메뉴 건너뛰기




Volumn 359, Issue 5, 2006, Pages 1249-1260

The Structure of the Exopolyphosphatase (PPX) from Escherichia coli O157:H7 Suggests a Binding Mode for Long Polyphosphate Chains

Author keywords

E. coli; exopolyphosphatase; polyphosphate; pppGpp; stationary phase

Indexed keywords

ENZYME; EXOPOLYPHOSPHATASE; POLYPHOSPHATE; RIBONUCLEASE H; RNA BINDING PROTEIN; UNCLASSIFIED DRUG;

EID: 33745170717     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.04.031     Document Type: Article
Times cited : (50)

References (50)
  • 1
    • 9244221616 scopus 로고    scopus 로고
    • Inorganic polyphosphate in the origin and survival of species
    • Brown M.R., and Kornberg A. Inorganic polyphosphate in the origin and survival of species. Proc. Natl Acad. Sci. USA 101 (2004) 16085-16087
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 16085-16087
    • Brown, M.R.1    Kornberg, A.2
  • 2
    • 0032836258 scopus 로고    scopus 로고
    • Inorganic polyphosphate: a molecule of many functions
    • Kornberg A., Rao N.N., and Ault-Riche D. Inorganic polyphosphate: a molecule of many functions. Annu. Rev. Biochem. 68 (1999) 89-125
    • (1999) Annu. Rev. Biochem. , vol.68 , pp. 89-125
    • Kornberg, A.1    Rao, N.N.2    Ault-Riche, D.3
  • 3
    • 0023937323 scopus 로고
    • Biological aspects of inorganic polyphosphates
    • Wood H.G., and Clark J.E. Biological aspects of inorganic polyphosphates. Annu. Rev. Biochem. 57 (1988) 235-260
    • (1988) Annu. Rev. Biochem. , vol.57 , pp. 235-260
    • Wood, H.G.1    Clark, J.E.2
  • 4
    • 0028221239 scopus 로고
    • Genetically altered levels of inorganic polyphosphate in Escherichia coli
    • Crooke E., Akiyama M., Rao N.N., and Kornberg A. Genetically altered levels of inorganic polyphosphate in Escherichia coli. J. Biol. Chem. 269 (1994) 6290-6295
    • (1994) J. Biol. Chem. , vol.269 , pp. 6290-6295
    • Crooke, E.1    Akiyama, M.2    Rao, N.N.3    Kornberg, A.4
  • 5
    • 0035958678 scopus 로고    scopus 로고
    • Role of inorganic polyphosphate in promoting ribosomal protein degradation by the Lon protease in E. coli
    • Kuroda A., Nomura K., Ohtomo R., Kato J., Ikeda T., Takiguchi N., Ohtake H., and Kornberg A. Role of inorganic polyphosphate in promoting ribosomal protein degradation by the Lon protease in E. coli. Science 293 (2001) 705-708
    • (2001) Science , vol.293 , pp. 705-708
    • Kuroda, A.1    Nomura, K.2    Ohtomo, R.3    Kato, J.4    Ikeda, T.5    Takiguchi, N.6    Ohtake, H.7    Kornberg, A.8
  • 6
    • 0034712760 scopus 로고    scopus 로고
    • Inorganic polyphosphate is needed for swimming, swarming, and twitching motilities of Pseudomonas aeruginosa
    • Rashid M.H., and Kornberg A. Inorganic polyphosphate is needed for swimming, swarming, and twitching motilities of Pseudomonas aeruginosa. Proc. Natl Acad. Sci. USA 97 (2000) 4885-4890
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 4885-4890
    • Rashid, M.H.1    Kornberg, A.2
  • 8
    • 0037188498 scopus 로고    scopus 로고
    • Inorganic polyphosphate is essential for long-term survival and virulence factors in Shigella and Salmonella spp
    • Kim K.S., Rao N.N., Fraley C.D., and Kornberg A. Inorganic polyphosphate is essential for long-term survival and virulence factors in Shigella and Salmonella spp. Proc. Natl Acad. Sci. USA 99 (2002) 7675-7680
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 7675-7680
    • Kim, K.S.1    Rao, N.N.2    Fraley, C.D.3    Kornberg, A.4
  • 9
    • 10344257548 scopus 로고    scopus 로고
