Crystal structure of 2-oxoisovalerate and dehydrogenase and the architecture of 2-oxo acid dehydrogenase multienzyme complexes (original) (raw)

References

1. Reed, L.J. Multienzyme complexes. Accounts Chem. Res. 7, 40–46 (1974).
   Article CAS Google Scholar
2. Perham, R.N. Domains, motifs, and linkers in 2-oxo acid dehydrogenase multienzyme complexes: a paradigm in the design of a multifunctional protein. Biochemistry 30, 8501–8512 ( 1991).
   Article CAS Google Scholar
3. Izard, T. et al. Principles of quasi-equivalence and Euclidean geometry govern the assembly of cubic and dodecahedral cores of pyruvate dehydrogenase complexes. Proc. Natl. Acad. Sci. USA 96, 1240– 1245 (1999).
   Article CAS Google Scholar
4. Patel, M.S. & Roche, T.M. Molecular biology and biochemistry of pyruvate dehydrogenase complexes. FASEB J. 4, 3224–3233 (1990).
   Article CAS Google Scholar
5. Wynn, R.M., Davie, J.R., Meng, M. & Chuang, D.T. In Alpha-keto acid dehydrogenase complexes (eds Patel, M.S., Roche, T.E. & Harris, R.A.) 101–117 (Birkhäuser Verlag, Basel; 1996).
   Book Google Scholar
6. Chuang, D.T. & Shih, V.E. In The metabolic and molecular bases of inherited disease (eds Scriver, C.R., Beudet, A.L., Sly, W.S. & Valle, D.) 1239–1227 (McGraw-Hill, New York; 1995).
   Google Scholar
7. Kerr, D.S., Wexler, I.D., Tripatara, A. & Patel, M.S. In Alpha-keto acid dehydrogenase complexes. (eds Patel, M.S., Roche, T.E. & Harris, R.A.) 249–267 (Birkhäuser Verlag, Basel; 1996).
   Book Google Scholar
8. Massey, L.K., Sokatch, J.R., & Conrad, R.S. Branched-chain amino acid catabolism in bacteria. Bacteriol. Rev. 40, 42– 54 (1976).
   CAS PubMed PubMed Central Google Scholar
9. Hawkins, C.F., Borges, A. & Perham, R.N. A common structural motif in thiamin pyrophosphate-binding enzymes. FEBS Lett. 255, 77– 82 (1989).
   Article CAS Google Scholar
10. Perham, R.N. & Packman, L.C. 2-Oxo acid dehydrogenase multienzyme complexes: domains, dynamics and design. Ann. N.Y. Acad. Sci. 573, 1–20 (1989).
    Article CAS Google Scholar
11. Burns, G., Brown, T., Hatter, K., Idriss, J.M. & Sokatch, J.R. Similarity of the E1 subunits of branched-chain-oxoacid dehydrogenase from Pseudomonas putida to the corresponding subunits of mammalian branched-chain-oxoacid and pyruvate dehydrogenases. Eur. J. Biochem. 176, 311–317 (1988).
    Article CAS Google Scholar
12. Nikkola, M., Lindqvist, Y. & Schneider, G. Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 Å resolution. J. Mol. Biol. 238, 387–404 (1994).
    Article CAS Google Scholar
13. Muller, Y.A. et al. A thiamin diphosphate binding fold revealed by comparison of the crystal structures of transketolase, pyruvate oxidase and pyruvate decarboxylase. Structure 1, 95– 103 (1993).
    Article CAS Google Scholar
14. Hasson, M.S. et al. The crystal structure of benzoylformate decarboxylase at 1.6 Å resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes. Biochemistry 37, 9918– 9930 (1998).
    Article CAS Google Scholar
15. Chabrière, E., Charon, M.-H., Volbeda, A., Pieulle, L., Hatchikian, E.C. & Fontecilla-Camps, J.-C. Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate. Nature Struct. Biol. 6, 182– 190 (1999).
