User:R. Jeremy Johnson/VKOR: Difference between revisions

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== Introduction ==

Vitamin K ~~epoxide reductase~~ (VKOR) is the ~~enzyme responsible for regenerating~~ vitamin K ~~from vitamin~~ K ~~epoxide~~ to ~~support~~ blood coagulation.

<scene name='90/904314/Vkor_structure/1'>Vitamin K Epoxide Reductase</scene> (VKOR) is a reducing enzyme composed of 4-helices that spans the endoplasmic reticulum as a transmembrane protein<ref>DOI 10.1126/science.abc5667</ref>. Its enzymatic role is reducing <scene name='90/904314/Vkor_with_ko/7'>vitamin K epoxide</scene> (KO) to Vitamin K Hydroquinone (KH2)<ref>DOI 10.1021/bi700527j</ref> (Figure 1). One of VKOR's primary roles is to assist in blood coagulation through this KH2 regeneration mechanism.

[[Image:Vitamin_k_cycle_5.jpg|350 px|left|thumb|'''Figure 1. Vitamin K Cycle''' The three states of Vitamin K are shown along with important enzymes, including VKOR. ]]

~~=== Vitamin K Cycle ===~~

[https://en.wikipedia.org/wiki/Vitamin_K Vitamin K] is essential for [https://en.wikipedia.org/wiki/Coagulation#Coagulation_cascade blood clotting] in the body and is recycled by means of the Vitamin K Cycle <ref name="Stafford">PMID:16102054</ref> (Figure 1). The fully reduced form, KH2, is used by [https://en.wikipedia.org/wiki/Gamma-glutamyl_carboxylase#:~:text=Gamma-glutamyl%20carboxylase%20is%20an%20enzyme%20that%20catalyzes%20the,of%20the%20encoded%20enzyme%20is%20essential%20for%20hemostasis gamma-glutamyl carboxylase] to carboxylate protein-bound glutamate residues in blood clotting cofactor precursors <ref name="Blanchard">PMID:6165889</ref>. After carboxylation, the clotting cofactors (such as [https://proteopedia.org/wiki/index.php/Thrombin prothrombin]) can bind to calcium and initiatw the coagulation cascade <ref name="Swanson">PMID:6758841</ref>. During this process, KH2 becomes oxidized to Vitamin K epoxide, or KO <ref name="Blanchard">PMID:6165889</ref>. VKOR returns the epoxide to the fully reduced form for reuse by [https://en.wikipedia.org/wiki/Gamma-glutamyl_carboxylase#:~:text=Gamma-glutamyl%20carboxylase%20is%20an%20enzyme%20that%20catalyzes%20the,of%20the%20encoded%20enzyme%20is%20essential%20for%20hemostasis gamma-glutamyl carboxylase]. This transformation happens in two steps: 1) converting the epoxide to the partially oxidized Vitamin K quinone and 2) converting the quinone to the fully reduced hydroquinone (KH2) (Figure 1) <ref name="Stafford">PMID:16102054</ref>.

[https://en.wikipedia.org/wiki/Vitamin_K Vitamin K] is essential for [https://en.wikipedia.org/wiki/Coagulation#Coagulation_cascade blood clotting] in the body and is recycled by means of the Vitamin K Cycle <ref name="Stafford">PMID:16102054</ref> (Figure 1). The fully reduced form, KH2, is used by [https://en.wikipedia.org/wiki/Gamma-glutamyl_carboxylase#:~:text=Gamma-glutamyl%20carboxylase%20is%20an%20enzyme%20that%20catalyzes%20the,of%20the%20encoded%20enzyme%20is%20essential%20for%20hemostasis gamma-glutamyl carboxylase] to carboxylate protein-bound glutamate residues in blood clotting cofactor precursors <ref name="Blanchard">PMID:6165889</ref>. After carboxylation, the clotting cofactors (such as [https://proteopedia.org/wiki/index.php/Thrombin prothrombin]) can bind to calcium and ~~can proceed to~~ the coagulation cascade <ref name="Swanson">PMID:6758841</ref>. During this process, KH2 becomes oxidized to Vitamin K epoxide, or KO <ref name="Blanchard">PMID:6165889</ref>. VKOR ~~turns~~ the epoxide ~~back~~ to the fully reduced form ~~so the reduced form can be used again~~. This transformation happens in two steps: 1) converting the epoxide to the partially oxidized Vitamin K quinone and 2) converting the quinone to the fully reduced hydroquinone (KH2) (Figure 1) <ref name="Stafford">PMID:16102054</ref>.

