Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Novel active site in Escherichia coli fructose 1,6-bisphosphate aldolase

Nature Structural Biology volume 3, pages 856–862 (1996)Cite this article

Abstract

The molecular architecture of the Class II E. coli fructose 1,6-bisphosphate aldolase dimer was determined to 1.6 Å resolution. The subunit fold corresponds to a singly wound α/β-barrel with an active site located on the β-barrel carboxyl side of each subunit. In each subunit there are two mutually exclusive zinc metal ion binding sites, 3.2 Å apart; the exclusivity is mediated by a conformational transition involving side-chain rotations by chelating histidine residues. A binding site for K+ and NH4+ activators was found near the β-barrel centre. Although Class I and Class II aldolases catalyse identical reactions, their active sites do not share common amino acid residues, are structurally dissimilar, and from sequence comparisons appear to be evolutionary distinct.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

References

  1. Horecker, B.L., Tsolas, O. & Lai, C.Y. In The Enzymes 3rd ed. Vol 7 (ed. RD. Boyer) 213–258 (New York: Academic Press, 1972).

    Google Scholar 

  2. Sygusch, J., Beaudry, D. & Allaire, M. Molecular architecture of rabbit skeletal muscle aldolase at 2.7 Å resolution. Proc. Natl. Acad. Sci. USA 84, 7846–7850 (1987).

    Article  CAS  Google Scholar 

  3. Gamblin, S.J. et al. Activity and specificity of human aldolases. J. Molec. Biol. 219, 573–576 (1991).

    Article  CAS  Google Scholar 

  4. Hester, G. et al. The crystal structure of fructose-1,6-bisphosphate aldolase from Drosophila melanogaster at 2.5 Å resolution. FEBS Lett. 292, 237–242 (1991).

    Article  CAS  Google Scholar 

  5. Rutter, W.J. Evolution of aldolase. FASEB. J. 23, 1248–1257 (1964).

    CAS  Google Scholar 

  6. Naismith, J.H. et al. Initiating a crystallographic study of a class II fructose-1,6-bisphosphate aldolase, J. Molec. Biol. 225, 1137–1141 (1992).

    Article  CAS  Google Scholar 

  7. Bergmeyer, H.U. In Methods of Enzymatic Analysis 4 (eds H.U. Bergmeyer & K. Gewahn) 2272–2274 (Weinheim,Verlag Chemie, 1974).

    Google Scholar 

  8. den Hollander, J.A., Brown, T.R., Ugurbil, K. & Shulman, R.G. 13C nuclear magnetic resonance studues of anaerobic glycolysis in suspension of yeast cells. Proc. Natl. Acad. Sci. USA 76, 6096–6100 (1979).

    Article  CAS  Google Scholar 

  9. Lowry, O.H., Carter, J., Ward, J.B. & Galser, L. The effect of carbon and nitorgen sources on the level of metabolic intermediates in Escherichia coli. J. Biol Chem. 246, 6511–6521 (1971).

    CAS  PubMed  Google Scholar 

  10. Ugurbil, K., Brown, T.R., den Hollander, J.A., Glynn, P. & Shulman, R.G. High-resolution 13C nuclear magnetic resonance studies of glucose metabolism in Escherichia coli. Proc. Natl. Acd. Sci. USA 75, 3742–3746 (1978).

    Article  CAS  Google Scholar 

  11. Szwergold, B.S., Ugurbil, K. & Brown, T.R. Propeties of fructose-1,6-bisphosphate aldolase from Escherichia coli: An NMR anlysis. Arch. Biochem. Biophys. 317, 224–252 (1995).

    Article  Google Scholar 

  12. Kitagawa, Y., Leonard, G.A., Harrop, S.J., Peterson, M.R. & Hunter, W.N. Additional crystal forms of the E. coli class II fructose-1,6-bisphosphate aldolase. Acta Crystallogr. D51, 833–834 (1995).

    CAS  Google Scholar 

  13. International Tables for X-ray Crystallography Vol III, 257–259 (Birmingham:TheKynoch Press (IUCR), 1968).

  14. Brünger, A.T. The free R factor value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472–474 (1992).

    Article  Google Scholar 

  15. Richardson, J.S. Describing patterns of protein tertiary structure. Metha. Enzymol. 115, 341–358 (1985).

    Article  CAS  Google Scholar 

  16. Ren, J., Stuart, D.I. & Acharya, K.R. α-Lactalbumin possesses a distinct zinc binding site. J. Biol. Chem. 268, 19292–19298 (1993).