    Article Google Scholar
16. Sundström, M., Lindqvist, Y., Schneider, G., Hellman, U. & Ronne, H. Yeast TKL1 gene encodes a transketolase that is required for efficient glycolysis and biosynthesis of aromatic amino acids. J. Biol. Chem. 268, 24346– 24352 (1993).
    PubMed Google Scholar
17. Schneider, G. & Lindqvist, Y. Crystallography and mutagenesis of transketolase: mechanistic implications for enzymatic thiamin catalysis. Biochim. Biophys. Acta 1385, 387– 398 (1998).
    Article CAS Google Scholar
18. Guo, F., Zhang, D., Kahyaoglu, A., Farid, R.S. & Jordan, F. Is a hydrophobic amino acid required to maintain the reactive V conformation of thiamin at the active center of thiamin diphosphate-requiring enzymes? Experimental and computational studies of isoleucine 415 of yeast pyruvate decarboxylase. Biochemistry 37, 13379–13391 (1998).
    Article CAS Google Scholar
19. Schellenberger, A. Sixty years of thiamin diphosphate biochemistry. Biochim. Biophys. Acta 1385, 177–186 ( 1998).
    Article CAS Google Scholar
20. Hübner, G. et al. Activation of thiamin diphosphate in enzymes. Biochim. Biophys. Acta 1385, 221–228 (1998).
    Article Google Scholar
21. Harris, R.A., Paxton, R. & DePaoli-Roach, A.A. Inhibition of branched chain α-ketoacid dehydrogenase kinase activity by α-chloroisocaproate. J. Biol. Chem. 257, 13915–13918 (1982).
    CAS PubMed Google Scholar
22. Bürgi, H.B., Dunitz, J.D., Lehn, J.M. & Wipff, G. Stereochemistry of reaction paths at carbonyl centres. Tetrahedron 30, 1563–1572 (1974).
    Article Google Scholar
23. Hawes, J.W. et al. Roles of amino acid residues surrounding phosphorylation site 1 of branched-chain α-ketoacid dehydrogenase (BCKDH) in catalysis and phophorylation site recognition by BCKDH kinase. J. Biol. Chem. 270, 31071–31076 ( 1995).
    Article CAS Google Scholar
24. Hester, K., Luo, J., Burns, G., Braswell, E.H. & Sokatch, J.R. Purification of active E1α2β 2 of Pseudomonas putida branched-chain-oxoacid dehydrogenase. Eur. J. Biochem. 233, 828– 836 (1995).
    Article CAS Google Scholar
25. Korotchkina, L.G., Ali, M.S. & Patel, M.S. In Alpha-keto acid dehydrogenase complexes (eds Patel, M.S., Roche, T.E. & Harris, R.A.) 17–32 (Birkhäuser Verlag, Basel; 1996).
    Book Google Scholar
26. Berg, A. & de Kok, A. 2-Oxo acid dehydrogenase multienzyme complexes. The central role of the lipoyl domain. Biol. Chem. 378, 617–634 (1997).
    CAS PubMed Google Scholar
27. Pan, K. & Jordan, F. D,L-_S_-Methyllipoic acid methyl ester, a kinetically viable model for _S_-protonated lipoic acid as the oxidizing agent in reductive acyl transfers catalyzed by the 2-oxoacid dehydrogenase multienzyme complexes. Biochemistry 37, 1357–1364 (1998).
    Article CAS Google Scholar
28. Yang, Y.S. & Frey, P.A. Dihydrolipoyl transacetylase of Escherichia coli. Formation of 8-S-acetyldihydrolipoamide. Biochemistry 25, 8173–8178 (1986).
    Article CAS Google Scholar
29. Perham, R.N. In Alpha-keto acid dehydrogenase complexes (eds Patel, M.S., Roche, T.E. & Harris, R.A.) 1–15 (Birkhäuser Verlag, Basel; 1996).
