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. 1995 Jan;4(1):84–92. doi: 10.1002/pro.5560040111

Modeling substrate binding in Thermus thermophilus isopropylmalate dehydrogenase.

T Zhang 1, D E Koshland Jr 1
PMCID: PMC2142962  PMID: 7773180

Abstract

The Thermus thermophilus 3-isopropylmalate dehydrogenase (IPMDH) and Escherichia coli isocitrate dehydrogenase (ICDH) are two functionally and evolutionarily related enzymes with distinct substrate specificities. To understand the determinants of substrate specificities of the two proteins, the substrate and coenzyme in IPMDH were docked into their respective binding sites based on the published structure for apo IPMDH and its sequence and structural homology to ICDH. This modeling study suggests that (1) the substrate and coenzyme (NAD) binding modes of IPMDH are significantly different from those of ICDH, (2) the interactions between the substrates and coenzymes help explain the differences in substrate specificities of IPMDH and ICDH, and (3) binding of the substrate and coenzyme should induce a conformational change in the structure of IPMDH.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Dean A. M., Koshland D. E., Jr Electrostatic and steric contributions to regulation at the active site of isocitrate dehydrogenase. Science. 1990 Aug 31;249(4972):1044–1046. doi: 10.1126/science.2204110. [DOI] [PubMed] [Google Scholar]
  2. Dean A. M., Koshland D. E., Jr Kinetic mechanism of Escherichia coli isocitrate dehydrogenase. Biochemistry. 1993 Sep 14;32(36):9302–9309. doi: 10.1021/bi00087a007. [DOI] [PubMed] [Google Scholar]
  3. Ehrlich R. S., Colman R. F. Histidine in the nucleotide-binding site of NADP-linked isocitrate dehydrogenase from pig heart. Eur J Biochem. 1978 Sep 1;89(2):575–587. doi: 10.1111/j.1432-1033.1978.tb12562.x. [DOI] [PubMed] [Google Scholar]
  4. Eklund H., Samama J. P., Jones T. A. Crystallographic investigations of nicotinamide adenine dinucleotide binding to horse liver alcohol dehydrogenase. Biochemistry. 1984 Dec 4;23(25):5982–5996. doi: 10.1021/bi00320a014. [DOI] [PubMed] [Google Scholar]
  5. Goodsell D. S., Olson A. J. Automated docking of substrates to proteins by simulated annealing. Proteins. 1990;8(3):195–202. doi: 10.1002/prot.340080302. [DOI] [PubMed] [Google Scholar]
  6. Grissom C. B., Cleland W. W. Use of intermediate partitioning to calculate intrinsic isotope effects for the reaction catalyzed by malic enzyme. Biochemistry. 1985 Feb 12;24(4):944–948. doi: 10.1021/bi00325a020. [DOI] [PubMed] [Google Scholar]
  7. Hurley J. H., Dean A. M., Koshland D. E., Jr, Stroud R. M. Catalytic mechanism of NADP(+)-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP+ complexes. Biochemistry. 1991 Sep 3;30(35):8671–8678. doi: 10.1021/bi00099a026. [DOI] [PubMed] [Google Scholar]
  8. Imada K., Sato M., Tanaka N., Katsube Y., Matsuura Y., Oshima T. Three-dimensional structure of a highly thermostable enzyme, 3-isopropylmalate dehydrogenase of Thermus thermophilus at 2.2 A resolution. J Mol Biol. 1991 Dec 5;222(3):725–738. doi: 10.1016/0022-2836(91)90508-4. [DOI] [PubMed] [Google Scholar]
  9. Miyazaki K., Eguchi H., Yamagishi A., Wakagi T., Oshima T. Molecular cloning of the isocitrate dehydrogenase gene of an extreme thermophile, Thermus thermophilus HB8. Appl Environ Microbiol. 1992 Jan;58(1):93–98. doi: 10.1128/aem.58.1.93-98.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Miyazaki K., Kakinuma K., Terasawa H., Oshima T. Kinetic analysis on the substrate specificity of 3-isopropylmalate dehydrogenase. FEBS Lett. 1993 Oct 11;332(1-2):35–36. doi: 10.1016/0014-5793(93)80477-c. [DOI] [PubMed] [Google Scholar]
  11. Miyazaki K., Oshima T. Tyr-139 in Thermus thermophilus 3-isopropylmalate dehydrogenase is involved in catalytic function. FEBS Lett. 1993 Oct 11;332(1-2):37–38. doi: 10.1016/0014-5793(93)80478-d. [DOI] [PubMed] [Google Scholar]
  12. Needleman S. B., Wunsch C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970 Mar;48(3):443–453. doi: 10.1016/0022-2836(70)90057-4. [DOI] [PubMed] [Google Scholar]
  13. Stoddard B. L., Dean A., Koshland D. E., Jr Structure of isocitrate dehydrogenase with isocitrate, nicotinamide adenine dinucleotide phosphate, and calcium at 2.5-A resolution: a pseudo-Michaelis ternary complex. Biochemistry. 1993 Sep 14;32(36):9310–9316. doi: 10.1021/bi00087a008. [DOI] [PubMed] [Google Scholar]

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