Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 Å resolution: The role of Glu88 in the unique substrate-recognition mechanism

Structure

Volumn 6, Issue 8, 1998, Pages 971-982

  Imada, Katsumi ^a,d   Inagaki, Kenji ^b   Matsunami, Hideyuki ^b   Kawaguchi, Hiroshi ^b   Tanaka, Hidehiko ^b   Tanaka, Nobuo ^c   Namba, Keiichi ^a  

^a ADVANCED TELECOMMUNICATIONS RESEARCH INSTITUTE INTERNATIONAL   (Japan)

^b OKAYAMA UNIVERSITY   (Japan)

^c TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^d JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

3 isopropylmalate dehydrogenase; Conformational change; Substrate binding; X ray crystallography

Indexed keywords

ACIDITHIOBACILLUS FERROOXIDANS; BACTERIA (MICROORGANISMS); HALOTHIOBACILLUS NEAPOLITANUS; THIOBACILLUS;

EID: 0032528935     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(98)00099-9     Document Type: Article

References (37)

1. Tanaka, T., Kawano, N. & Oshima, T. (1981). Cloning of 3-isopropylmalate dehydrogenase gene of an extreme thermophile and partial purification of the gene product. J. Biochem. 89, 677-682.
2. Kagawa, Y., et al., & Oshima, T. (1984). High guanine plus cytosine content in the third letter of codons of an extreme thermophile: DNA sequence of the isopropylmalate dehydrogenase of Thermus thermophilus. J. Biol. Chem. 259, 2956-2960.
3. Oshima, T. (1994). Stabilization of proteins by evolutionary molecular engineering techniques. Curr. Opin. Struct. Biol. 4, 623-628.
4. Imada, K., et al., & Oshima, T. (1991). Three-dimensional structure of a highly thermostable enzyme, 3-isopropylmalate dehydrogenase of Thermus thermophilus. J. Mol. Biol. 222, 725-738.
5. Hurley, J.H., et al., & Stroud, R.M. (1989). Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase. Proc. Natl Acad. Sci. USA 86, 8635-8639.
6. Tipton, P.A. & Beecher, B.S. (1994). Tartrate dehydrogenase, a new member of the family of metal-dependent decarboxylating R-hydroxyacid dehydrogenases. Arch. Biochem. Biophys. 313, 15-21.
7. Miyazaki, K., Kakinuma, K., Terasawa, H. & Oshima, T. (1993). Kinetic analysis on the substrate specificity of 3-isopropylmalate dehydrogenase. FEBS Lett. 332, 35-36.
8. Dean, A.M. & Dvorak, L. (1995). The role of glutamate 87 in the kinetic mechanism of Thermus thermophilus isopropylmalate dehydrogenase. Protein Sci. 4, 2156-2167.
9. Matsunami, H., et al., & Tanaka, H. (1998). 3-Isopropylmalate dehydrogenase from Thiobacillus ferrooxidans: overproduction and substrate specificity. Biosci. Biotech. Biochem. 62, 372-373.
10. Hurley, J.H, Dean, A.M., Sohl, J.L., Koshland, D.E., Jr. & Stroud, R.M. (1990). Regulation of an enzyme by phosphorylation at the active site. Science 249, 1012-1016.
11. + complexes. Biochemistry 30, 8671-8678.
12. Stoddard, B.L., Dean, A.M. & Koshland, D.E., Jr. (1993). Structure of isocitrate dehydrogenase with isocitrate, nicotinamide adenine dinucleotide phosphate, and calcium at 2.5 Å-resolution: a pseudo-Michaelis ternary complex. Biochemistry 32, 9310-9316.
13. Stoddard, B.L & Koshland, D.E., Jr. (1993). Structure of isocitrate dehydrogenase with α-ketoglutarate at 2.7 Å resolution: conformational changes induced by decarboxylation of isocitrate. Biochemistry 32, 9317-9322.
14. Bolduc, J.M., et al., & Stoddard, B.L. (1995). Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase. Science 268, 1312-1318.
15. Mesecar, A.D., Stoddard, B.L. & Koshland, D.E., Jr. (1997). Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences. Science 277, 202-206.
16. Finer-Moore, J., et al., & Stroud, R.M. (1997). Access to phosphorylation in isocitrate dehydrogenase may occur by domain shifting. Biochemistry 36, 13890-13896.
17. Dean, A.M. & Koshland, D.E., Jr. (1990). Electrostatic and steric contributions to regulation at the active site of isocitrate dehydrogenase. Science 249, 1044-1046.
18. Dean, A.M. & Koshland, D.E., Jr. (1993). Kinetic mechanism of Escherichia coli isocitrate dehydrogenase. Biochemistry 32, 9302-9309.
19. +-dependent isocitrate dehydrogenase from Escherichia coli. Biochemistry 34, 378-384.
20. +: ligand-induced loop closing and mechanism for cofactor specificity. Structure 2, 1007-1016.
21. Kadono, S., et al., & Tanaka, N. (1995). Ligand-induced changes in the conformation of 3-isopropylmalate dehydrogenase from Thermus thermophilus. J. Biochem. 118, 745-752.
22. Wallon, G., et al., & Petsko, G.A. (1997). Crystal structure of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus. J. Mol. Biol. 266, 1016-1031.
23. Yaoi, T., Miyazaki, K. & Oshima, T. (1997). Substrate recognition of isocitrate dehydrogenase and 3-isopropylmalate dehydrogenase from Thermus thermophilus HB8. J. Biochem. 121, 77-81.
24. Chen, R., Grobler, J.A. & Dean, A.M. (1996). Second-site suppression of regulatory phosphorylation in Escherichia coli isocitrate dehydrogenase. Protein Sci. 5, 287-295.
25. Inagaki, K., et al., & Tano, T. (1990). Cloning and expression of the Thiobacillus ferrooxidans 3-isopropylmalate dehydrogenase gene in Escherichia coli. J. Ferment. Bioeng. 70, 71-74.
26. Kawaguchi, H., Inagaki, K., Kuwata, Y., Tanaka, H. & Tano, T. (1993). 3-Isopropylmalate dehydrogenase from chemolithoautotroph Thiobacillus ferrooxidans: DNA sequence, enzyme purification, and characterization. J. Biochem. 114, 370-377.
27. Stura, E.A. & Wilson, A. (1992). Seeding techniques. In Crystallization of Nucleic Acids and Proteins: A Practical Approach (Ducruix, A. & Giege, R., eds), pp. 99-126, IRL Press, Oxford.
28. Sato, M., et al., & Higashi, T. (1992). A high-speed data-collection system for large-unit-cell crystals using an imaging plate as a detector. J. Appl. Cryst. 25, 348-357.
29. Higashi, T. (1990). Auto-indexing of oscillation images. J. Appl. Cryst. 23, 253-257.
30. Collaborative Computational Project No.4 (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D 50, 760-763.
31. Navaza, J. (1994). An automated package for molecular replacement. Acta Cryst. A 50, 157-163.
32. Jones, T.A., Zhou, J.Y., Cowan, S.W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A 47, 110-119.
33. Brünger, AT., Kuriyan, J. & Karplus, M. (1987). Crystallographic R factor refinement by molecular dynamics. Science 235, 458-460.
34. Brünger, AT. (1992). Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475.
35. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: program to check the stereochemistry of protein structures. J. Appl. Cryst. 26, 283-291.
36. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.
37. Merritt, E.A. & Murphy, M. (1994). Raster 3D version 2.0: a program for photorealistic molecular graphics. Acta Cryst. D 50, 869-873.