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Reversible Inhibition of Escherichia coli Inorganic Pyrophosphatase by Fluoride: Trapped Catalytic Intermediates in Cryo-crystallographic Studies

Samygina, V.R., Moiseev, V.M., Rodina, E.V., Vorobyeva, N.N., Popov, A.N., Kurilova, S.A., Nazarova, T.I., Avaeva, S.M., Bartunik, H.D.·2007·Journal of Molecular Biology
DOI 10.1016/j.jmb.2006.11.082
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Abstract

Here, we describe high-resolution X-ray structures of Escherichia coli inorganic pyrophosphatase (E-PPase) complexed with the substrate, magnesium, or manganese pyrophosphate. The structures correspond to steps in the catalytic synthesis of enzyme-bound pyrophosphate (PP(i)) in the presence of fluoride as an inhibitor of hydrolysis. The catalytic reaction intermediates were trapped applying a new method that we developed for initiating hydrolytic activity in the E-PPase crystal. X-ray structures were obtained for three consecutive states of the enzyme in the course of hydrolysis. Comparative analysis of these structures showed that the Mn2+-supported hydrolysis of the phosphoanhydride bond is followed by a fast release of the leaving phosphate from the P1 site. The electrophilic phosphate P2 is trapped in the "down" conformation. Its movement into the "up" position most likely represents the rate-limiting step of Mn2+-supported hydrolysis. We further determined the crystal structure of the Arg43Gln mutant variant of E-PPase complexed with one phosphate and four Mn ions.

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  • In pyrophosphatase, F− displaces the hydrolytic water in the coordination sphere of the enzyme-bound Mg2+, acting as a transition state analogue of the activated water molecule.

    “For example, in pyrophosphatase, F− displaces the hydrolytic water in the coordination sphere of the enzyme-bound Mg2+, acting as a transition state analogue of the activated water molecule(17, 18) (Figure 2a).”

    From Membrane exporters of fluoride ion (2021) · cites this paper as [17]

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Research works printed but not linked: 20

  1. Marquis, 2003, Fluoride and organic weak acids as modulators of microbial physiology, FEMS Microbiology Rev., 26, 493, 10.1111/j.1574-6976.2003.tb00627.x · DOI · Paper page
  2. Islam, 2003, Inorganic pyrophosphatase in the round worm Ascaris and its role in the development and molting process of the larval stage parasites, Eur. J. Biochem., 270, 2814, 10.1046/j.1432-1033.2003.03658.x · DOI
  3. Baykov, 2000, Fluoride effect along the reaction pathway of pyrophosphatase: evidence for a second enzyme.pyrophosphate intermediate, Biochemistry, 39, 11939, 10.1021/bi000627u · DOI · Paper page
  4. Heikinheimo, 2001, Toward a quantum-mechanical description of metal-assisted phosphoryl transfer in pyrophosphatase, Proc. Natl Acad. Sci. USA, 98, 3121, 10.1073/pnas.061612498 · DOI · Paper page
  5. Samygina, 2000, Improving the X-ray resolution by reversible flash-cooling combined with concentration screening? As axemplified with PPase, Acta Crystallog. sect. D, 65, 595, 10.1107/S0907444900002493 · DOI
  6. Avaeva, 1996, Escherichia coli inorganic pyrophosphatase: site directed mutagenesis of the metal binding sites, FEBS Letters, 399, 99, 10.1016/S0014-5793(96)01296-3 · DOI
  7. Tuominen, 1998, The R78K and D117E active-site variants of Saccharomyces cerevisiae soluble inorganic pyrophosphatase: structural studies and mechanistic implication, J. Mol. Biol., 284, 1565, 10.1006/jmbi.1998.2266 · DOI
  8. Avaeva, 1996, Effect of D42N substitution in Escherichia coli inorganic pyrophosphatase on catalytic activity and Mg2+ binding, FEBS Letters, 392, 91, 10.1016/0014-5793(96)00791-0 · DOI
  9. Zyryanov, 2001, The electrophilic and leaving group phosphates in the catalytic mechanism of yeast pyrophosphatase, J. Biol. Chem., 276, 17629, 10.1074/jbc.M100343200 · DOI
  10. Vainonen, 2001, Some features of hydrolysis of organic and inorganic substrates by Escherichia coli inorganic pyrophosphatase in the presence of various activator cations, Russ. Chem. Bull., 50, 1877, 10.1023/A:1014394415781 · DOI
  11. Avaeva, 1999, Stabilization of the enzyme-substrate compound of the mutant Asp-67Asn inorganic pyrophosphatase from Escherichia coli by fluoride, Biochemistry (Russia), 64, 212
  12. de Grotthuss, 1806, Memoire sur la decompostion de l'eau et des corps qu'elle tient en dissolution a l'aide de l'electricite galvanicue, Ann. Chim., 58, 54
  13. Oganessyan, 1994, X-ray crystallographic studies of recombinant inorganic pyrphosphatase from Escherichia coli, FEBS Letters, 348, 301, 10.1016/0014-5793(94)00605-9 · DOI
  14. Samygina, 2001, The structures of Escherichia coli inorganic pyrophosphatase complexed with Ca2+ or CaPPi at atomic resolution and their mechanistic implications, J. Mol. Biol., 314, 643, 10.1006/jmbi.2001.5149 · DOI
  15. Popov, 2003, Choice of data-collection parameters based on statistic modelling, Acta Crystallog. sect. D, 59, 1145, 10.1107/S0907444903008163 · DOI
  16. Otwinowski, 1997, Processing of X-ray diffraction data collected in oscillation mode, Methods Enzymol., 276, 307, 10.1016/S0076-6879(97)76066-X · DOI · Paper page
  17. Sheldrick, 1997, SHELX: high-resolution refinement, Methods Enzymol., 227, 319, 10.1016/S0076-6879(97)77018-6 · DOI
  18. Laskowski, 1993, PROCHECK: a programm to check the stereochemical quality of orotein structures, J. Appl. Crystallog., 26, 283, 10.1107/S0021889892009944 · DOI · Paper page
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Authors
Samygina, V. R., Moiseev, V. M., Rodina, E. V., Vorobyeva, N. N., Popov, A. N., Kurilova, S. A., Nazarova, T. I., Avaeva, S. M., & Bartunik, H. D.
Venue
Journal of Molecular Biology
Publisher
Elsevier BV
Published
2007-03
Volume
366
Issue
4
Pages
1305-1317
ISSN
0022-2836
DOI
10.1016/j.jmb.2006.11.082
Cited by
50
References
0
Language
en
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)

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