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Escherichia coli K-12 substr. MG1655 Polypeptide: K+ transporting ATPase - ATP binding subunit

Gene: kdpB Accession Numbers: EG10514 (EcoCyc), b0697, ECK0685

Synonyms: kac

Regulation Summary Diagram

Regulation summary diagram for kdpB

Component of: K+ transporting ATPase (extended summary available)

Gene Citations: [Nakashima93, Asha93, Hesse84]

Locations: inner membrane

Map Position: [724,211 <- 726,259] (15.61 centisomes, 56°)
Length: 2049 bp / 682 aa

Molecular Weight of Polypeptide: 72.199 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002376, CGSC:587, EchoBASE:EB0509, EcoGene:EG10514, EcoliWiki:b0697, Mint:MINT-8188849, ModBase:P03960, OU-Microarray:b0697, PortEco:kdpB, PR:PRO_000023051, Pride:P03960, Protein Model Portal:P03960, RefSeq:NP_415225, RegulonDB:EG10514, SMR:P03960, String:511145.b0697, UniProt:P03960

Relationship Links: InterPro:IN-FAMILY:IPR001757, InterPro:IN-FAMILY:IPR006391, InterPro:IN-FAMILY:IPR008250, InterPro:IN-FAMILY:IPR018303, InterPro:IN-FAMILY:IPR023214, InterPro:IN-FAMILY:IPR023299, Panther:IN-FAMILY:PTHR24093, PDB:Structure:1SVJ, PDB:Structure:1U7Q, PDB:Structure:2A00, PDB:Structure:2A29, Pfam:IN-FAMILY:PF00122, Pfam:IN-FAMILY:PF00702, Prints:IN-FAMILY:PR00119, Prosite:IN-FAMILY:PS00154

In Paralogous Gene Group: 183 (3 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for kdpB

GO Terms:
Biological Process:
Inferred from experimentInferred by computational analysisGO:0006813 - potassium ion transport [UniProtGOA11a, Becker07a, Buurman95]
Inferred from experimentInferred by computational analysisGO:0071805 - potassium ion transmembrane transport [GOA06, GOA01, GOA01a, Becker07a]
Inferred by computational analysisGO:0006810 - transport [UniProtGOA11a]
Inferred by computational analysisGO:0006811 - ion transport [UniProtGOA11a]
Inferred by computational analysisGO:0008152 - metabolic process [UniProtGOA11a]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Irzik11]
Inferred from experimentInferred by computational analysisGO:0008556 - potassium-transporting ATPase activity [GOA06, GOA01, GOA01a, Becker07a]
Inferred by computational analysisGO:0000166 - nucleotide binding [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0000287 - magnesium ion binding [GOA06]
Inferred by computational analysisGO:0005524 - ATP binding [UniProtGOA11a, GOA06, GOA01a]
Inferred by computational analysisGO:0016787 - hydrolase activity [UniProtGOA11a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a, GOA01a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
Inferred from experimentInferred by computational analysisGO:0016021 - integral component of membrane [UniProtGOA11a, GOA01a, Becker07a]
Inferred by computational analysisGO:0005887 - integral component of plasma membrane [Gaudet10, GOA06]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a]
Inferred by computational analysisGO:0043231 - intracellular membrane-bounded organelle [Gaudet10]

MultiFun Terms: cell structuremembrane
transportChannel-type TransportersPyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active TransportersThe P-type ATPase (P-ATPase) Superfamily

Essentiality data for kdpB knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Subunit of: K+ transporting ATPase

Subunit composition of K+ transporting ATPase = [KdpF][KdpA][KdpB][KdpC]
         K+ transporting ATPase - KdpF subunit = KdpF
         K+ transporting ATPase - K+ channel forming subunit = KdpA
         K+ transporting ATPase - ATP binding subunit = KdpB
         K+ transporting ATPase - KdpC subunit = KdpC

The kdpFABC genes encode an ATP-dependent high affinity P-Type ATPase potassium ion transporter [Siebers88, Siebers89]. The transporter has a high affinity and substrate specificity for potassium ion (Km= 10 μM). It is activated by magnesium ion with an affinity constant of 80 μM [Siebers88]. ATP-driven potassium ion transport has been observed when the Kdp complex is reconstituted in vesicles [Buurman95].