    CAS  PubMed  Google Scholar 

  17. Kobes, R.D., Simpson, R.T., Vallee, B.L. & Rutter, W.J. A functional role of metal ions in class II aldolase. Biochemistry 8, 585–588 (1969).

    Article  CAS  Google Scholar 

  18. Smith, G.M. & Mildvan, A.S. Nuclear magnetic resonance and chemical modification studies of the role of the metal in yeast aldolase Biochemistry 20, 4340–4346 (1981).

    Article  CAS  Google Scholar 

  19. Belasco, J.G. & Knowles, J.R. Polarization of substrate carbonyl groups by yeast aldolase: investigation by Fourier transform infrared spectroscopy Biochemistry 22, 122–129 (1983).

    Article  CAS  Google Scholar 

  20. Baldwin, S.A., Perham, R.N. & Stribling, D. Purification and characterization of the class II D-fructose 1,6-bisphosphate aldolase from Escherichia coli (Crookes'strain), Biochem. J. 169, 633–641 (1978).

    Article  CAS  Google Scholar 

  21. Sobieszek, A. & Bremel, R.D. Preparation and properties of vertebrate smooth-muscle myofibrils and actomyosin. Eur. J. Biochem. 55, 49–60 (1975).

    Article  CAS  Google Scholar 

  22. Takio, K., Blumenthal, D.K., Walsh, K.A., Titani, K. & Krebs, E.G. Amino acid sequence of rabbit skeletal muscle myosin light chain kinase. Biochemistry 25, 8049–8057 (1986).

    Article  CAS  Google Scholar 

  23. Qamar, S., March, K. & Berry, A. Identification of arginine 331 as an important active site residue in the class II fructose-1,6-bisphosphate aldolase of Escherichia coli. Prot. Sci. 5, 154–161 (1996).

    Article  CAS  Google Scholar 

  24. Vallee, B.L. & Auld, D.S. Zinc coordination, function, and structure of zinc enzymes and other proteins. Biochemistry 29, 5647–5659 (1990).

    Article  CAS  Google Scholar 

  25. Chakravarty, S. & Kannan, K.K. Drug-protein interactions. Refined structures of three sulfonamide drug complexes of human carbonic anhydrase I enzyme. J. Molec. Biol. 243, 298–309 (1994).

    Article  CAS  Google Scholar 

  26. Teplyakov, A., Wilson, K.S., Orioli, P. & Mangani, S. The high resolution crystal structure of the complex between carboxypeptidase A and L-phenyl lactate. Acta Crystallogr. D49, 534–540 (1993).

    CAS  Google Scholar 

  27. Dreyer, M.K. & Schulz, G.E. The spatial structure of the class II L-fuculose-1-phosphate aldolase from Escherichia coli. J. Molec. Biol. 231, 549–553 (1993).

    Article  CAS  Google Scholar 

  28. Wilson, D.K., Rudolph, F.B. & Quiocho, F. Atomic structure of adenosine deaminase complex with a transition-state analog: understanding catalysis and immunodeficiency mutations. Science 252, 1278–1284 (1991).

    Article  CAS  Google Scholar 

  29. Jabri, E., Carr, M., Hausinger, R. & Karplus, P.A. The crystal structure of urease from Klebsiella aerogenes. Science 268, 998–1004 (1995).

    Article  CAS  Google Scholar 

  30. Chothia, C. & Lesk, A.M. The relation between the divergence of sequence and structure in proteins, EMBO J. 5, 823–826 (1986).

    Article  CAS  Google Scholar 

  31. Freeze, H & Brock, T.D. Thermostable aldolase from Thermus aquaticus. J. Bact. 101, 541–550 (1970).

    CAS  PubMed  Google Scholar 

  32. Yoshino, M. & Murakami, K. AMP deaminase reaction as a control system of glycolysis in yeast. Role of ammonium ion in the interaction of phosphofructokinase and purivate kinase activity with the adenylate energy charge. J. Biol. Chem. 260, 4729–4732 (1985).

    CAS  PubMed  Google Scholar 

  33. Meury, J. & Kepes, A. The regulation of potassium fluxes for the adjustment and maintenance of potassium levels in Escherichia coli. Eur. J. Biochem. 119, 165–170 (1981).

