Sandbox Reserved 1709: Difference between revisions

Line 4:

== Introduction==

=== Biological Role ===

<scene name='90/906893/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</ref>. Its enzymatic role is reducing <scene name='90/906893/Vkor_with_ko/1'>vitamin K epoxide</scene> (KO) to Vitamin K Hydroquinone (KH2) <ref>DOI 10.1021</ref> (Figure 1). The mechanism first occurs through the binding KO and using two cysteine residues to reduce KO into [https://en.wikipedia.org/wiki/Vitamin_K Vitamin K]. Then, a second pair of cysteine residues will reduce Vitamin K into the final product, KH2 (Figure 1). One of VKORs primary roles is to assist in blood coagulation through this KH2 regeneration mechanism.[[Image:VKOR_mechanism_2D.png|400 px|right|thumb|Figure 1. Mechanism of KO ~~oxidation~~ into KH2.]] With Vitamin K as a cofactor, the [https://www.britannica.com/science/bleeding/The-extrinsic-pathway-of-blood-coagulation#ref64617 γ-carboxylase] enzyme will enact post-translational modification on KH2, oxidizing it back to KO. The oxidation of KH2 by γ-carboxylase is coupled with the carboxylation of a glutamate residue to form γ-carboxyglutamate. The coupling of this oxidation and carboxylation will activate several clotting factors in the coagulation cascade.

<scene name='90/906893/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</ref>. Its enzymatic role is reducing <scene name='90/906893/Vkor_with_ko/1'>vitamin K epoxide</scene> (KO) to Vitamin K Hydroquinone (KH2) <ref>DOI 10.1021</ref> (Figure 1). The mechanism first occurs through the binding KO and using two cysteine residues to reduce KO into [https://en.wikipedia.org/wiki/Vitamin_K Vitamin K]. Then, a second pair of cysteine residues will reduce Vitamin K into the final product, KH2 (Figure 1). One of VKORs primary roles is to assist in blood coagulation through this KH2 regeneration mechanism.[[Image:VKOR_mechanism_2D.png|400 px|right|thumb|Figure 1. Mechanism of KO reduction into KH2.]] With Vitamin K as a cofactor, the [https://www.britannica.com/science/bleeding/The-extrinsic-pathway-of-blood-coagulation#ref64617 γ-carboxylase] enzyme will enact post-translational modification on KH2, oxidizing it back to KO. The oxidation of KH2 by γ-carboxylase is coupled with the carboxylation of a glutamate residue to form γ-carboxyglutamate. The coupling of this oxidation and carboxylation will activate several clotting factors in the coagulation cascade.

=== Author's Notes ===

Structural characterization of VKOR has been difficult due to its in vitro instability. Recently, a series of atomic structures have been determined utilizing anticoagulant stabilization and VKOR-like [https://pubmed.ncbi.nlm.nih.gov/33154105/ homologs]. Crystal structures of VKOR were captured with a bound substrate (KO) or vitamin K antagonist (VKA)<ref>DOI 10.1126</ref>. VKA substrates utilized were anticoagulants, namely [https://en.wikipedia.org/wiki/Warfarin Warfarin], [https://en.wikipedia.org/wiki/Brodifacoum Brodifacoum], [https://en.wikipedia.org/wiki/Phenindione Phenindione], and [https://en.wikipedia.org/wiki/Chlorophacinone Chlorophacinone]. Second, VKOR-like homologs were utilized to aid in structure classification. Homologs refer to specific cysteine residues that have been mutated to serine to facilitate capturing a stable conformation state. Homologs were mainly isolated from human VKOR with some isolated from the pufferfish ''Takifugu rubripes''. Furthermore, all of the structures used have been processed to remove a beta barrel at the south end of VKOR that served no purpose in function of the enzyme. This also allowed for the residue numbering to be reassigned and more closely replicate the human VKOR.

Line 24:

=== Brief Overview ===

The overall mechanism works to convert Vitamin K epoxide to an activated form of Vitamin K, as noted in Figure 1. The <scene name='90/906893/Open_conformation/1'>open conformation</scene> ~~will be prepped~~ and ~~waiting for a substrate or ligand to bind. Once the substrate binds, this will~~ induce the <scene name='90/906893/Closed_conformation/4'>closed conformation</scene> 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.

The overall mechanism works to convert Vitamin K epoxide to an activated form of Vitamin K hydroquinone, as noted in Figure 1. The substrate will bind VKOR at the binding pocket in the <scene name='90/906893/Open_conformation/1'>open conformation</scene> and induce the <scene name='90/906893/Closed_conformation/4'>closed conformation</scene>. Transition from open to closed conformation occurs with the oxidation of the C43-C51 disulfide bridge. Here, VKOR will utilize the second pair of catalytic cysteines, C132 and C135, to reduce KO into Vitamin K and Vitamin K into KH2. KH2 will be released from the binding fully activated and ready for use in the body. VKOR will reset, returning to the open conformation again, prepared for another substrate to bind.