The kdp genes are expressed when growth is limited by the availability of potassium ion [Siebers88]. A decline in extracellular K+ concentration stimulates expression of kdpFABC and kdpFABC expression decreases with increasing extracellular K+ concentration [Laermann13]. The kdp genes are also induced upon exposure to methylglyoxal where they probably act to counter the loss of potassium that occurs due to activation of the Kef potassium efflux systems as a result of methylglyoxal detoxification [Ozyamak13]

Kdp is unusual among P- type ATPases in having three subunits: one for energy coupling (KdpB), one for substrate binding and transport (KdpA), and one for associating the first two subunits together (KdpC) [Buurman95]. The largest subunit, KdpB, is the homologue of other P-type ATPases. Neither of the other two subunits, KdpA or KdpC, has homologues in other P-type ATPases. Mutation experiments have shown that all three subunits are required for normal Kdp activity [Buurman95]. KdpA is highly hydrophobic with many predicted membrane-spanning segments [Buurman95]. The fact that most mutants displaying lower affinity for potassium ion had mutations that altered KdpA implies that KdpA has a major role in determining affinity for potassium ion [Buurman95]. A truncated version of KdpA with only the N-terminal 135 amino acids (which contains two transmembrane segments) is able to rescue a K+ transporter mutant in media with low K+ concentration even without KdpA and KdpB. This is predicted to occur in response to the membrane potential [Sardesai01]. KdpC is predicted to have only a single membrane-spanning segment [Buurman95]. Complementation experiments with complete and truncated KdpC proteins and hybrids as well as sequence analysis of KdpC proteins have identified 4 major parts to the protein. There are two highly conserved regions (regions 2 and 4) and two highly variable regions (1 and 3). Region 1, the N-terminal region, is predicted to be the membrane spanning segment [Gassel01]. Mutational analysis also showed that KdpC is involved in linking KdpA and KdpB together, serving to assemble and stabilize the KdpFABC complex [Gassel98]. A fourth gene on the same operon, kdpF, encodes a small non-essential polypeptide, which was shown by SDS-polyacrylamide gel analysis of the transporter complex to be associated with and stabilize the KdpFABC complex in vivo [Altendorf98, Gassel99].

Two other important potassium ion uptake systems in E. coli include Trk and Kup [Buurman95].

Review: [Greie07]

Enzymatic reaction of: K+ transporting ATPase

Inferred from experiment

EC Number:

Transport reaction diagram for K+ transporting ATPase

Kinetic Parameters:
Substrate Km (μM) Citations
K+ 2.0 [Gassel99, BRENDA14]
K+ 10.0 [Siebers88, BRENDA14]

Sequence Features

Protein sequence of K+ transporting ATPase - ATP binding subunit with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 36 -> 58
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 63 -> 85
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Sequence-Conflict 111 -> 112
Inferred by curator[Hesse84, UniProt15]
UniProt: (in Ref. 1; AAB96336).
Transmembrane-Region 220 -> 242
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 252 -> 274
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Active-Site 307
Inferred by computational analysis[UniProt15]
UniProt: 4-aspartylphosphate intermediate.
Metal-Binding-Site 518
Inferred by computational analysis[UniProt15]
UniProt: Magnesium.
Metal-Binding-Site 522
Inferred by computational analysis[UniProt15]
UniProt: Magnesium.
Transmembrane-Region 578 -> 600
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 615 -> 634
Inferred by computational analysis[UniProt15]
UniProt: Helical.
Transmembrane-Region 654 -> 676
Inferred by computational analysis[UniProt15]
UniProt: Helical.

Sequence Pfam Features

Protein sequence of K+ transporting ATPase - ATP binding subunit with features indicated

Feature Class Location Citations Comment
Pfam PF00122 72 -> 296
Inferred by computational analysis[Finn14]
E1-E2_ATPase : E1-E2 ATPase
Pfam PF00702 301 -> 530
Inferred by computational analysis[Finn14]
Hydrolase : haloacid dehalogenase-like hydrolase

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram


10/20/97 Gene b0697 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10514; confirmed by SwissProt match.


