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Millisecond Laue structures of an enzyme–product complex using photocaged substrate analogs

Nature Structural Biology volume 5, pages 891–897 (1998)Cite this article

Abstract

The structure of a rate-limited product complex formed during a single initial round of turnover by isocitrate dehydrogenase has been determined. Photolytic liberation of either caged substrate or caged cofactor and Laue X-ray data collection were used to visualize the complex, which has a minimum half-life of approximately 10 milliseconds. The experiment was conducted with three different photoreactive compounds, each possessing a unique mechanism leading to the formation of the enzyme–substrate (ES) complex. Photoreaction efficiency and subsequent substrate affinities and binding rates in the crystal are critical parameters for these experiments. The structure suggests that CO2 dissociation is a rapid event that may help drive product formation, and that small conformational changes may contribute to slow product release .

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Figure 1: a, General kinetic mechanism of isocitrate dehdyrogenase.
Figure 2: Chemical structures of the three caged substrate analogs used in this study.
Figure 3: Fo - Fc difference maps after initial protein refinement against merged Laue data, displayed over the substrate/product binding site.
Figure 4: Superimposed structures of product complex (blue) and protein side chains from the initial refinement model (isocitrate–NADP+ complex, red).

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Acknowledgements

We thank W. Scott, J. Bolduc, D. Dyer, M. Holmes, R. Strong, and K. Zhang for advice and help with X-ray crystallography, R.M. Sweet, P. Singer, and G. Shea for assistance and technical support at NSLS Beamline X-26C (Brookhaven National Laboratories), D. Ringe and G. Petsko for extended use of their Xe flashlamp, and K. Moffat for extremely helpful advice and criticism at all stages of our time-resolved studies. B.L.S. is funded for this project by the NIH, DEK by the NSF and DOE.

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Authors and Affiliations

  1. Division of Basic Sciences, Program in Structural Biology, Fred Hutchinson Cancer Research Center, A3-023, 1100 Fairview Ave. N., Seattle, 98109, Washington, USA

    Barry L. Stoddard

  2. Department of Chemistry, University of California, Berkeley, 94720, California, USA

    Bruce E. Cohen

  3. Department of Molecular and Cell Biology, Stanley Hall, University of California, Berkeley, 94720, California, USA

    Michael Brubaker, Andrew D. Mesecar & Daniel E. Koshland Jr

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Stoddard, B., Cohen, B., Brubaker, M. et al. Millisecond Laue structures of an enzyme–product complex using photocaged substrate analogs. Nat Struct Mol Biol 5, 891–897 (1998). https://doi.org/10.1038/2331

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