Sandbox Reserved 1724

This is a default text for your page '. 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 ^[1] or to the article describing Jmol ^[2] to the rescue.

Introduction

Vitamin K Cycle

Vitamin K is essential for blood clotting in the body. The fully reduced form, KH2, allows the gamma carboxylation of blood clotting cofactors and is turned into the epoxide form in the process. Vitamin K epoxide reductase turns the epoxide back to the fully reduced form so the reduced form can be used again. This transformation happens in two steps including converting the epoxide to partially oxidized Vitamin K then converting the partially oxidized Vitamin K to the fully reduced hydroquinone. ^[3]

Structural Overview

Function

Catalytic Cycle

Overview

The main story of vitamin K epoxide reductase can be shown through the steps of the catalytic cycle shown on this slide. The first step of the catalytic cycle I want to highlight is the top right confirmation in which KOH is bound in the active site of VKOR. Later Emma will go into some details about the bonds that occur within VKOR that stabilize this bond, but right now the most important thing to know is that KOH exists within the closed conformation of vKOR. In the second stage the conformation of VKOR changes, the amino acid residues behave differently, but the KH substrate still exists within the closed conformation. The third step to highlight is the open conformation of VKOR. On this diagram it is shown in many different ways, first with each of our previously mentioned substrates and finally with warfarin bound (which is called a closed conformation). This is labeled a closed conformation not because the actual cap is bound to the helices like in previous steps but because warfarin is a vitamin K antagonist and prevents KOH from binding the active site of our protein. Finally VKOR can also exist in the closed conformation with warfarin because as Emma mentioned there are a lot of similarities in the interactions between KOH and warfarin with vitamin k epoxide reductase.

Catalytic Cysteines

There are 4 catalytic cysteines that are important to VKOR, 43, 51, 132, and 135. To explain how this works, it is easiest to start with the second state. In the second state, an oxidized or partially oxidized Vitamin K has entered the active site. The stabilizing 51-132 disulfide bond is shown. Then in the third state, 43 has attacked the disulfide bond and made its own bond with 51. You can see 132 has an oxygen. That is because the researchers made a mutation from S to O to force the reaction to stop at that step so the structure could be deduced. In the natural VKOR, that would be a sulfur. The next state, the open state, results from 132 forming a bridge with 135. This allows release of the reduced or partially reduced Vitamin K. All of this disulfide rearranging was working to reduce the Vitamin K, particularly in the 135 position. If we go back to State 2, when Vitamin K first binds, you can see that 135 is not tied up in a disulfide bond. It is available to help the Vitamin K bond. So, it makes sense that once 135 gets forced to bond, the now reduced Vitamin K is released. State 5 is interesting because the disulfide bonds are similar to the open state, but warfarin is actually bound. This represents the binding of warfarin to the fully oxidized VKOR at the end of its cycle. Going back to State 1, the researchers used a mutation at 43 to mimic VKOR’s partially oxidized state. Warfarin can also bind to this state and notice that the disulfide bonds are the same as State 2. Also it is worth pointing out how the disulfide bonds contribute to conformational changes and are affected by conformational changes, which affects their proximity to each other and the active site.

Tyrosine 138 and Asparagine 80

Hydrophobic Interactions

Medical Relevance

Warfarin

Warfarin is a structural mimic of Vitamin K that is used clinically as an anticoagulant.

Superwarfarins

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.