Sandbox Reserved 1716: Difference between revisions

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===Step I===

===Step I ===

Step I of reforming Vitamin K Epoxide through the enzyme Vitamin K Reductase (VKOR) begins in a partially oxidized open conformation. In this state, catalytic cysteines 51 and 132 form a disulfide bond. Cysteines 43 and 135 are considered "free" because they are not bound to anything in this state. The <scene name='90/904321/I/2'>central binding pocket</scene> (highlighted in hot pink) is also empty because Vitamin K Epoxide has not bound yet. In order to get to the next step, Vitamin K epoxide will enter through the isoprenyl-chain tunnel.<ref name=”Shixuan”>PMID:33154105</ref>

<scene name='90/904321/I/1'>Step I</scene> of reforming Vitamin K Epoxide through the enzyme Vitamin K Reductase (VKOR) begins in a partially oxidized open conformation. In this state, catalytic cysteines 51 and 132 form a disulfide bond. Cysteines 43 and 135 are considered "free" because they are not bound to anything in this state. The <scene name='90/904321/I/2'>central binding pocket</scene> (highlighted in hot pink) is also empty because Vitamin K Epoxide has not bound yet. In order to get to the next step, Vitamin K epoxide will enter through the isoprenyl-chain tunnel.<ref name=”Shixuan”>PMID:33154105</ref>

===Step II===

After Vitamin K Epoxide enters through the isoprenyl-chain tunnel, Asn80 on TM2 and Tyr139 on TM4 <scene name='90/904322/Tyr_asn_binding_warfarin/2'>hydrogen bond</scene>. to Vitamin K Epoxide. When Vitamin K Epoxide binds, there is a shift in the bonds between the cap domain, beta hairpin, and anchor. <scene name='90/904321/Vkobound_cys/1'>Cys135</scene> also forms a disulfide bond with the 3' OH group on Vitamin K Epoxide.

<scene name='90/904321/Ii/2'>After</scene> Vitamin K Epoxide enters through the isoprenyl-chain tunnel, Asn80 on TM2 and Tyr139 on TM4 <scene name='90/904322/Tyr_asn_binding_warfarin/2'>hydrogen bond</scene>. to Vitamin K Epoxide. When Vitamin K Epoxide binds, there is a shift in the bonds between the cap domain, beta hairpin, and anchor. <scene name='90/904321/Vkobound_cys/1'>Cys135</scene> also forms a disulfide bond with the 3' OH group on Vitamin K Epoxide.

===Step III===

<scene name='90/904321/Iii/1'>Step III</scene> is within this partially <scene name='90/904321/Iii/2'>oxidized state</scene> and free Cys43 forms a bond with Cys 51. Cys51 kicks its electrons to Cys132, and Cys 132 forms a disulfide bond with Cys135. Cys135 then reduces the epoxide ring on Vitamin K Epoxide after donating its electrons. The epoxide ring opens and reforms Vitamin K Quinone.

===Step IV===

<scene name='90/904321/Iv/1'>Step IV</scene> is the last step of this cycle. Vitamin K Quinone will exit the central binding pocket and the open conformation will form. VKOR is in its fully oxidized state after donating its electrons to Vitamin K Epoxide. This is when the luminal helix will be visible. The cycle then repeats at Step I to keep reducing Vitamin K Epoxide to Vitamin K Quinone.

== Vitamin K Epoxide ==

Sandbox Reserved 1716: Difference between revisions

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@@ Line 40: / Line 40: @@
-===Step I===
+===Step I ===
-Step I of reforming Vitamin K Epoxide through the enzyme Vitamin K Reductase (VKOR) begins in a partially oxidized open conformation. In this state, catalytic cysteines 51 and 132 form a disulfide bond. Cysteines 43 and 135 are considered "free" because they are not bound to anything in this state. The <scene name='90/904321/I/2'>central binding pocket</scene> (highlighted in hot pink) is also empty because Vitamin K Epoxide has not bound yet. In order to get to the next step, Vitamin K epoxide will enter through the isoprenyl-chain tunnel.<ref name=”Shixuan”>PMID:33154105</ref>
+<scene name='90/904321/I/1'>Step I</scene> of reforming Vitamin K Epoxide through the enzyme Vitamin K Reductase (VKOR) begins in a partially oxidized open conformation. In this state, catalytic cysteines 51 and 132 form a disulfide bond. Cysteines 43 and 135 are considered "free" because they are not bound to anything in this state. The <scene name='90/904321/I/2'>central binding pocket</scene> (highlighted in hot pink) is also empty because Vitamin K Epoxide has not bound yet. In order to get to the next step, Vitamin K epoxide will enter through the isoprenyl-chain tunnel.<ref name=”Shixuan”>PMID:33154105</ref>
 ===Step II===
-After Vitamin K Epoxide enters through the isoprenyl-chain tunnel, Asn80 on TM2 and Tyr139 on TM4 <scene name='90/904322/Tyr_asn_binding_warfarin/2'>hydrogen bond</scene>. to Vitamin K Epoxide. When Vitamin K Epoxide binds, there is a shift in the bonds between the cap domain, beta hairpin, and anchor. <scene name='90/904321/Vkobound_cys/1'>Cys135</scene> also forms a disulfide bond with the 3' OH group on Vitamin K Epoxide.
+<scene name='90/904321/Ii/2'>After</scene> Vitamin K Epoxide enters through the isoprenyl-chain tunnel, Asn80 on TM2 and Tyr139 on TM4 <scene name='90/904322/Tyr_asn_binding_warfarin/2'>hydrogen bond</scene>. to Vitamin K Epoxide. When Vitamin K Epoxide binds, there is a shift in the bonds between the cap domain, beta hairpin, and anchor. <scene name='90/904321/Vkobound_cys/1'>Cys135</scene> also forms a disulfide bond with the 3' OH group on Vitamin K Epoxide.
+===Step III===
+<scene name='90/904321/Iii/1'>Step III</scene> is within this partially <scene name='90/904321/Iii/2'>oxidized state</scene> and free Cys43 forms a bond with Cys 51. Cys51 kicks its electrons to Cys132, and Cys 132 forms a disulfide bond with Cys135. Cys135 then reduces the epoxide ring on Vitamin K Epoxide after donating its electrons. The epoxide ring opens and reforms Vitamin K Quinone.
+===Step IV===
+<scene name='90/904321/Iv/1'>Step IV</scene> is the last step of this cycle. Vitamin K Quinone will exit the central binding pocket and the open conformation will form. VKOR is in its fully oxidized state after donating its electrons to Vitamin K Epoxide. This is when the luminal helix will be visible. The cycle then repeats at Step I to keep reducing Vitamin K Epoxide to Vitamin K Quinone.
 == Vitamin K Epoxide ==