Sandbox Reserved 1724
From Proteopedia
(Difference between revisions)
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{{Template:CH462_Biochemistry_II_2022}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | {{Template:CH462_Biochemistry_II_2022}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | ||
- | == | + | ==Vitamin K Epoxide Reductase== |
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> | <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> | ||
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | ||
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=== Vitamin K Cycle === | === 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. <ref name="Stafford">PMID:16102054</ref> | ||
=== Structural Overview === | === Structural Overview === | ||
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=== Function === | === Function === | ||
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===Overview=== | ===Overview=== | ||
===Catalytic Cysteines=== | ===Catalytic Cysteines=== | ||
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+ | 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. | ||
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===Tyrosine 138 and Asparagine 80=== | ===Tyrosine 138 and Asparagine 80=== | ||
===Hydrophobic Interactions=== | ===Hydrophobic Interactions=== | ||
== Medical Relevance == | == Medical Relevance == | ||
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===Warfarin=== | ===Warfarin=== | ||
+ | Warfarin is a structural mimic of Vitamin K that is used clinically as an anticoagulant. | ||
===Superwarfarins=== | ===Superwarfarins=== | ||
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This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | ||
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== References == | == References == | ||
<references/> | <references/> | ||
+ | ==Student Contributors== | ||
+ | Izabella Jordan, Emma Varness |
Revision as of 19:28, 17 March 2022
This Sandbox is Reserved from February 28 through September 1, 2022 for use in the course CH462 Biochemistry II taught by R. Jeremy Johnson at the Butler University, Indianapolis, USA. This reservation includes Sandbox Reserved 1700 through Sandbox Reserved 1729. |
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Vitamin K Epoxide Reductase
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References
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
- ↑ Stafford DW. The vitamin K cycle. J Thromb Haemost. 2005 Aug;3(8):1873-8. doi: 10.1111/j.1538-7836.2005.01419.x. PMID:16102054 doi:http://dx.doi.org/10.1111/j.1538-7836.2005.01419.x
Student Contributors
Izabella Jordan, Emma Varness