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Analysis of the structure and substrate binding of Phormidium lapideum alanine dehydrogenase

Nature Structural Biology volume 5, pages 561–567 (1998)Cite this article

Abstract

The structure of the hexameric L-alanine dehydrogenase from Phormidium lapideum reveals that the subunit is constructed from two domains, each having the common dinucleotide binding fold. Despite there being no sequence similarity, the fold of alanine dehydrogenase is closely related to that of the family of D-2-hydroxyacid dehydrogenases, with a similar location of the active site, suggesting that these enzymes are related by divergent evolution. L-alanine dehydrogenase and the 2-hydroxyacid dehydrogenases also use equivalent functional groups to promote substrate recognition and catalysis. However, they are arranged differently on the enzyme surface, which has the effect of directing opposite faces of the keto acid to the dinucleotide in each case, forcing a change in absolute configuration of the product.

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Figure 1: Assembly of the hexamer of AlaDH.
Figure 2: The aligned amino acid sequences of the AlaDHs from P. lapideum (Pla), B. stearothermophilus (Bst), M. tuberculosis (Mct), B. sphaericus (Bsp) and B. subtilis (Bsu).
Figure 3: a, The superposition of the structures of the binary complex of AlaDH with NAD+ (green) and the free enzyme (blue) showing the movement of the 238–246, the 266–271 and the 296–299 loops, which occurs on dinucleotide binding.
Figure 4: a, Close ups of the active sites of L-AlaDH, b, L-lactate dehydrogenase (1LDM) and c, D-2-hydroxyisocaproate dehydrogenase (1DXY).

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References

  1. Yoshida, A. & Freese, E. Meth. Enz. 17, 176–181 (1970).

    Article  Google Scholar 

  2. McCowen, S.M. & Phibs Jr, P.V. J. Bacteriol. 118 , 590–597 (1974).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Ohshima, T. & Soda, K. Adv. Biochem. Engineer. Biotechnol. 42, 187–209 ( 1990).

    CAS  Google Scholar 

  4. Vancura, A. et al. Eur. J. Biochem. 179, 221–227 (1989).

    Article  CAS  Google Scholar 

  5. Rowell, P. & Stewart, W.D. P Arch. Microbiol. 107, 115–124 (1976).

    Article  CAS  Google Scholar 

  6. Sawa, Y., Tani, M., Murata, K., Shibata, H. & Ochiai, H. J. Biochem. 116, 995– 1000 (1994).

    Article  CAS  Google Scholar 

  7. Andersen, A.B., Andersen, P. & Ljungqvist, L. Infection Immun. 60, 2317– 2323 (1992).

    CAS  Google Scholar 

  8. Itoh, N. & Morikawa, R. Agric. Biol. Chem. 47, 2511–2519 (1983).

    CAS  Google Scholar 

  9. Vancurova, I. et al. Arch. Microbiol. 150, 438–440 (1988).

    Article  CAS  Google Scholar 

  10. Smith, M.T. & Emerich, D.W. Arch. Biochem. Biophys. 304, 379–385 (1993).

    Article  CAS  Google Scholar 

  11. Porumb, H. et al. J. Biol. Chem. 262, 4610–4615 (1987).

    CAS  PubMed  Google Scholar 

  12. Ohshima, T. & Soda, K. Eur. J. Biochem. 100, 29–39 (1979).

    Article  Google Scholar 

  13. Grimshaw, C.E. & Cleland, W.W. Biochemistry 20, 5650–5655 (1981).

    Article  CAS  Google Scholar 

  14. Grimshaw, C.E, Cook, P.F. & Cleland, W.W. Biochemistry 20, 5655– 5661 (1981).

    Article  CAS  Google Scholar 

  15. Kuroda, S., Tanizawa, K., Sakamoto, Y., Hidehiko, T. & Soda, K. Biochemistry, 29, 1009–1015 (1990).

    Article  CAS  Google Scholar 

  16. Siranosian, K.J., Ireton, K. & Grossmann, A.D. J. Bacteriol. 175, 6789– 6796 (1993).

    Article  CAS  Google Scholar 

  17. Williams, R., Cotton, N.P.J., Thomas, C.M. & Jackson, J.B. Microbiol. 140, 1595–1604 ( 1994).

    Article  CAS  Google Scholar 

  18. Rossmann, M.G., Liljas, A., Branden, C-I. & Banaszak, L.J. In The enzymes, third edition. (ed. Boyer, P.D.) 61– 102 (Academic Press, New York; 1975).

    Google Scholar 

  19. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. J. Appl. Crystallogr. 26, 283– 291 (1993).

    Article  CAS  Google Scholar 

  20. Lee, B. & Richards, F.M J. Mol. Biol. 55, 379–400 (1971).

    Article  CAS  Google Scholar 

  21. Eklund, H & Branden, C.-I. In Coenzymes & cofactors – Pyridine nucleotide coenzymes (eds Dolphin, D., Avramovic, O. & Poulson, R.) 51–98 (J. Wiley, New York; 1987).