    • Inorganic polyphosphate in Bacillus cereus: motility, biofilm formation, and sporulation
    • Shi X., Rao N.N., and Kornberg A. Inorganic polyphosphate in Bacillus cereus: motility, biofilm formation, and sporulation. Proc. Natl Acad. Sci. USA 101 (2004) 17061-17065
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 17061-17065
    • Shi, X.1    Rao, N.N.2    Kornberg, A.3
  • 10
    • 26444588756 scopus 로고    scopus 로고
    • Inorganic polyphosphate in the social life of Myxococcus xanthus: motility, development, and predation
    • Zhang H., Rao N.N., Shiba T., and Kornberg A. Inorganic polyphosphate in the social life of Myxococcus xanthus: motility, development, and predation. Proc. Natl Acad. Sci. USA 102 (2005) 13416-13420
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 13416-13420
    • Zhang, H.1    Rao, N.N.2    Shiba, T.3    Kornberg, A.4
  • 11
    • 0034462888 scopus 로고    scopus 로고
    • Inorganic polyphosphate in Vibrio cholerae: genetic, biochemical, and physiologic features
    • Ogawa N., Tzeng C.M., Fraley C.D., and Kornberg A. Inorganic polyphosphate in Vibrio cholerae: genetic, biochemical, and physiologic features. J. Bacteriol. 182 (2000) 6687-6693
    • (2000) J. Bacteriol. , vol.182 , pp. 6687-6693
    • Ogawa, N.1    Tzeng, C.M.2    Fraley, C.D.3    Kornberg, A.4
  • 12
    • 0032485896 scopus 로고    scopus 로고
    • Engineering polyphosphate metabolism in Escherichia coli: implications for bioremediation of inorganic contaminants
    • Keasling J.D., Van Dien S.J., and Pramanik J. Engineering polyphosphate metabolism in Escherichia coli: implications for bioremediation of inorganic contaminants. Biotechnol. Bioeng. 58 (1998) 231-239
    • (1998) Biotechnol. Bioeng. , vol.58 , pp. 231-239
    • Keasling, J.D.1    Van Dien, S.J.2    Pramanik, J.3
  • 13
    • 0032552494 scopus 로고    scopus 로고
    • Optimization of polyphosphate degradation and phosphate secretion using hybrid metabolic pathways and engineered host strains
    • Van Dien S.J., and Keasling J.D. Optimization of polyphosphate degradation and phosphate secretion using hybrid metabolic pathways and engineered host strains. Biotechnol. Bioeng. 59 (1998) 754-761
    • (1998) Biotechnol. Bioeng. , vol.59 , pp. 754-761
    • Van Dien, S.J.1    Keasling, J.D.2
  • 14
    • 0141594599 scopus 로고    scopus 로고
    • Inorganic polyphosphate stimulates mammalian TOR, a kinase involved in the proliferation of mammary cancer cells
    • Wang L., Fraley C.D., Faridi J., Kornberg A., and Roth R.A. Inorganic polyphosphate stimulates mammalian TOR, a kinase involved in the proliferation of mammary cancer cells. Proc. Natl Acad. Sci. USA 100 (2003) 11249-11254
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 11249-11254
    • Wang, L.1    Fraley, C.D.2    Faridi, J.3    Kornberg, A.4    Roth, R.A.5
  • 15
    • 14544308372 scopus 로고    scopus 로고
    • Inorganic polyphosphate in Dictyostelium discoideum: influence on development, sporulation, and predation
    • Zhang H., Gomez-Garcia M.R., Brown M.R., and Kornberg A. Inorganic polyphosphate in Dictyostelium discoideum: influence on development, sporulation, and predation. Proc. Natl Acad. Sci. USA 102 (2005) 2731-2735
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 2731-2735
    • Zhang, H.1    Gomez-Garcia, M.R.2    Brown, M.R.3    Kornberg, A.4
  • 16
    • 0035902596 scopus 로고    scopus 로고
    • The endopolyphosphatase gene: essential in Saccharomyces cerevisiae