    Book Google Scholar
30. Wynn, R.M. et al. Cloning and expression in Escherichia coli of mature _E_1β subunit of bovine mitochondrial branched-chain α-keto acid dehydrogenase complex. J. Biol. Chem. 267, 1881–1887 (1992).
    CAS PubMed Google Scholar
31. Mande, S.S., Sarfaty, S., Allen, M.D., Perham, R.N. & Hol, W.G.J. Protein–protein interactions in the pyruvate dehydrogenase multienzyme complex: dihydrolipoamide dehydrogenase complexed with the binding domain of dihydrolipoamide acetyltransferase. Structure 4, 277–286 (1996).
    Article CAS Google Scholar
32. Mattevi, A. et al. Atomic structure of the cubic core of the pyruvate dehydrogenase multienzyme complex. Science 255, 1544– 1550 (1992).
    Article CAS Google Scholar
33. Mattevi, A., Obmolova, G., Sokatch, J.R., Betzel, C. & Hol, W.G.J. The refined crystal structure of Pseudomonas putida lipoamide dehydrogenase complexed with NAD+ at 2.45 Å resolution. Proteins 13, 336–351 (1992).
    Article CAS Google Scholar
34. Kalia, Y.N. et al. The high-resolution structure of the peripheral subunit-binding domain of dihydrolipoamide acetyltransferase from the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. J. Mol. Biol. 230, 323–341 ( 1993).
    Article CAS Google Scholar
35. Dardel, F., Davis, A.L., Laue, E.D. & Perham, R.N. Three-dimensional structure of the lipoyl domain from Bacillus stearothermophilus pyruvate dehydrogenase multienzyme complex. J. Mol. Biol. 229 , 1037–1048 (1993).
    Article CAS Google Scholar
36. Mattevi, A., Obmolova, G., Kalk, K.H., Teplyakov, A. & Hol, W.G.J. Crystallographic analysis of substrate binding and catalysis in dihydrolipoyl transacetylase. Biochemistry 32, 3887–3901 (1993).
    Article CAS Google Scholar
37. Bagdasarian, M.M. et al. Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas. Gene 16, 237–247 (1981).
    Article CAS Google Scholar
38. Sykes, P.J., Menard, J., McCully, V. & Sokatch, J.R. Conjugative mapping of pyruvate, 2-ketoglutarate, and branched-chain keto acid dehydrogenase genes in Pseudomonas putida mutants. J. Bacteriol. 162, 203–208 (1985).
    CAS PubMed PubMed Central Google Scholar
39. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 277, 307–326 ( 1997).
    Article Google Scholar
40. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 ( 1994).
41. Navazza, J. AMoRe, an automated package for molecular replacement. Acta Crystallogr. A 50, 157–163 ( 1994).
    Article Google Scholar
42. de La Fortelle, E. & Bricogne, G. Maximum-likelihood heavy-atom parameter refinement in the MIR and MAD methods. Methods Enzymol. 276, 472–494 (1997).
    Article CAS Google Scholar
43. Abrahams, J.P. & Leslie, A.G.W. Methods used in the structure determination of bovine mitochondral F1 ATPase. Acta Crystallogr. D 52, 30– 42 (1996).
    Article CAS Google Scholar
44. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).
    Article Google Scholar
45. Brünger, A.T., Krukowski, A. & Erickson, J.W. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallogr. A 46, 585–593 (1990).
    Article Google Scholar
46. Brünger, A.T., et al. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998).
    Article Google Scholar
47. 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
48. Esnouf, R.M. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J. Mol. Graph. 15, 132–134 (1997).
    Article CAS Google Scholar
49. Nicholls, A., Shar, K.A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Gen. 11, 282–296 (1991).
    Article Google Scholar
50. Merritt, E.A. & Murphy, M.E.P. Raster3D Version 2.0—a program for photorealistic molecular graphics. Acta Crystallogr. D 50, 869–873 ( 1994).
    Article CAS Google Scholar

Download references