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Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair

Nature Structural & Molecular Biology volume 11, pages 945–949 (2004)Cite this article

Abstract

A fundamental question is how enzymes can accelerate chemical reactions. Catalysis is not only defined by actual chemical steps, but also by enzyme structure and dynamics. To investigate the role of protein dynamics in enzymatic turnover, we measured residue-specific protein dynamics in hyperthermophilic and mesophilic homologs of adenylate kinase during catalysis. A dynamic process, the opening of the nucleotide-binding lids, was found to be rate-limiting for both enzymes as measured by NMR relaxation. Moreover, we found that the reduced catalytic activity of the hyperthermophilic enzyme at ambient temperatures is caused solely by a slower lid-opening rate. This comparative and quantitative study of activity, structure and dynamics revealed a close link between protein dynamics and catalytic turnover.

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Figure 1: Kinetic models and catalytic activity of Adk.
Figure 2: Characterization of protein dynamics during catalysis.
Figure 3: Identification of lid-opening and closing as the rate-limiting step for catalysis.
Figure 4: Ligand titration experiments provide additional evidence for the slow dynamic process in thermoAdk.

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Acknowledgements

We thank The Swedish NMR Centre for 800 MHz NMR spectrometer time, V. Orekhov for valuable technical advice on the acquisition of NMR relaxation dispersion experiments, L. Kay for providing pulse programs and D. Korzhnev for sharing software for NMR relaxation data analysis. We are grateful to A. Wittinghofer for supplying the plasmid for E. coli adenylate kinase and K.O. Stetter for providing DNA isolated from Aquifex aeolicus. This work was supported by US National Institutes of Health (NIH) grants GM067963 and GM62117 to D.K. and a postdoctoral fellowship from the Swedish Research Council to M.W.W. and from the NIH to K.H.W.

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  1. Department of Biochemistry, Brandeis University, Waltham, 02454, Massachusetts, USA

    Magnus Wolf-Watz, Vu Thai, Katherine Henzler-Wildman, Georgia Hadjipavlou, Elan Z Eisenmesser & Dorothee Kern

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  1. Magnus Wolf-Watz
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Correspondence to Dorothee Kern.

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Wolf-Watz, M., Thai, V., Henzler-Wildman, K. et al. Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair. Nat Struct Mol Biol 11, 945–949 (2004). https://doi.org/10.1038/nsmb821

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