The Vitamin K Cycle and VKOR enzyme are common drug targets for thromboembolic diseases, as coagulant factor activation promotes blood clotting, which in high amounts can be dangerous and cause thromboembolic diseases such as [https://en.wikipedia.org/wiki/Stroke stroke], [https://en.wikipedia.org/wiki/Deep_vein_thrombosis deep vein thrombosis], and/or [https://en.wikipedia.org/wiki/Pulmonary_embolism pulmonary embolism].

Vitamin K Epoxide Reductase is found and primarily synthesized in the [https://en.wikipedia.org/wiki/Liver liver].

[[Image:VKOR_in_membrane.jpg|300 px|right|thumb|'''Figure 2. VKOR in Membrane''' Transmembrane helices are teal. The tan sections are the loops (loop 1, beta hairpin, cap loop, 3-4 loop). The cap helix is light blue and the anchor is dark blue.]]

=== Author's Note ===

To deduce VKOR structures, superfolder green flourescent protein (sGFP) was appended to the N and C termini of VKOR to provide added stability during crystallization. In some of the resolved structures, a catalytic cysteine was also mutated to serine to freeze VKOR in specific catalytic conformations. Also, due to stability issues, some experiments used human VKOR and others used VKOR from ''Takifugu rubripes''. The barrel domain has been removed from all structures used in this page and the amino acids renumbered to more closely match the published numbering in the referenced article <ref name="Liu">PMID:33154105</ref>. In the human VKOR (HsVKOR), the catalytic cysteines that play an intricate role in the reduction of Vitamin K epoxide are <scene name='90/904321/Cysteines/7'>cysteines</scene> 43, 51, 132, and 135. In ''T. rubripes''(TrVKORL), the cysteines are 52, 55, 141, and 144.

==Protein Structure==

=== Structural Overview ===

VKOR consists of four <scene name='90/904330/Transmembranehelices1/5'>transmembrane helices</scene> embedded in the endoplasmic reticulum membrane (Figure 2). Helices one and two are <scene name='90/904330/Betahairpin2/5'>connected</scene> by Loop 1 and the beta hairpin region which contains two of the active cysteines, Cys43 and Cys51; these cysteines, along with Cys132 and Cys135, are essential for reduction and structural changes discussed in the next section<ref name="Liu">PMID:33154105</ref>. VKOR also has a <scene name='90/904330/Capdomain/3'>cap domain</scene> consisting of a helix, loop, and anchor. The anchor stabilizes the cap domain by attaching it to the surface of the ER membrane<ref name="Liu">PMID:33154105</ref>. The loop helps stabilize one of the substrate-binding amino acids, Asn80<ref name="Liu">PMID:33154105</ref>. The helix is involved in stabilization of certain disulfide bonds and structural changes as part of the catalytic cycle discussed below<ref name="Liu">PMID:33154105</ref>.

~~=== Author's Note ===~~

In order to deduce VKOR structures, Liu <ref name="Liu">PMID:33154105</ref> and colleagues used various strategies worthy of note. They incorporated a barrel-like domain that is not part of the catalytic VKOR protein to help with stability during experimentation. In some of the resolved structures, a catalytic cysteine was mutated to serine to force the reaction to stop with VKOR in that certain conformation. Also, due to stability issues, some of the experiments used human VKOR and others used VKOR of ''Takifugu rubripes'' which is similar to humans. The barrel domain has been removed from all structures used in this page and the amino acids renumbered to more closely match the published numbering in the referenced article <ref name="Liu">PMID:33154105</ref>.

