


Sequence Features

Feature Class Location Citations Comment State
Transmembrane-Region 401 -> 423
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: probable;
 
Transmembrane-Region 428 -> 444
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: probable;
 
Transmembrane-Region 446 -> 466
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: probable;
 
Transmembrane-Region 475 -> 498
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: probable;
 
Conserved-Region 670 -> 883
[UniProt09]
UniProt: Histidine kinase;
 
Phosphorylation-Modification 673
[UniProt13]
UniProt: Phosphohistidine; by autocatalysis; Non-Experimental Qualifier: by similarity.
Unmodified


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0695 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10516; confirmed by SwissProt match.


References

Asha93: Asha H, Gowrishankar J (1993). "Regulation of kdp operon expression in Escherichia coli: evidence against turgor as signal for transcriptional control." J Bacteriol 1993;175(14);4528-37. PMID: 8331081

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

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

Burmeister69: Burmeister M (1969). "Chromosomal Location of a Gene Involved in Potassium Ion Uptake in Escherichia coli B." J Bacteriol 100(2);796-802. PMID: 16559072

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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

Facey03: Facey SJ, Kuhn A (2003). "The sensor protein KdpD inserts into the Escherichia coli membrane independent of the Sec translocase and YidC." Eur J Biochem 270(8);1724-34. PMID: 12694185

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, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Hamann08: Hamann K, Zimmann P, Altendorf K (2008). "Reduction of turgor is not the stimulus for the sensor kinase KdpD of Escherichia coli." J Bacteriol 190(7);2360-7. PMID: 18245296

Heermann00: Heermann R, Altendorf K, Jung K (2000). "The hydrophilic N-terminal domain complements the membrane-anchored C-terminal domain of the sensor kinase KdpD of Escherichia coli." J Biol Chem 275(22);17080-5. PMID: 10747873

Heermann03: Heermann R, Fohrmann A, Altendorf K, Jung K (2003). "The transmembrane domains of the sensor kinase KdpD of Escherichia coli are not essential for sensing K+ limitation." Mol Microbiol 47(3);839-48. PMID: 12535080

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

Heermann09a: Heermann R, Lippert ML, Jung K (2009). "Domain swapping reveals that the N-terminal domain of the sensor kinase KdpD in Escherichia coli is important for signaling." BMC Microbiol 9;133. PMID: 19589130

Heermann98: Heermann R, Altendorf K, Jung K (1998). "The turgor sensor KdpD of Escherichia coli is a homodimer." Biochim Biophys Acta 1415(1);114-24. PMID: 9858704

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

Jung01: Jung K, Krabusch M, Altendorf K (2001). "Cs(+) induces the kdp operon of Escherichia coli by lowering the intracellular K(+) concentration." J Bacteriol 183(12);3800-3. PMID: 11371546

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

Jung98a: Jung K, Altendorf K (1998). "Individual substitutions of clustered arginine residues of the sensor kinase KdpD of Escherichia coli modulate the ratio of kinase to phosphatase activity." J Biol Chem 273(41);26415-20. PMID: 9756874

Jung98b: Jung K, Heermann R, Meyer M, Altendorf K (1998). "Effect of cysteine replacements on the properties of the turgor sensor KdpD of Escherichia coli." Biochim Biophys Acta 1372(2);311-22. PMID: 9675324

Laermann13: Laermann V, Cudic E, Kipschull K, Zimmann P, Altendorf K (2013). "The sensor kinase KdpD of Escherichia coli senses external K(+)." Mol Microbiol 88(6);1194-204. PMID: 23651428

Laimins81: Laimins LA, Rhoads DB, Epstein W (1981). "Osmotic control of kdp operon expression in Escherichia coli." Proc Natl Acad Sci U S A 78(1);464-8. PMID: 6787588

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

Maier08: Maier KS, Hubich S, Liebhart H, Krauss S, Kuhn A, Facey SJ (2008). "An amphiphilic region in the cytoplasmic domain of KdpD is recognized by the signal recognition particle and targeted to the Escherichia coli membrane." Mol Microbiol 68(6);1471-84. PMID: 18433452

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, Mizuno T (1993). "Functional reconstitution of the putative Escherichia coli osmosensor, KdpD, into liposomes." J Biochem (Tokyo) 1993;114(4);615-21. PMID: 8276778

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

Puppe96: Puppe W, Zimmann P, Jung K, Lucassen M, Altendorf K (1996). "Characterization of truncated forms of the KdpD protein, the sensor kinase of the K+-translocating Kdp system of Escherichia coli." J Biol Chem 1996;271(40);25027-34. PMID: 8798785

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

Rhoads78a: Rhoads DB, Laimins L, Epstein W (1978). "Functional organization of the kdp genes of Escherichia coli K-12." J Bacteriol 135(2);445-52. PMID: 355227

Rothenbucher06: Rothenbucher MC, Facey SJ, Kiefer D, Kossmann M, Kuhn A (2006). "The cytoplasmic C-terminal domain of the Escherichia coli KdpD protein functions as a K+ sensor." J Bacteriol 188(5);1950-8. PMID: 16484207

Stallkamp02: Stallkamp I, Altendorf K, Jung K (2002). "Amino acid replacements in transmembrane domain 1 influence osmosensing but not K+ sensing by the sensor kinase KdpD of Escherichia coli." Arch Microbiol 178(6);525-30. PMID: 12420175

Stallkamp99: Stallkamp I, Dowhan W, Altendorf K, Jung K (1999). "Negatively charged phospholipids influence the activity of the sensor kinase KdpD of Escherichia coli." Arch Microbiol 172(5);295-302. PMID: 10550471

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 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

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Zimmann07: Zimmann P, Steinbrugge A, Schniederberend M, Jung K, Altendorf K (2007). "The extension of the fourth transmembrane helix of the sensor kinase KdpD of Escherichia coli is involved in sensing." J Bacteriol 189(20);7326-34. PMID: 17704218

Zimmann95: Zimmann P, Puppe W, Altendorf K (1995). "Membrane topology analysis of the sensor kinase KdpD of Escherichia coli." J Biol Chem 270(47);28282-8. PMID: 7499326


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 21, 2014, biocyc14.