=== ~~Catalytic~~ Mechanism ===

=== Enzymatic Mechanism ===

[[Image:Catalytic Mech Pic.png |350 px| right| thumb]]

Sandbox Reserved 1709: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 4: / Line 4: @@
 == Introduction==
 === Biological Role ===
-<scene name='90/906893/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</ref>. Its enzymatic role is reducing <scene name='90/906893/Vkor_with_ko/1'>vitamin K epoxide</scene> (KO) to Vitamin K Hydroquinone (KH2) <ref>DOI 10.1021</ref> (Figure 1). The mechanism first occurs through the binding KO and using two cysteine residues to reduce KO into [https://en.wikipedia.org/wiki/Vitamin_K Vitamin K]. Then, a second pair of cysteine residues will reduce Vitamin K into the final product, KH2 (Figure 1). One of VKORs primary roles is to assist in blood coagulation through this KH2 regeneration mechanism.[[Image:VKOR_mechanism_2D.png|400 px|right|thumb|Figure 1. Mechanism of KO oxidation into KH2.]] With Vitamin K as a cofactor, the [https://www.britannica.com/science/bleeding/The-extrinsic-pathway-of-blood-coagulation#ref64617 γ-carboxylase] enzyme will enact post-translational modification on KH2, oxidizing it back to KO. The oxidation of KH2 by γ-carboxylase is coupled with the carboxylation of a glutamate residue to form γ-carboxyglutamate. The coupling of this oxidation and carboxylation will activate several clotting factors in the coagulation cascade.
+<scene name='90/906893/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</ref>. Its enzymatic role is reducing <scene name='90/906893/Vkor_with_ko/1'>vitamin K epoxide</scene> (KO) to Vitamin K Hydroquinone (KH2) <ref>DOI 10.1021</ref> (Figure 1). The mechanism first occurs through the binding KO and using two cysteine residues to reduce KO into [https://en.wikipedia.org/wiki/Vitamin_K Vitamin K]. Then, a second pair of cysteine residues will reduce Vitamin K into the final product, KH2 (Figure 1). One of VKORs primary roles is to assist in blood coagulation through this KH2 regeneration mechanism.[[Image:VKOR_mechanism_2D.png|400 px|right|thumb|Figure 1. Mechanism of KO reduction into KH2.]] With Vitamin K as a cofactor, the [https://www.britannica.com/science/bleeding/The-extrinsic-pathway-of-blood-coagulation#ref64617 γ-carboxylase] enzyme will enact post-translational modification on KH2, oxidizing it back to KO. The oxidation of KH2 by γ-carboxylase is coupled with the carboxylation of a glutamate residue to form γ-carboxyglutamate. The coupling of this oxidation and carboxylation will activate several clotting factors in the coagulation cascade.
 === Author's Notes ===
 Structural characterization of VKOR has been difficult due to its in vitro instability. Recently, a series of atomic structures have been determined utilizing anticoagulant stabilization and VKOR-like [https://pubmed.ncbi.nlm.nih.gov/33154105/ homologs]. Crystal structures of VKOR were captured with a bound substrate (KO) or vitamin K antagonist (VKA)<ref>DOI 10.1126</ref>. VKA substrates utilized were anticoagulants, namely [https://en.wikipedia.org/wiki/Warfarin Warfarin], [https://en.wikipedia.org/wiki/Brodifacoum Brodifacoum], [https://en.wikipedia.org/wiki/Phenindione Phenindione], and [https://en.wikipedia.org/wiki/Chlorophacinone Chlorophacinone]. Second, VKOR-like homologs were utilized to aid in structure classification. Homologs refer to specific cysteine residues that have been mutated to serine to facilitate capturing a stable conformation state. Homologs were mainly isolated from human VKOR with some isolated from the pufferfish ''Takifugu rubripes''. Furthermore, all of the structures used have been processed to remove a beta barrel at the south end of VKOR that served no purpose in function of the enzyme. This also allowed for the residue numbering to be reassigned and more closely replicate the human VKOR.
@@ Line 24: / Line 24: @@
 === Brief Overview ===
-The overall mechanism works to convert Vitamin K epoxide to an activated form of Vitamin K, as noted in Figure 1. The <scene name='90/906893/Open_conformation/1'>open conformation</scene> will be prepped and waiting for a substrate or ligand to bind. Once the substrate binds, this will induce the <scene name='90/906893/Closed_conformation/4'>closed conformation</scene> 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.
+The overall mechanism works to convert Vitamin K epoxide to an activated form of Vitamin K hydroquinone, as noted in Figure 1. The substrate will bind VKOR at the binding pocket in the <scene name='90/906893/Open_conformation/1'>open conformation</scene> and induce the <scene name='90/906893/Closed_conformation/4'>closed conformation</scene>. Transition from open to closed conformation occurs with the oxidation of the C43-C51 disulfide bridge. Here, VKOR will utilize the second pair of catalytic cysteines, C132 and C135, to reduce KO into Vitamin K and Vitamin K into KH2. KH2 will be released from the binding fully activated and ready for use in the body. VKOR will reset, returning to the open conformation again, prepared for another substrate to bind.
-=== Catalytic Mechanism ===
+=== Enzymatic Mechanism ===
 [[Image:Catalytic Mech Pic.png |350 px| right| thumb]]