=== Active Site ===

@@ Line 3: / Line 3: @@
 == Introduction ==
-Vitamin K epoxide reductase (VKOR) is the enzyme responsible for regenerating vitamin K from vitamin K epoxide to support blood coagulation.
+<scene name='90/904314/Vkor_structure/1'>Vitamin K Epoxide Reductase</scene> (VKOR) is a reducing enzyme composed of 4-helices that spans the endoplasmic reticulum as a transmembrane protein<ref>DOI 10.1126/science.abc5667</ref>. Its enzymatic role is reducing <scene name='90/904314/Vkor_with_ko/7'>vitamin K epoxide</scene> (KO) to Vitamin K Hydroquinone (KH2)<ref>DOI 10.1021/bi700527j</ref> (Figure 1). One of VKOR's primary roles is to assist in blood coagulation through this KH2 regeneration mechanism.
 [[Image:Vitamin_k_cycle_5.jpg|350 px|left|thumb|'''Figure 1. Vitamin K Cycle''' The three states of Vitamin K are shown along with important enzymes, including VKOR. ]]
-=== Vitamin K Cycle ===
+[https://en.wikipedia.org/wiki/Vitamin_K Vitamin K] is essential for [https://en.wikipedia.org/wiki/Coagulation#Coagulation_cascade blood clotting] in the body and is recycled by means of the Vitamin K Cycle <ref name="Stafford">PMID:16102054</ref> (Figure 1). The fully reduced form, KH2, is used by [https://en.wikipedia.org/wiki/Gamma-glutamyl_carboxylase#:~:text=Gamma-glutamyl%20carboxylase%20is%20an%20enzyme%20that%20catalyzes%20the,of%20the%20encoded%20enzyme%20is%20essential%20for%20hemostasis gamma-glutamyl carboxylase] to carboxylate protein-bound glutamate residues in blood clotting cofactor precursors <ref name="Blanchard">PMID:6165889</ref>. After carboxylation, the clotting cofactors (such as [https://proteopedia.org/wiki/index.php/Thrombin prothrombin]) can bind to calcium and initiatw the coagulation cascade <ref name="Swanson">PMID:6758841</ref>. During this process, KH2 becomes oxidized to Vitamin K epoxide, or KO <ref name="Blanchard">PMID:6165889</ref>. VKOR returns the epoxide to the fully reduced form for reuse by [https://en.wikipedia.org/wiki/Gamma-glutamyl_carboxylase#:~:text=Gamma-glutamyl%20carboxylase%20is%20an%20enzyme%20that%20catalyzes%20the,of%20the%20encoded%20enzyme%20is%20essential%20for%20hemostasis gamma-glutamyl carboxylase]. This transformation happens in two steps: 1) converting the epoxide to the partially oxidized Vitamin K quinone and 2) converting the quinone to the fully reduced hydroquinone (KH2) (Figure 1) <ref name="Stafford">PMID:16102054</ref>.
-[https://en.wikipedia.org/wiki/Vitamin_K Vitamin K] is essential for [https://en.wikipedia.org/wiki/Coagulation#Coagulation_cascade blood clotting] in the body and is recycled by means of the Vitamin K Cycle <ref name="Stafford">PMID:16102054</ref> (Figure 1). The fully reduced form, KH2, is used by [https://en.wikipedia.org/wiki/Gamma-glutamyl_carboxylase#:~:text=Gamma-glutamyl%20carboxylase%20is%20an%20enzyme%20that%20catalyzes%20the,of%20the%20encoded%20enzyme%20is%20essential%20for%20hemostasis gamma-glutamyl carboxylase] to carboxylate protein-bound glutamate residues in blood clotting cofactor precursors <ref name="Blanchard">PMID:6165889</ref>. After carboxylation, the clotting cofactors (such as [https://proteopedia.org/wiki/index.php/Thrombin prothrombin]) can bind to calcium and can proceed to the coagulation cascade <ref name="Swanson">PMID:6758841</ref>. During this process, KH2 becomes oxidized to Vitamin K epoxide, or KO <ref name="Blanchard">PMID:6165889</ref>. VKOR turns the epoxide back to the fully reduced form so the reduced form can be used again. This transformation happens in two steps: 1) converting the epoxide to the partially oxidized Vitamin K quinone and 2) converting the quinone to the fully reduced hydroquinone (KH2) (Figure 1) <ref name="Stafford">PMID:16102054</ref>.