    • Sethuraman A., Rao N.N., and Kornberg A. The endopolyphosphatase gene: essential in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 98 (2001) 8542-8547
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 8542-8547
    • Sethuraman, A.1    Rao, N.N.2    Kornberg, A.3
  • 17
    • 0025315968 scopus 로고
    • Polyphosphate kinase from Escherichia coli. Purification and demonstration of a phosphoenzyme intermediate
    • Ahn K., and Kornberg A. Polyphosphate kinase from Escherichia coli. Purification and demonstration of a phosphoenzyme intermediate. J. Biol. Chem. 265 (1990) 11734-11739
    • (1990) J. Biol. Chem. , vol.265 , pp. 11734-11739
    • Ahn, K.1    Kornberg, A.2
  • 18
    • 23744488104 scopus 로고    scopus 로고
    • Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis
    • Zhu Y., Huang W., Lee S.S., and Xu W. Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis. EMBO Rep. 6 (2005) 681-687
    • (2005) EMBO Rep. , vol.6 , pp. 681-687
    • Zhu, Y.1    Huang, W.2    Lee, S.S.3    Xu, W.4
  • 19
    • 0027439691 scopus 로고
    • An exopolyphosphatase of Escherichia coli. The enzyme and its ppx gene in a polyphosphate operon
    • Akiyama M., Crooke E., and Kornberg A. An exopolyphosphatase of Escherichia coli. The enzyme and its ppx gene in a polyphosphate operon. J. Biol. Chem. 268 (1993) 633-639
    • (1993) J. Biol. Chem. , vol.268 , pp. 633-639
    • Akiyama, M.1    Crooke, E.2    Kornberg, A.3
  • 20
    • 0034721791 scopus 로고    scopus 로고
    • Polyphosphate binding and chain length recognition of Escherichia coli exopolyphosphatase
    • Bolesch D.G., and Keasling J.D. Polyphosphate binding and chain length recognition of Escherichia coli exopolyphosphatase. J. Biol. Chem. 275 (2000) 33814-33819
    • (2000) J. Biol. Chem. , vol.275 , pp. 33814-33819
    • Bolesch, D.G.1    Keasling, J.D.2
  • 21
    • 0021099181 scopus 로고
    • Guanosine 5′-triphosphate, 3′-diphosphate 5′-phosphohydrolase. Purification and substrate specificity
    • Hara A., and Sy J. Guanosine 5′-triphosphate, 3′-diphosphate 5′-phosphohydrolase. Purification and substrate specificity. J. Biol. Chem. 258 (1983) 1678-1683
    • (1983) J. Biol. Chem. , vol.258 , pp. 1678-1683
    • Hara, A.1    Sy, J.2
  • 22
    • 0027219719 scopus 로고
    • Guanosine pentaphosphate phosphohydrolase of Escherichia coli is a long-chain exopolyphosphatase
    • Keasling J.D., Bertsch L., and Kornberg A. Guanosine pentaphosphate phosphohydrolase of Escherichia coli is a long-chain exopolyphosphatase. Proc. Natl Acad. Sci. USA 90 (1993) 7029-7033
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 7029-7033
    • Keasling, J.D.1    Bertsch, L.2    Kornberg, A.3
  • 23
    • 3142666890 scopus 로고    scopus 로고
    • Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family
    • Kristensen O., Laurberg M., Liljas A., Kastrup J.S., and Gajhede M. Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family. Biochemistry 43 (2004) 8894-8900
    • (2004) Biochemistry , vol.43 , pp. 8894-8900
    • Kristensen, O.1    Laurberg, M.2    Liljas, A.3    Kastrup, J.S.4    Gajhede, M.5
  • 24
    • 0027159053 scopus 로고
    • Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp 70 superfamily
    • Reizer J., Reizer A., Saier Jr. M.H., Bork P., and Sander C. Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp 70 superfamily. Trends Biochem. Sci. 18 (1993) 247-248
    • (1993) Trends Biochem. Sci. , vol.18 , pp. 247-248
    • Reizer, J.1    Reizer, A.2    Saier Jr., M.H.3    Bork, P.4    Sander, C.5
