Sandbox Reserved 1709

spinqualitylabelsall models VKOR with KO bound. Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D This is a default text for your page George G. Papadeas/Sandbox VKOR. Click above on edit this page to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia or to the article describing Jmol to the rescue. Introduction History of VKOR Vitamin K epoxide reductase (VKOR) is an enzyme that, as its name implies, promotes the reduction of vitamin K epoxide (KO). VKOR is a transmembrane protein spanning the endoplasmic reticulum and composed of 4 transmembrane helical proteins. One of its primary roles is to assist in blood coagulation by regenerating hydroquinone (KH2). KH2 acts as a γ-carboxylase cofactor that drives the γ-carboxylation of several coagulation factors. Structural characterization of VKOR has been difficult, though, due to its in vitro instability. Nonetheless, a near perfect atomic structure has been determined utilization anticoagulant stabilization and VKOR-like homologs. Author's Notes As previously mentioned, the VKOR structure has been challenging to qualify. Thus it is important to note that to date all VKOR structures discovered were done so from 2 methods. First, crystal structures of Human VKOR were captured with a bound substrate (KO) or vitamin K antagonist (VKA). VKA substrates utilized were anticoagulants, namely Warfarin, brodifacoum, phenindione, and chlorophacinone. Second, VKOR-like homologs, specifically isolated from the pufferfish Takifugu rubripes, aided in structure classification as well. Structural Highlights Active Site Within the four transmembrane helices lies the active site. The active site is comprised of a hydrophobic pocket containing two hydrophilic residues, A80 and Y139, that interact with substrates and ligands alike. The hydrophobic pocket provides specificity to the region while the hydrophilic residues have potential to hydrogen bond, allowing recognition and increasing specificity as well. Slightly above the active site is a crucial disulfide bridge that provides stabilization when a substrate is bound. This bridge occurs between C132 and C135, recurrent residues that continually aid in VKOR function. The active site plays a vital role in binding of any substrate or ligand to the VKOR. Upon binding, the VKOR will transition into a closed conformation that will allow its catalytic mechanism to commence. Cap Domain A key part of VKOR is the function of the VKOR Cap Domain, which is located right above the helices of VKOR towards the intracellular part of the membrane. The cap is in a helical shape and is located in close proximity to the Anchor and beta hairpin to maintain in the proper orientation. The cap domain assists with activating Vitamin K as it induces the structural change of VKOR from the open conformation to the closed conformation when the substrate binds. This initiates a domino effect through the catalytic mechanism. The cap domain has critical interactions that stabilize the closed conformation including a Disulfide Bridge between S43 and S51, and polar interactions from D44. Anchor The Anchor Domain sticks out from the side of VKOR with the primary role of stabilizing the enzyme within the membrane. To accomplish this, hydrophilic and hydrophobic residues are highly conserved with hydrophilic residues located to interact with the outer hydrophilic leaflet of the bilipid membrane, while the hydrophobic residues on the anchor have strong interactions with the inner hydrophobic leaflet of the bilipid membrane. These sufficient interactions allow for VKOR to remain in the proper arrangement and proximity within the membrane for Vitamin K to properly bind to be activated to achieve its biological function. Function: Method of Coagulation Brief Overview The open conformation will be prepped and waiting for a substrate or ligand to bind. Once the substrate binds, this will induce the closed conformation of VKOR, where the catalytic mechanism will activate Vitamin K via reactive cysteine residues. Vitamin K will then be released from the binding pocket once it is fully activated for use in the body, and VKOR will resume the open conformation once again. The enzyme will then reset into its reactive state to prep for another molecule of Vitamin K to bind. Catalytic Mechanism The catalytic mechanism of VKOR is a critical part of its overall function in the body. Highly regulated enzymatic activity through the reactivity of catalytic cysteines allows VKOR to properly activate Vitamin K for its use in the body. The enzyme begins in stage 1, where it's in the open conformation with the cap domain open to allow in a substrate to bind to the active site. Once a substrate binds, the cap domain is initiated into the closed conformation. VKOR is now in stage 2. To further stabilize the closed conformation with the substrate bound, the cap domain helps initiate a catalytic reaction of cysteines to break the disulfide bridge that was stabilizing stage 1. Free cysteines are now available that provide strong stabilization of the closed conformation through interactions with the cap domain and the bound substrate. This puts the enzyme in Stage 3, where the catalytic free cysteines react to form a new disulfide bridge, releasing the activated substrate into the blood stream to promote anticoagulation. With two stable disulfide bridges and VKOR unbound, the enzyme is now in its final, unreactive Stage 4. VKOR must undergo conformational changes to return to Stage 1 and restart the catalytic process to activate Vitamin K again. Disease and Treatment Afflictions Since activated Vitamin K plays a crucial role in blood coagulation in the body, any defects in the function and enzymatic activity of VKOR may have detrimental effects on Vitamin K's ability to promote important blood clotting. Ultimately, mutations in VKOR may lead to increased susceptibility to vascular diseases, such as a stroke. Vitamin K has also been shown to have an important role in maintaining bone health, so inactivity of VKOR could also be linked to decreased bone density and osteoporosis. Inhibition The most inexpensive and common way to treat blood clotting is through the VKOR inhibitor, Warfarin. Warfarin is able to do so by outcompeting KO. It will enter the binding pocket of VKOR, creating strong hydrogen bonds with the active site. Mutations Some key mutations that can be detrimental to the VKOR structure are mutations of the active site. The two main residues, N80 and Y139, can be mutated to A80 and F139 creating a decrease in recognition and stabilization This is a sample scene created with SAT to color by Group, and another to make a transparent representation of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

References

1. Elshaikh, A. O., Shah, L., Joy Mathew, C., Lee, R., Jose, M. T., & Cancarevic, I. "Influence of Vitamin K on Bone Mineral Density and Osteoporosis" (2020) Cureus, 12(10), e10816. [1]

2. Li, Weikai et al. “Structure of a bacterial homologue of vitamin K epoxide reductase.” Nature vol. 463,7280 (2010): 507-12. doi:10.1038/nature08720.

3. Liu S, Li S, Shen G, Sukumar N, Krezel AM, Li W. Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation. Science. 2021 Jan 1;371(6524):eabc5667. doi: 10.1126/science.abc5667. Epub 2020 Nov 5. PMID: 33154105; PMCID: PMC7946407.

4. “Warfarin.” Wikipedia, Wikimedia Foundation, 10 Feb. 2022, https://en.wikipedia.org/wiki/Warfarin.

5. Yang W., et. al. “VKORC1 Haplotypes Are Associated With Arterial Vascular Diseases (Stroke, Coronary Heart Disease, and Aortic Dissection)” (2006) Circulation. ;113:1615–1621 [2]