    Google Scholar 

  22. Birktoft, J.J & Banasak, L.J. J. Biol. Chem. 258 , 472–282, (1983).

    CAS  PubMed  Google Scholar 

  23. Dunn, C.R. et al. Phil. Trans. R. Soc. London, 332, 177– 181 (1991).

    Article  CAS  Google Scholar 

  24. Grindley, H.M., Artymiuk, P.J., Rice, D.W. & Willett, P. J. Mol. Biol. 229, 707–721 (1993).

    Article  CAS  Google Scholar 

  25. Bernstein, F.C. et al J. Mol. Biol. 112, 535–542 (1977).

    Article  CAS  Google Scholar 

  26. Goldberg, J.D., Yoshida, T. & Brick, P. J. Mol. Biol. 236, 1123– 1140 (1994).

    Article  CAS  Google Scholar 

  27. Lamzin, V.S., Dauter, Z., Popov, V.O., Harutyunyan, E.H. & Wilson, K.S. J. Mol. Biol. 236, 759–764 (1994).

    Article  CAS  Google Scholar 

  28. Schuller, D.J., Grant, G.A. & Banaszak, L.J. Nature Struct. Biol. 2, 69 –76 (1995).

    Article  CAS  Google Scholar 

  29. Dengler, U., Niefind, K., Kiess, M. & Schomburg, D. J. Mol. Biol. 267 640–660 ( 1997).

    Article  CAS  Google Scholar 

  30. Matthews, B.W. & Rossmann, M.G. Meth. Enz. 115, 397–420 (1985).

    Article  CAS  Google Scholar 

  31. Sali, A. & Blundell, T.L. J. Mol. Biol. 212 , 403–428 (1990).

    Article  CAS  Google Scholar 

  32. Baker, P.J., Turnbull, A.P., Sedelnikova, S.E., Stillman, T.J. & Rice, D.W. Structure 3, 693–705 (1995).

    Article  CAS  Google Scholar 

  33. Wright, C.S., Alden, R.A. & Kraut, J. Nature 221, 235–242 (1969).

    Article  CAS  Google Scholar 

  34. Sedelnikova, S.E., Rice, D.W., Shibata, H., Sawa, Y. & Baker, P.J. Acta Crystallogr. D 54, 407 –408 (1998).

    Article  CAS  Google Scholar 

  35. Xuong, N.H., Nielsen, C., Hamlin, R. & Anderson, D. J. Appl. Crystallogr. 18, 324–350 ( 1985).

    Article  Google Scholar 

  36. Collaborative Computing Project no.4. Acta Crystallogr. D50, 760–763 (1994).

  37. Leslie, A.G.W. In Joint CCP4 & ESF-EACBM newsletter on protein crystallography, no.26. (SERC Laboratory, Daresbury, Warrington, WA4 4AD, UK; 1992).

  38. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Acta Crystallogr. A 47, 110–119 ( 1991).

    Article  Google Scholar 

  39. Tronrud, D.E., Ten Eyck, L.F. & Matthews, B.W. Acta Crystallogr. A 43, 489 –501 (1987).

    Article  Google Scholar 

  40. Ferrin, T.E., Huang, C.C., Jarvis, L.E. & Langridge, R. J. Mol. Graphics 6, 13–27 ( 1988).

    Article  CAS  Google Scholar 

  41. Huang, C.C., Pettersen, E.F., Klein, T.E., Ferrin, T.E. & Langridge, R. J. Mol. Graphics 9, 230–236 (1991).

    Article  CAS  Google Scholar 

  42. Enouf, R.M. J. Mol. Graphics 15, 133–138 ( 1997).

    Google Scholar 

  43. Barton, G.J. Prot. Engng . 6, 37–40 ( 1993).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank the BBSRC, The New Energy and Industrial Development Organization, The Wellcome Trust and the British Council/ The Royal Society Anglo-Japanese Scientific Exchange Scheme for financial help. The Krebs Institute is a BBSRC designated Biomolecular Sciences center and a member of the North of England Structural Biology Centre.

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Authors and Affiliations

  1. The Department of Molecular Biology & Biotechnology, The Krebs Institute, The University of Sheffield, Western Bank, S10 2TN, Sheffield, UK

    Patrick J. Baker, Svetlana E. Sedelnikova & David W. Rice

  2. Department of Life Science & Biotechnology, Shimane University, 1060 Nishikawatsu, Matsue, Shimane, 690, Japan

    Yoshihisa Sawa & Hitoshi Shibata

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Correspondence to Patrick J. Baker.

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Baker, P., Sawa, Y., Shibata, H. et al. Analysis of the structure and substrate binding of Phormidium lapideum alanine dehydrogenase. Nat Struct Mol Biol 5, 561–567 (1998). https://doi.org/10.1038/817

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