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Structure of a bacterial homologue of vitamin K epoxide reductase

Nature volume 463, pages 507–512 (2010)Cite this article

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Abstract

Vitamin K epoxide reductase (VKOR) generates vitamin K hydroquinone to sustain γ-carboxylation of many blood coagulation factors. Here, we report the 3.6 Å crystal structure of a bacterial homologue of VKOR from Synechococcus sp. The structure shows VKOR in complex with its naturally fused redox partner, a thioredoxin-like domain, and corresponds to an arrested state of electron transfer. The catalytic core of VKOR is a four transmembrane helix bundle that surrounds a quinone, connected through an additional transmembrane segment with the periplasmic thioredoxin-like domain. We propose a pathway for how VKOR uses electrons from cysteines of newly synthesized proteins to reduce a quinone, a mechanism confirmed by in vitro reconstitution of vitamin K-dependent disulphide bridge formation. Our results have implications for the mechanism of the mammalian VKOR and explain how mutations can cause resistance to the VKOR inhibitor warfarin, the most commonly used oral anticoagulant.

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Figure 1: Architecture of Synechococcus VKOR in complex with its redox partner.
Figure 2: The active site of VKOR.
Figure 3: Mutations causing warfarin resistance in mammalian VKOR.
Figure 4: Electron transfer pathway.
Figure 5: In vitro reconstitution of vitamin K-dependent oxidative folding.
Figure 6: Comparison of VKOR with DsbB.

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Acknowledgements

We thank C. Jao for help with mass spectroscopy, S. Harrison for insightful comments on the structure, B. Furie, B. C. Furie and Y. Yu. for discussion, A. Osborne, B. van den Berg, J. Zimmer, and Y. Chen for critical reading of the manuscript, R. Zhang for help with the figures, the staff at Advanced Photon Source beamline ID-24C, and the SBGrid consortium at Harvard Medical School. S.S. is supported by an NIH Medical Scientist Training Program fellowship. J.B. is supported by grant GMO41883 from the National Institute of General Medical Sciences. W. L. is supported by a Charles King Trust fellowship and K99 grant 1K99HL097083 from the National Heart, Lung, and Blood Institute (NIH). T.A.R. is an HHMI investigator.

Author Contributions J.B., R.J.D. and D.B. conceived the project. W.L. purified and crystallized the proteins, and determined the structures. S.S. generated constructs and aided in crystallization. S.S. and W.L. performed biochemical analysis. W.L., S.S. and T.A.R. analysed the data and wrote the paper.

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  1. Weikai Li and Sol Schulman: These authors contributed equally to this work.

Authors and Affiliations

  1. Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA,

    Weikai Li, Sol Schulman & Tom A. Rapoport

  2. Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA,

    Rachel J. Dutton, Dana Boyd & Jon Beckwith

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Correspondence to Weikai Li or Tom A. Rapoport.

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Supplementary information

Supplementary Information

This file contains Supplementary Table S1, Supplementary Figures S1- S10 with Legends and Legends for Supplementary Movies 1-2. (PDF 9103 kb)

Supplementary Movie 1

This movie shows the overall structure of the protein, consisting of VKOR (pink) and the thioredoxin (Trx)-like domain (blue) - see Supplementary Information file for full Legend. (AVI 24126 kb)

Supplementary Movie 2

In this movie the active site of VKOR is shown together with the experimental electron density map - see Supplementary Information file for full Legend. (AVI 27723 kb)

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Li, W., Schulman, S., Dutton, R. et al. Structure of a bacterial homologue of vitamin K epoxide reductase. Nature 463, 507–512 (2010). https://doi.org/10.1038/nature08720

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