Altendorf98: Altendorf K, Gassel M, Puppe W, Mollenkamp T, Zeeck A, Boddien C, Fendler K, Bamberg E, Drose S (1998). "Structure and function of the Kdp-ATPase of Escherichia coli." Acta Physiol Scand Suppl 1998;643;137-46. PMID: 9789555

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

Becker07a: Becker D, Fendler K, Altendorf K, Greie JC (2007). "The conserved dipole in transmembrane helix 5 of KdpB in the Escherichia coli KdpFABC P-type ATPase is crucial for coupling and the electrogenic K+-translocation step." Biochemistry 46(48);13920-8. PMID: 17994765

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Buurman95: Buurman ET, Kim KT, Epstein W (1995). "Genetic evidence for two sequentially occupied K+ binding sites in the Kdp transport ATPase." J Biol Chem 1995;270(12);6678-85. PMID: 7896809

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

Gassel01: Gassel M, Altendorf K (2001). "Analysis of KdpC of the K(+)-transporting KdpFABC complex of Escherichia coli." Eur J Biochem 268(6);1772-81. PMID: 11248697

Gassel98: Gassel M, Siebers A, Epstein W, Altendorf K (1998). "Assembly of the Kdp complex, the multi-subunit K+-transport ATPase of Escherichia coli." Biochim Biophys Acta 1998;1415(1);77-84. PMID: 9858692

Gassel99: Gassel M, Mollenkamp T, Puppe W, Altendorf K (1999). "The KdpF subunit is part of the K(+)-translocating Kdp complex of Escherichia coli and is responsible for stabilization of the complex in vitro." J Biol Chem 1999;274(53);37901-7. PMID: 10608856

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Greie07: Greie JC, Altendorf K (2007). "The K+-translocating KdpFABC complex from Escherichia coli: a P-type ATPase with unique features." J Bioenerg Biomembr 39(5-6);397-402. PMID: 18058005

Hesse84: Hesse JE, Wieczorek L, Altendorf K, Reicin AS, Dorus E, Epstein W (1984). "Sequence homology between two membrane transport ATPases, the Kdp-ATPase of Escherichia coli and the Ca2+-ATPase of sarcoplasmic reticulum." Proc Natl Acad Sci U S A 81(15);4746-50. PMID: 6146979

Irzik11: Irzik K, Pfrotzschner J, Goss T, Ahnert F, Haupt M, Greie JC (2011). "The KdpC subunit of the Escherichia coli K+-transporting KdpB P-type ATPase acts as a catalytic chaperone." FEBS J 278(17);3041-53. PMID: 21711450

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

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

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

Ozyamak13: Ozyamak E, de Almeida C, de Moura AP, Miller S, Booth IR (2013). "Integrated stress response of Escherichia coli to methylglyoxal: transcriptional readthrough from the nemRA operon enhances protection through increased expression of glyoxalase I." Mol Microbiol 88(5);936-50. PMID: 23646895

Rhoads78: 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

Sardesai01: Sardesai AA, Gowrishankar J (2001). "Improvement in K+-limited growth rate associated with expression of the N-terminal fragment of one subunit (KdpA) of the multisubunit Kdp transporter in Escherichia coli." J Bacteriol 183(11);3515-20. PMID: 11344160

Siebers88: Siebers A, Altendorf K (1988). "The K+-translocating Kdp-ATPase from Escherichia coli. Purification, enzymatic properties and production of complex- and subunit-specific antisera." Eur J Biochem 1988;178(1);131-40. PMID: 2849541

Siebers89: Siebers A, Altendorf K (1989). "Characterization of the phosphorylated intermediate of the K+-translocating Kdp-ATPase from Escherichia coli." J Biol Chem 1989;264(10);5831-8. PMID: 2522440

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." 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."

Other References Related to Gene Regulation

Narayanan12: 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. PMID: 22291906

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

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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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