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Volumn 375, Issue 5, 2008, Pages 1469-1476

Structure of the PPX/GPPA Phosphatase from Aquifex aeolicus in Complex with the Alarmone ppGpp

Author keywords

Aquifex aeolicus; exopolyphosphatase; guanosine pentaphosphate; stringent response

Indexed keywords

EXOPOLYPHOSPHATASE; GUANOSINE PENTAPHOSPHATE PHOSPHOHYDROLASE; PHOSPHATASE; UNCLASSIFIED DRUG;

EID: 37549035447     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.11.073     Document Type: Article
Times cited : (31)

References (40)
  • 1
    • 0036651767 scopus 로고    scopus 로고
    • The stringent response genes relA and spoT are important for Escherichia coli biofilms under slow-growth conditions
    • Balzer G.J., and McLean R.J. The stringent response genes relA and spoT are important for Escherichia coli biofilms under slow-growth conditions. Can. J. Microbiol. 48 (2002) 675-680
    • (2002) Can. J. Microbiol. , vol.48 , pp. 675-680
    • Balzer, G.J.1    McLean, R.J.2
  • 3
    • 0035958643 scopus 로고    scopus 로고
    • Cell biology. Surviving starvation
    • Gottesman S., and Maurizi M.R. Cell biology. Surviving starvation. Science 293 (2001) 614-615
    • (2001) Science , vol.293 , pp. 614-615
    • Gottesman, S.1    Maurizi, M.R.2
  • 4
    • 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., et al. 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
  • 6
    • 0017757724 scopus 로고
    • Synthesis of guanosine polyphosphates (pppGpp and ppGpp) and its regulation by aminoacyl-tRNA
    • Ogawa Y., and Sy J. Synthesis of guanosine polyphosphates (pppGpp and ppGpp) and its regulation by aminoacyl-tRNA. J. Biochem. (Tokyo) 82 (1977) 947-953
    • (1977) J. Biochem. (Tokyo) , vol.82 , pp. 947-953
    • Ogawa, Y.1    Sy, J.2
  • 8
    • 0035150018 scopus 로고    scopus 로고
    • Regulation of Escherichia coli RelA requires oligomerization of the C-terminal domain
    • Gropp M., Strausz Y., Gross M., and Glaser G. Regulation of Escherichia coli RelA requires oligomerization of the C-terminal domain. J. Bacteriol. 183 (2001) 570-579
    • (2001) J. Bacteriol. , vol.183 , pp. 570-579
    • Gropp, M.1    Strausz, Y.2    Gross, M.3    Glaser, G.4
  • 9
    • 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
  • 10
    • 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
  • 11
    • 0030771435 scopus 로고    scopus 로고
    • Guanosine tetra- and pentaphosphate promote accumulation of inorganic polyphosphate in Escherichia coli
    • Kuroda A., Murphy H., Cashel M., and Kornberg A. Guanosine tetra- and pentaphosphate promote accumulation of inorganic polyphosphate in Escherichia coli. J. Biol. Chem. 272 (1997) 21240-21243
    • (1997) J. Biol. Chem. , vol.272 , pp. 21240-21243
    • Kuroda, A.1    Murphy, H.2    Cashel, M.3    Kornberg, A.4
  • 12
    • 33746826565 scopus 로고    scopus 로고
    • Origin of exopolyphosphatase processivity: fusion of an ASKHA phosphotransferase and a cyclic nucleotide phosphodiesterase homolog
    • Alvarado J., Ghosh A., Janovitz T., Jauregui A., Hasson M.S., and Sanders D.A. Origin of exopolyphosphatase processivity: fusion of an ASKHA phosphotransferase and a cyclic nucleotide phosphodiesterase homolog. Structure 14 (2006) 1263-1272
    • (2006) Structure , vol.14 , pp. 1263-1272
    • Alvarado, J.1    Ghosh, A.2    Janovitz, T.3    Jauregui, A.4    Hasson, M.S.5    Sanders, D.A.6
  • 13
    • 0037168609 scopus 로고    scopus 로고
    • A polyphosphate kinase (PPK2) widely conserved in bacteria
    • Zhang H., Ishige K., and Kornberg A. A polyphosphate kinase (PPK2) widely conserved in bacteria. Proc. Natl Acad. Sci. USA 99 (2002) 16678-16683
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 16678-16683
    • Zhang, H.1    Ishige, K.2    Kornberg, A.3
  • 14
    • 33745170717 scopus 로고    scopus 로고
    • The structure of the exopolyphosphatase (PPX) from Escherichia coli O157:H7 suggests a binding mode for long polyphosphate chains
    • Rangarajan E.S., Nadeau G., Li Y., Wagner J., Hung M.N., Schrag J.D., et al. The structure of the exopolyphosphatase (PPX) from Escherichia coli O157:H7 suggests a binding mode for long polyphosphate chains. J. Mol. Biol. 359 (2006) 1249-1260
    • (2006) J. Mol. Biol. , vol.359 , pp. 1249-1260
    • Rangarajan, E.S.1    Nadeau, G.2    Li, Y.3    Wagner, J.4    Hung, M.N.5    Schrag, J.D.6
  • 16
    • 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
  • 17
  • 18
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 19
    • 0346432073 scopus 로고    scopus 로고
    • Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service
    • Reddy V., Swanson S.M., Segelke B., Kantardjieff K.A., Sacchettini J.C., and Rupp B. Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service. Acta Crystallogr., Sect. D: Biol. Crystallogr. 59 (2003) 2200-2210
    • (2003) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.59 , pp. 2200-2210
    • Reddy, V.1    Swanson, S.M.2    Segelke, B.3    Kantardjieff, K.A.4    Sacchettini, J.C.5    Rupp, B.6
  • 20
    • 0032006209 scopus 로고    scopus 로고
    • Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme
    • Hayward S., and Berendsen H.J.C. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins: Struct. Funct. Genet. 30 (1998) 144-154
    • (1998) Proteins: Struct. Funct. Genet. , vol.30 , pp. 144-154
    • Hayward, S.1    Berendsen, H.J.C.2
  • 21
    • 0026687729 scopus 로고
    • An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins
    • Bork P., Sander C., and Valencia A. An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc. Natl Acad. Sci. USA 89 (1992) 7290-7294
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 7290-7294
    • Bork, P.1    Sander, C.2    Valencia, A.3
  • 22
    • 0035909233 scopus 로고    scopus 로고
    • ATPase activity and conformational changes in the regulation of actin
    • Schuler H. ATPase activity and conformational changes in the regulation of actin. Biochim. Biophys. Acta 1549 (2001) 137-147
    • (2001) Biochim. Biophys. Acta , vol.1549 , pp. 137-147
    • Schuler, H.1
  • 23
    • 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
  • 24
    • 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
  • 25
    • 0028153795 scopus 로고
    • Planar stacking interactions of arginine and aromatic side-chains in proteins
    • Flocco M.M., and Mowbray S.L. Planar stacking interactions of arginine and aromatic side-chains in proteins. J. Mol. Biol. 235 (1994) 709-717
    • (1994) J. Mol. Biol. , vol.235 , pp. 709-717
    • Flocco, M.M.1    Mowbray, S.L.2
  • 26
    • 0036100338 scopus 로고    scopus 로고
    • An improved hydrogen bond potential: impact on medium resolution protein structures
    • Fabiola F., Bertram R., Korostelev A., and Chapman M.S. An improved hydrogen bond potential: impact on medium resolution protein structures. Protein Sci. 11 (2002) 1415-1423
    • (2002) Protein Sci. , vol.11 , pp. 1415-1423
    • Fabiola, F.1    Bertram, R.2    Korostelev, A.3    Chapman, M.S.4
  • 27
    • 0018593773 scopus 로고
    • Regulatory nucleotides involved in the Rel function of Bacillus subtilis
    • Nishino T., Gallant J., Shalit P., Palmer L., and Wehr T. Regulatory nucleotides involved in the Rel function of Bacillus subtilis. J. Bacteriol. 140 (1979) 671-679
    • (1979) J. Bacteriol. , vol.140 , pp. 671-679
    • Nishino, T.1    Gallant, J.2    Shalit, P.3    Palmer, L.4    Wehr, T.5
  • 28
    • 21744436486 scopus 로고    scopus 로고
    • Characterization of disulfide bonds in human nucleoside triphosphate diphosphohydrolase 3 (NTPDase3): implications for NTPDase structural modeling
    • Ivanenkov V.V., Meller J., and Kirley T.L. Characterization of disulfide bonds in human nucleoside triphosphate diphosphohydrolase 3 (NTPDase3): implications for NTPDase structural modeling. Biochemistry 44 (2005) 8998-9012
    • (2005) Biochemistry , vol.44 , pp. 8998-9012
    • Ivanenkov, V.V.1    Meller, J.2    Kirley, T.L.3
  • 29
    • 0017077373 scopus 로고
    • Occurrence of pppApp-synthesizing activity in actinomycetes and isolation of purine nucleotide pyrophosphotransferase
    • Oki T., Yoshimoto A., Ogasawara T., Sato S., and Takamatsu A. Occurrence of pppApp-synthesizing activity in actinomycetes and isolation of purine nucleotide pyrophosphotransferase. Arch. Microbiol. 107 (1976) 183-187
    • (1976) Arch. Microbiol. , vol.107 , pp. 183-187
    • Oki, T.1    Yoshimoto, A.2    Ogasawara, T.3    Sato, S.4    Takamatsu, A.5
  • 30
    • 0016747976 scopus 로고
    • Purine nucleotide pyrophosphotransferase from Streptomyces morookaensis, capable of synthesizing pppApp and pppGpp
    • Oki T., Yoshimoto A., Sato S., and Takamatsu A. Purine nucleotide pyrophosphotransferase from Streptomyces morookaensis, capable of synthesizing pppApp and pppGpp. Biochim. Biophys. Acta 410 (1975) 262-272
    • (1975) Biochim. Biophys. Acta , vol.410 , pp. 262-272
    • Oki, T.1    Yoshimoto, A.2    Sato, S.3    Takamatsu, A.4
  • 32
    • 0027879008 scopus 로고
    • Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants
    • Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26 (1993) 795-800
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 795-800
    • Kabsch, W.1
  • 35
    • 33644872571 scopus 로고    scopus 로고
    • LAFIRE: software for automating the refinement process of protein-structure analysis
    • Yao M., Zhou Y., and Tanaka I. LAFIRE: software for automating the refinement process of protein-structure analysis. Acta Crystallogr., Sect. D: Biol. Crystallogr. 62 (2006) 189-196
    • (2006) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.62 , pp. 189-196
    • Yao, M.1    Zhou, Y.2    Tanaka, I.3
  • 39
    • 0027412196 scopus 로고
    • ALSCRIPT: a tool to format multiple sequence alignments
    • Barton G.J. ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng. 6 (1993) 37-40
    • (1993) Protein Eng. , vol.6 , pp. 37-40
    • Barton, G.J.1
  • 40
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford P.J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 28 (1985) 849-857
    • (1985) J. Med. Chem. , vol.28 , pp. 849-857
    • Goodford, P.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.