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bioRxiv · 10.1101/2025.02.09.637231

Molecular basis of vitamin K-dependent protein γ-glutamyl carboxylation

Zhong, Q.·Chen, D.·Xu, J.·Li, Y.·Meng, Y.·Wen, Q.·Ye, Q.·Wang, G.·Pan, K.·Tao, L.·Qiao, J.·Hang, J.
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Abstract

Gamma-glutamyl carboxylase (GGCX) in human is the sole enzyme responsible for catalyzing the carboxylation of glutamate (Glu) to {gamma}-carboxyglutamate (Gla), a process that relies on the deprotonation of reduced vitamin K. This post-translational modification of vitamin K-dependent proteins (VKDPs) plays a pivotal role in numerous biological processes. Mutations in GGCX are responsible for multiple clinical phenotypes; however, the molecular mechanisms of GGCX activity and its pathology remain poorly understood. In this study, we reported the cryo-electron microscopy (cryo-EM) structures of GGCX bound with the either FIX or FX, two VKDPs and vitamin K, and employed the biochemical and cellular assays as well as molecular dynamics simulations to elucidate its dual-catalytic properties. The enzyme comprises a transmembrane domain that anchors the vitamin K-binding site, along with an ER luminal domain that facilitates binding of coagulation factor IX (FIX) at the exosite. The catalytic center orchestrates the oxidation of vitamin K and the carboxylation of Glu residues through a Cap-H2 coupling mechanism, along where disease-associated mutations in GGCX are predominantly clustered. These findings offer a comprehensive molecular framework for understanding the allosteric regulation of GGCXs dual enzymatic activities and provide valuable insights for developing strategies to monitor and therapeutically target vitamin K metabolism in related diseases.

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Zhong, Q., Chen, D., Xu, J., Li, Y., Meng, Y., Wen, Q., Ye, Q., Wang, G., Pan, K., Tao, L., Qiao, J., Hang, J.. 2025-02-09. Molecular basis of vitamin K-dependent protein γ-glutamyl carboxylation. https://doi.org/10.1101/2025.02.09.637231

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