  • 25
    • 1842766260 scopus 로고    scopus 로고
    • Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response
    • Hogg T., Mechold U., Malke H., Cashel M., and Hilgenfeld R. Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response. Cell 117 (2004) 57-68
    • (2004) Cell , vol.117 , pp. 57-68
    • Hogg, T.1    Mechold, U.2    Malke, H.3    Cashel, M.4    Hilgenfeld, R.5
  • 26
    • 0003174053 scopus 로고    scopus 로고
    • The stringent response
    • Neidhart III F.C., Curtiss R., Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W.S., Riley M., Schaechter M., and Umbarger H.E. (Eds), ASM Press, Washington, DC
    • Cashel M., Gentry D.R., Hernandez V.J., and Vinella D. The stringent response. In: Neidhart III F.C., Curtiss R., Ingraham J.L., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W.S., Riley M., Schaechter M., and Umbarger H.E. (Eds). Escherichia coli and Salmonella: Cellular and Molecular Biology (1996), ASM Press, Washington, DC 341-356
    • (1996) Escherichia coli and Salmonella: Cellular and Molecular Biology , pp. 341-356
    • Cashel, M.1    Gentry, D.R.2    Hernandez, V.J.3    Vinella, D.4
  • 27
    • 0035945586 scopus 로고    scopus 로고
    • Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
    • Perna N.T., Plunkett G.I., Blattner F.R., Mau B., and Blattner F.R. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409 (2001) 529-533
    • (2001) Nature , vol.409 , pp. 529-533
    • Perna, N.T.1    Plunkett, G.I.2    Blattner, F.R.3    Mau, B.4    Blattner, F.R.5
  • 28
    • 0025262173 scopus 로고
    • Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure
    • Hendrickson W.A., Horton J.R., and LeMaster D.M. Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 9 (1990) 1665-1672
    • (1990) EMBO J. , vol.9 , pp. 1665-1672
    • Hendrickson, W.A.1    Horton, J.R.2    LeMaster, D.M.3
  • 29
    • 0014432781 scopus 로고
    • Solvent content of protein crystals
    • Matthews B.W. Solvent content of protein crystals. J. Mol. Biol. 33 (1968) 491-497
    • (1968) J. Mol. Biol. , vol.33 , pp. 491-497
    • Matthews, B.W.1
  • 30
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 31
    • 0036006755 scopus 로고    scopus 로고
    • Sine-enhanced Shake-and-Bake: the theoretical basis and applications to Se-atom substructures
    • Xu H., Hauptman H.A., and Weeks C.M. Sine-enhanced Shake-and-Bake: the theoretical basis and applications to Se-atom substructures. Acta Crystallog. sect. D 58 (2002) 90-96
    • (2002) Acta Crystallog. sect. D , vol.58 , pp. 90-96
    • Xu, H.1    Hauptman, H.A.2    Weeks, C.M.3
  • 32
    • 0036848846 scopus 로고    scopus 로고
    • Automated structure solution, density modification and model building
    • Terwilliger T.C. Automated structure solution, density modification and model building. Acta Crystallog. sect. D 58 (2002) 1937-1940
    • (2002) Acta Crystallog. sect. D , vol.58 , pp. 1937-1940
    • Terwilliger, T.C.1
  • 33
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: an automated program for molecular replacement
    • Vagin A., and Teplyakov A. MOLREP: an automated program for molecular replacement. J. Appl. Crystallog. 30 (1997) 1022-1025
    • (1997) J. Appl. Crystallog. , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 34
    • 0032964481 scopus 로고    scopus 로고
    • Automated protein model building combined with iterative structure refinement
    • Perrakis A., Morris R., and Lamzin V.S. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6 (1999) 458-463
