Escherichia coli K-12 substr. MG1655 Enzyme: exopolyphosphatase

Gene: ppx Accession Numbers: EG11403 (EcoCyc), b2502, ECK2498

Regulation Summary Diagram: ?

Regulation summary diagram for ppx

Subunit composition of exopolyphosphatase = [Ppx]2
         exopolyphosphatase monomer = Ppx

Exopolyphosphatase (PPX) degrades inorganic polyphosphates (polyP). It has a strong preference for long-chain polyphosphates; activity decreases with smaller size polyP of about 15 residues. PPX acts on the ends of the polyP chain, removing orthophosphate processively [Akiyama93]. pppGpp is also a substrate for PPX, but GppA is the major source of pppGppase activity in the cell [Kuroda97].

Steady-state levels of polyP are dependent on the level of PPX in the cell [Van97].

Crystal structures of the enzyme have been solved at 1.9 Å [Alvarado06] and 2.2 Å [Rangarajan06] (using E. coli O157:H7, with 100% identical sequence) resolution. The enzyme consists of four domains, with the active site located at the interface between domains I and II. The location of the active site was confirmed by deletions and site-directed mutagenesis [Alvarado06]. The active site region opens to a "canyon" that extends along the dimer interface, which may represent the polyP binding site [Rangarajan06, Alvarado06].

A strain overexpressing ppx together with ppk has increased tolerance to cadmium compared to a strain that only expresses ppk [Keasling96]. A ppx mutant accumulates polyP that is dispersed throughout the cell; under wild type conditions, polyP forms foci primarily at the cell poles. Diffuse polyP localization is correlated with diffuse localization of LtrA, a Group II intron protein, and other basic proteins such as XapR. PolyP can bind to LtrA and inhibit its reverse transcriptase activity [Zhao08].

Citations: [Reizer93]

Gene Citations: [Maciag11]

Locations: cytosol, inner membrane

Map Position: [2,623,137 -> 2,624,678] (56.54 centisomes, 204°)
Length: 1542 bp / 513 aa

Molecular Weight of Polypeptide: 58.136 kD (from nucleotide sequence), 57.0 kD (experimental) [Akiyama93 ]

Molecular Weight of Multimer: 120.0 kD (experimental) [Akiyama93]

pI: 7.07

Unification Links: ASAP:ABE-0008238 , CGSC:32899 , DIP:DIP-29140N , EchoBASE:EB1375 , EcoGene:EG11403 , EcoliWiki:B2502 , Mint:MINT-1285895 , OU-Microarray:b2502 , PortEco:ppx , PR:PRO_000023584 , Pride:P0AFL6 , Protein Model Portal:P0AFL6 , RefSeq:NP_416997 , RegulonDB:EG11403 , SMR:P0AFL6 , String:511145.b2502 , Swiss-Model:P0AFL6 , UniProt:P0AFL6

Relationship Links: InterPro:IN-FAMILY:IPR003695 , InterPro:IN-FAMILY:IPR022371 , PDB:Structure:1U6Z , Pfam:IN-FAMILY:PF02541

In Paralogous Gene Group: 423 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006798 - polyphosphate catabolic process Inferred from experiment [Van97]
Molecular Function: GO:0004309 - exopolyphosphatase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Akiyama93]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: metabolism metabolism of other compounds phosphorous metabolism

Essentiality data for ppx 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]
Yes [Feist07, Comment 4]

Last-Curated ? 08-Jul-2008 by Keseler I , SRI International

Enzymatic reaction of: exopolyphosphatase

Synonyms: metaphosphatase, polyphosphate phosphohydrolase, Pxp

EC Number:

(polyphosphate)(n) + H2O <=> (polyphosphate)(n-1) + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is irreversible in the direction shown.

Alternative Products for long chain polyphosphate: pppGpp [Kuroda97 ]

The Km for pppGpp is 6.7 µM [Kuroda97].

Cofactors or Prosthetic Groups: Mg2+ [Bolesch00, Akiyama93]

Activators (Unknown Mechanism): ammonium sulfate [Akiyama93] , K+ [Akiyama93, Comment 5]

Inhibitors (Competitive): pppGpp [Kuroda97]

Inhibitors (Unknown Mechanism): ppGpp [Kuroda97] , phosphate [Akiyama93]

Primary Physiological Regulators of Enzyme Activity: ppGpp , K+ , phosphate , pppGpp

Kinetic Parameters:

Km (μM)
long chain polyphosphate

T(opt): 37 °C [BRENDA14, Akiyama93]

pH(opt): 7 [BRENDA14, Proudfoot04], 8 [Akiyama93]

Sequence Features

Protein sequence of exopolyphosphatase monomer with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
Chain 2 -> 513
UniProt: Exopolyphosphatase;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b2502 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11403; confirmed by SwissProt match.


Akiyama93: Akiyama M, Crooke E, Kornberg A (1993). "An exopolyphosphatase of Escherichia coli. The enzyme and its ppx gene in a polyphosphate operon." J Biol Chem 1993;268(1);633-9. PMID: 8380170

Alvarado06: Alvarado J, Ghosh A, Janovitz T, Jauregui A, Hasson MS, Sanders DA (2006). "Origin of exopolyphosphatase processivity: Fusion of an ASKHA phosphotransferase and a cyclic nucleotide phosphodiesterase homolog." Structure 14(8);1263-72. PMID: 16905100

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

Bolesch00: Bolesch DG, Keasling JD (2000). "The effect of monovalent ions on polyphosphate binding to Escherichia coli exopolyphosphatase." Biochem Biophys Res Commun 274(1);236-41. PMID: 10903924

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

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

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."

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

Keasling96: Keasling JD, Hupf GA (1996). "Genetic manipulation of polyphosphate metabolism affects cadmium tolerance in Escherichia coli." Appl Environ Microbiol 62(2);743-6. PMID: 8593078

Kuroda97: Kuroda A, Murphy H, Cashel M, Kornberg A (1997). "Guanosine tetra- and pentaphosphate promote accumulation of inorganic polyphosphate in Escherichia coli." J Biol Chem 1997;272(34);21240-3. PMID: 9261133

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Proudfoot04: Proudfoot M, Kuznetsova E, Brown G, Rao NN, Kitagawa M, Mori H, Savchenko A, Yakunin AF (2004). "General enzymatic screens identify three new nucleotidases in Escherichia coli. Biochemical characterization of SurE, YfbR, and YjjG." J Biol Chem 279(52);54687-94. PMID: 15489502

Rangarajan06: Rangarajan ES, Nadeau G, Li Y, Wagner J, Hung MN, Schrag JD, Cygler M, Matte A (2006). "The structure of the exopolyphosphatase (PPX) from Escherichia coli O157:H7 suggests a binding mode for long polyphosphate chains." J Mol Biol 359(5);1249-60. PMID: 16678853

Reizer93: Reizer J, Reizer A, Saier MH, Bork P, Sander C (1993). "Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp 70 superfamily." Trends Biochem Sci 1993;18(7);247-8. PMID: 8212131

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

Van97: Van Dien SJ, Keyhani S, Yang C, Keasling JD (1997). "Manipulation of independent synthesis and degradation of polyphosphate in Escherichia coli for investigation of phosphate secretion from the cell." Appl Environ Microbiol 1997;63(5);1689-95. PMID: 9143103

Zhao08: Zhao J, Niu W, Yao J, Mohr S, Marcotte EM, Lambowitz AM (2008). "Group II intron protein localization and insertion sites are affected by polyphosphate." PLoS Biol 6(6);e150. PMID: 18593213

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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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