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The ternary complex of antithrombin–anhydrothrombin–heparin reveals the basis of inhibitor specificity

Nature Structural & Molecular Biology volume 11, pages 863–867 (2004)Cite this article

Abstract

Antithrombin, the principal physiological inhibitor of the blood coagulation proteinase thrombin, requires heparin as a cofactor. We report the crystal structure of the rate-determining encounter complex formed between antithrombin, anhydrothrombin and an optimal synthetic 16-mer oligosaccharide. The antithrombin reactive center loop projects from the serpin body and adopts a canonical conformation that makes extensive backbone and side chain contacts from P5 to P6′ with thrombin's restrictive specificity pockets, including residues in the 60-loop. These contacts rationalize many earlier mutagenesis studies on thrombin specificity. The 16-mer oligosaccharide is just long enough to form the predicted bridge between the high-affinity pentasaccharide-binding site on antithrombin and the highly basic exosite 2 on thrombin, validating the design strategy for this synthetic heparin. The protein-protein and protein-oligosaccharide interactions together explain the basis for heparin activation of antithrombin as a thrombin inhibitor.

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Figure 1: Synthetic 16-mer heparin mimetic, SR123781A, used in this study.
Figure 2: Stereo ribbon representation of the ternary complex.
Figure 3: The antithrombin reactive center loop conformation and contacts with thrombin.
Figure 4: Stereo representation of the overlay of the RCL conformations of the antithrombin in the present structure (cyan) and in pentasaccharide-activated antithrombin (gold).
Figure 5: The defined heparin-binding regions in the ternary complex.

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Acknowledgements

This work was supported by grants HL49234 and HL64013 from the US National Institutes of Health. Data were collected on the SERCAT ID beamline at the Advanced Photon Source (APS), Argonne National Laboratory. Use of APS is supported by the US Department of Energy.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, 900 S. Ashland, Chicago, 60607, Illinois, USA

    Alexey Dementiev & Peter G W Gettins

  2. Sanofi-Synthélabo, 185 Route d'Espagne, Toulouse, 31036, Cedex, France

    Maurice Petitou & Jean-Marc Herbert

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  1. Alexey Dementiev
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Correspondence to Peter G W Gettins.

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M.P. and J.-M.H. are currently employees of Sanofi, the manufacturer of the heparin mimetic SR123781A, which was used in this study.

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Dementiev, A., Petitou, M., Herbert, JM. et al. The ternary complex of antithrombin–anhydrothrombin–heparin reveals the basis of inhibitor specificity. Nat Struct Mol Biol 11, 863–867 (2004). https://doi.org/10.1038/nsmb810

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