    Article  CAS  Google Scholar 

  34. Alefounder, P.R., Baldwin, S.A., Perham, R.N. & Short, N.J. Cloning, sequence analysis and over-expression of the gene for the class II fructose 1,6-bisphosphate aldolase from Escherichia coli. Biochem. J. 257, 529–534 (1989).

    Article  CAS  Google Scholar 

  35. Rondeau, J.M. et al. Novel NADPH-binding domain revealed by the crystal structure of aldolase reductase. Nature 355, 469–472 (1992).

    Article  CAS  Google Scholar 

  36. Klein, C. & Schulz, G.E. Structure of cyclodextrin glycosyltransferase refined at 2.0 Å resolution. J. Mol. Biol. 217, 737–750 (1991).

    Article  CAS  Google Scholar 

  37. Rao, V., Guan, C. & van Roey, P. Endo-β-N-acetylglucosaminidase H at 1.9 Å resolution: active site geometry and substrate recognition. Structure 3, 449–457 (1995).

    Article  CAS  Google Scholar 

  38. Lolis, E., Alber, T., Davenport, R.C., Rose, D., Hartman, F.C. & Petsko, G.A. Structure of Yeast triosephosphate isomerase at 1.9 Å resolution. Biochemistry 29, 6609–6618 (1990).

    Article  CAS  Google Scholar 

  39. Farber, G.K. An α/β-barrel full of evolutionary trouble. Curr. Opin. Struct. Biol. 3, 409–412 (1993).

    Article  CAS  Google Scholar 

  40. Howard, A.J., Nielsen, C. & Xuong, N.H. Software for diffractometer with multiwire area detector. Meths. Enzymol. 114, 416–452 (1985).

    Article  Google Scholar 

  41. Reeke, Jr. G.N. The ROCKS system of computer programs for macromolecular crystallography. J.Appl. Crystallogr. 17, 125–130 (1984).

    Article  CAS  Google Scholar 

  42. Jones, T.A. FRODO: A graphics fitting program for macromolecules. In Computing Crystallography. (ed: Sayre D.) 303–317 (Clarendon Press, Oxford, 1982).

    Google Scholar 

  43. Brünger, A.T., Kuriyan, J. & Karplus, M. Crystallographic R-factor refinement by molecular dynamics. Science 235, 458–460 (1987).

    Article  Google Scholar 

  44. Brünger, A.T. X-PLOR Manual, Version 3.1 (Yale University Press, Connecticut, USA, 1992).

    Google Scholar 

  45. The SERC (UK) Collaborative Computing Project no. 4, A suite of programs for protein crystallography, Daresbury Laboratories, Warrington WA4 4AD UK(1979).

  46. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjelgaard, M. Improved methods for the building of protein models in electron density maps and the location of errors in these. Acta Crystallogr. 47, 110–119 (1991).

    Article  Google Scholar 

  47. Kleywegt, G.J. & Jones, T.A. Efficient rebuilding of protein structures. Acta Crystallogr. D52, 829–832 (1996).

    CAS  Google Scholar 

  48. Discover User Guide, version 3.1, (San Diego: Biosym Technologies, 1994).

  49. Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

  50. Merritt, E.A., Murphy, M.E.P. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr. D50, 869–673 (1994).

    CAS  Google Scholar 

  51. Drenth, J. in Principles of protein crystallography (ed. C.R. Cantor) 285–288 (New York: Springer Verlag, 1994).

    Book  Google Scholar 

Download references

Author information

Author notes

  1. René Coulombe

    Present address: Institut de Recherche en Biotechnologie, Conseil de Recherche National du Canada, 6100 Avenue Royalmount, Montréal, Canada, H4P2R2

Authors and Affiliations

  1. Département de biochimie, Université de Montréal, C.P. 6128, Station Centre-ville, Montréal, Canada, H3C 3J7

    Nick S. Blom, Steve Tétreault & Jurgen Sygusch

Authors
  1. Nick S. Blom
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Steve Tétreault
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. René Coulombe
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jurgen Sygusch
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Blom, N., Tétreault, S., Coulombe, R. et al. Novel active site in Escherichia coli fructose 1,6-bisphosphate aldolase. Nat Struct Mol Biol 3, 856–862 (1996). https://doi.org/10.1038/nsb1096-856

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb1096-856

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing