Supplementary Materials

Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation

Shixuan Liu, Shuang Li, Guomin Shen, Narayanasami Sukumar, Andrzej M. Krezel, Weikai Li

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Figs. S1 to S19
  • Tables S1 to S3
  • References
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Images, Video, and Other Media

Movie S1
Structure of HsVKOR with bound warfarin. The movie starts with a side view showing the overall architecture of HsVKOR with warfarin, followed by a top view showing the stabilization of the cap domain by peripheral regions. Subsequently, zoomed-in views are presented to show the binding interactions of warfarin, including those from the cap domain, the peripheral interactions stabilizing the cap domain, the membrane-interface interactions of the anchor domain, and its supporting interactions to stabilize the cap domain.
Movie S2
Warfarin binding induces the transition from open to closed conformation. The structure conversion between the apo- and warfarin-bound states of wild-type TrVKORL is modeled by the Morph program (64). The binding of warfarin induces the movement of Val44 and Phe55 (numbering in HsVKOR) and the formation of the cap helix. Interaction between Phe55 and Cys43-Cys51 brings this disulfide close and generates the β-hairpin. The newly formed cap helix, β-hairpin and loop1 interact with loop 3–4 and TM1e to form the closed conformation. Asp44 is a central residue that mediates interactions at the closed conformation.
Movie S3
Transition between open and closed conformations promotes the catalytic cycle of VKORs. HsVKOR and TrVKORL structures are superimposed and the structural transitions are modeled by the Morph program (64). The movie starts with the structure of apo TrVKORL in the fully oxidized state (as in Fig. 3D). Electron transfer in the ER generates the partially oxidized state, with the Cys51–Cys132 disulfide and reduced Cys43 and Cys135. The substrate, KO or K, may bind initially at the low affinity site (fig. S9) and then enter the active site to form a charge-transfer or covalent complex with Cys135 (Figs. 4A and 5A). Formation of this stable substrate adduct changes the conformation of the cap domain and in turn favors the formation of the β-hairpin. The closed conformation brings Cys43 close and allows it to attack Cys51–Cys132, generating a reduced Cys132 (mimicked by Cys132Ser in Fig. 4). Subsequently, Cys132 attacks the Cys135-substrate adduct. This adduct is resolved, resulting in the Cys132–Cys135 disulfide and the fully reduced product, K or KH2. K may bind at the low affinity site for the next round of the reaction. Release of the product from the active site changes the cap domain conformation, and the fully oxidized protein returns to the open conformation.