+The Vitamin K Cycle and VKOR enzyme are common drug targets for thromboembolic diseases, as coagulant factor activation promotes blood clotting, which in high amounts can be dangerous and cause thromboembolic diseases such as [https://en.wikipedia.org/wiki/Stroke stroke], [https://en.wikipedia.org/wiki/Deep_vein_thrombosis deep vein thrombosis], and/or [https://en.wikipedia.org/wiki/Pulmonary_embolism pulmonary embolism].
+Vitamin K Epoxide Reductase is found and primarily synthesized in the [https://en.wikipedia.org/wiki/Liver liver].
 [[Image:VKOR_in_membrane.jpg|300 px|right|thumb|'''Figure 2. VKOR in Membrane''' Transmembrane helices are teal. The tan sections are the loops (loop 1, beta hairpin, cap loop, 3-4 loop). The cap helix is light blue and the anchor is dark blue.]]
+=== Author's Note ===
+To deduce VKOR structures, superfolder green flourescent protein (sGFP) was appended to the N and C termini of VKOR to provide added stability during crystallization. In some of the resolved structures, a catalytic cysteine was also mutated to serine to freeze VKOR in specific catalytic conformations. Also, due to stability issues, some experiments used human VKOR and others used VKOR from ''Takifugu rubripes''. The barrel domain has been removed from all structures used in this page and the amino acids renumbered to more closely match the published numbering in the referenced article <ref name="Liu">PMID:33154105</ref>. In the human VKOR (HsVKOR), the catalytic cysteines that play an intricate role in the reduction of Vitamin K epoxide are <scene name='90/904321/Cysteines/7'>cysteines</scene> 43, 51, 132, and 135. In ''T. rubripes''(TrVKORL), the cysteines are 52, 55, 141, and 144.
 ==Protein Structure==
 === Structural Overview ===
 VKOR consists of four <scene name='90/904330/Transmembranehelices1/5'>transmembrane helices</scene> embedded in the endoplasmic reticulum membrane (Figure 2). Helices one and two are <scene name='90/904330/Betahairpin2/5'>connected</scene> by <b><span class="text-brown">Loop 1</span></b> and the <b><span class="text-orange">beta hairpin</span></b> region which contains two of the active cysteines, Cys43 and Cys51; these cysteines, along with Cys132 and Cys135, are essential for reduction and structural changes discussed in the next section<ref name="Liu">PMID:33154105</ref>. VKOR also has a <scene name='90/904330/Capdomain/3'>cap domain</scene> consisting of a <b><span class="text-blue">helix</span></b>, <b><span class="text-lightmagenta">loop</span></b>, and <b><span class="text-olive">anchor</span></b>. The <b><span class="text-olive">anchor</span></b> stabilizes the cap domain by attaching it to the surface of the ER membrane<ref name="Liu">PMID:33154105</ref>. The <b><span class="text-lightmagenta">loop</span></b> helps stabilize one of the substrate-binding amino acids, Asn80<ref name="Liu">PMID:33154105</ref>. The <b><span class="text-blue">helix</span></b> is involved in stabilization of certain disulfide bonds and structural changes as part of the catalytic cycle discussed below<ref name="Liu">PMID:33154105</ref>.
-=== Author's Note ===
-In order to deduce VKOR structures, Liu <ref name="Liu">PMID:33154105</ref> and colleagues used various strategies worthy of note. They incorporated a barrel-like domain that is not part of the catalytic VKOR protein to help with stability during experimentation. In some of the resolved structures, a catalytic cysteine was mutated to serine to force the reaction to stop with VKOR in that certain conformation. Also, due to stability issues, some of the experiments used human VKOR and others used VKOR of ''Takifugu rubripes'' which is similar to humans. The barrel domain has been removed from all structures used in this page and the amino acids renumbered to more closely match the published numbering in the referenced article <ref name="Liu">PMID:33154105</ref>.
 === Active Site ===