    • (1999) Nature Struct. Biol. , vol.6 , pp. 458-463
    • Perrakis, A.1    Morris, R.2    Lamzin, V.S.3
  • 35
    • 0032790081 scopus 로고    scopus 로고
    • XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density
    • McRee D.E. XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125 (1999) 156-165
    • (1999) J. Struct. Biol. , vol.125 , pp. 156-165
    • McRee, D.E.1
  • 36
    • 13244281317 scopus 로고    scopus 로고
    • Coot: model-building tools for molecular graphics
    • Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallog. sect. D 60 (2004) 2126-2132
    • (2004) Acta Crystallog. sect. D , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 37
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D 53 (1997) 240-255
    • (1997) Acta Crystallog. sect. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 38
    • 0000243829 scopus 로고
    • PROCHECK: a program to check the stereochemical quality of protein structures
    • Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26 (1993) 283-291
    • (1993) J. Appl. Crystallog. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 40
    • 0028871926 scopus 로고
    • Dali: a network tool for protein structure comparison
    • Holm L., and Sander C. Dali: a network tool for protein structure comparison. Trends Biochem. Sci. 20 (1995) 478-480
    • (1995) Trends Biochem. Sci. , vol.20 , pp. 478-480
    • Holm, L.1    Sander, C.2
  • 43
    • 0032408864 scopus 로고    scopus 로고
    • The HD domain defines a new superfamily of metal-dependent phosphohydrolases
    • Aravind L., and Koonin E.V. The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem. Sci. 23 (1998) 469-472
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 469-472
    • Aravind, L.1    Koonin, E.V.2
  • 44
    • 0037459257 scopus 로고    scopus 로고
    • Solution NMR structure of ribosome-binding factor A (RbfA), a cold-shock adaptation protein from Escherichia coli
    • Huang Y.J., Swapna G.V., Rajan P.K., Ke H., Xia B., Shukla K., et al. Solution NMR structure of ribosome-binding factor A (RbfA), a cold-shock adaptation protein from Escherichia coli. J. Mol. Biol. 327 (2003) 521-536
    • (2003) J. Mol. Biol. , vol.327 , pp. 521-536
    • Huang, Y.J.1    Swapna, G.V.2    Rajan, P.K.3    Ke, H.4    Xia, B.5    Shukla, K.6
  • 45
    • 33645314652 scopus 로고    scopus 로고
    • Inorganic polyphosphate interacts with ribosomes and promotes translation fidelity in vitro and in vivo
    • McInerney P., Mizutani T., and Shiba T. Inorganic polyphosphate interacts with ribosomes and promotes translation fidelity in vitro and in vivo. Mol. Microbiol. 60 (2006) 438-447
    • (2006) Mol. Microbiol. , vol.60 , pp. 438-447
    • McInerney, P.1    Mizutani, T.2    Shiba, T.3
  • 47
    • 0032522882 scopus 로고    scopus 로고
    • How do kinases transfer phosphoryl groups?
    • Matte A., Tari L.W., and Delbaere L.T. How do kinases transfer phosphoryl groups?. Structure 6 (1998) 413-419
    • (1998) Structure , vol.6 , pp. 413-419
    • Matte, A.1    Tari, L.W.2    Delbaere, L.T.3
  • 48
  • 50
    • 0043123208 scopus 로고    scopus 로고
    • ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins
    • Gouet P., Robert X., and Courcelle E. ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucl. Acids Res. 31 (2003) 3320-3323
    • (2003) Nucl. Acids Res. , vol.31 , pp. 3320-3323
    • Gouet, P.1    Robert, X.2    Courcelle, E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.