Sandbox Reserved 333
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:Mevalonate diphosphate decarboxylase exists as a symmetrical dimer<ref name = "Byres"/> <ref name = "Voynova"/> <ref name ="ByresMartin"/> . The C-terminal domains of each monomer are symmetrically oriented towards one another around a solvent-filled channel <ref name = "Byres"/>. The dimer is stabilized between alpha helices 6 and 10 on the monomers, and also through salt bridge interactions, tyrosine and proline stacking, and hydrophobic interactions <ref name = "Byres"/>. The interface between the monomers is very small, with only 7% of the total surface area of the monomer engaged in the interface interaction <ref name = "Voynova"/>. This small interface between monomers is a characteristic of GHMP kinases <ref name = "Voynova"/>. Each monomer consists of a single polypeptide chain with 331 amino acid residues. Each polypeptide chain has 13 alpha helices and 15 beta chains. The active site on each monomer is a deep, highly charged cleft made up seven segments of polypeptide chain, which is located away from the other monomer, and is unaffected by dimerization <ref name = "Byres"/>. An ATP binding polypeptide segment called the P loop is also located near the active site <ref name = "Byres"/>. A total of 19 amino acid residue side chains are involved with substrate binding in the active site <ref name = "Byres"/>. | :Mevalonate diphosphate decarboxylase exists as a symmetrical dimer<ref name = "Byres"/> <ref name = "Voynova"/> <ref name ="ByresMartin"/> . The C-terminal domains of each monomer are symmetrically oriented towards one another around a solvent-filled channel <ref name = "Byres"/>. The dimer is stabilized between alpha helices 6 and 10 on the monomers, and also through salt bridge interactions, tyrosine and proline stacking, and hydrophobic interactions <ref name = "Byres"/>. The interface between the monomers is very small, with only 7% of the total surface area of the monomer engaged in the interface interaction <ref name = "Voynova"/>. This small interface between monomers is a characteristic of GHMP kinases <ref name = "Voynova"/>. Each monomer consists of a single polypeptide chain with 331 amino acid residues. Each polypeptide chain has 13 alpha helices and 15 beta chains. The active site on each monomer is a deep, highly charged cleft made up seven segments of polypeptide chain, which is located away from the other monomer, and is unaffected by dimerization <ref name = "Byres"/>. An ATP binding polypeptide segment called the P loop is also located near the active site <ref name = "Byres"/>. A total of 19 amino acid residue side chains are involved with substrate binding in the active site <ref name = "Byres"/>. | ||
<Structure load= 2hk3 size='400' frame='true' align='left' caption='Fig 2: Active site of MDD' scene='Insert optional scene name here' /> | <Structure load= 2hk3 size='400' frame='true' align='left' caption='Fig 2: Active site of MDD' scene='Insert optional scene name here' /> | ||
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| + | :The mevalonate pathway encompasses 3 different enzymes that convert mevalonate to isopentenyl pyrophosphate, which is an important building block for all isoprenoids <ref name = "Andreassi"> 19485344 <ref/>. Mevalonate diphosphate decarboxylase is the last enzyme in this pathway, and it converts mevalonate diphosphate to IPP <ref name = "Andreassi"/>. The conversion of mevalonate diphosphate to isopentenyl pyrophosphate is a two-stage reaction <ref name = "Byres">. First, MDD binds an ATP molecule to the P loop near the active site, and the mevalonate diphosphate in the active site <ref name = "Byres"/>. Specifically, the Asp293 residue in the active site of MDD abstracts a proton from the C3 hydroxyl group of mevalonate diphosphate, creating a nucleophile that attacks the γ-phosphoryl group of ATP <ref name = "Byres"/>. The phosphorylation of the C3 carbon creates an unstable intermediate and a good leaving group on C3 <ref name = "Byres"/>. The second stage of the reaction is when MDD dephosphorylates and decarboxylates the substrate, releasing isopentenyl pyrophosphate, inorganic phosphate, ADP and a CO2 molecule <ref name = "Byres"/><ref name = "Voynova"/>. The IPP molecules can be joined together to make cholesterol or other isoprenoids. | ||
[[Image:Trial_1.png|thumb|Caption 1]] | [[Image:Trial_1.png|thumb|Caption 1]] | ||
Revision as of 07:24, 11 March 2011
| This Sandbox is Reserved from January 10, 2010, through April 10, 2011 for use in BCMB 307-Proteins course taught by Andrea Gorrell at the University of Northern British Columbia, Prince George, BC, Canada. |
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Introduction
- Mevalonate diphosphate decarboxylase (MDD) is an important enzyme required for the biosynthesis of cholesterol and other isoprenoids in mammals, bacteria, yeast and fungi [1]. MDD is a member of the GHMP (Galactokinase, Homoserine kinase, mevalonate kinase and phosphomevalonate kinase) enzyme family, and is responsible for the conversion of mevalonate diphosphate to isopentenyl pyrophosphate with the help of 1 ATP molecule[1] [2]. Even though the kinases in the GHMP family differ in quaternary structure and ability to bind a wide variety of substrates, they share a characteristic alpha/beta fold and similar sequences [1] [3]. Some GHMP kinases exist as dimers, some as tetramers and some as monomers [1]. The amino acid residues in MDD are highly conserved across all species, indicating the specific important activity of the enzyme [1].
Structure
- Mevalonate diphosphate decarboxylase exists as a symmetrical dimer[1] [2] [3] . The C-terminal domains of each monomer are symmetrically oriented towards one another around a solvent-filled channel [1]. The dimer is stabilized between alpha helices 6 and 10 on the monomers, and also through salt bridge interactions, tyrosine and proline stacking, and hydrophobic interactions [1]. The interface between the monomers is very small, with only 7% of the total surface area of the monomer engaged in the interface interaction [2]. This small interface between monomers is a characteristic of GHMP kinases [2]. Each monomer consists of a single polypeptide chain with 331 amino acid residues. Each polypeptide chain has 13 alpha helices and 15 beta chains. The active site on each monomer is a deep, highly charged cleft made up seven segments of polypeptide chain, which is located away from the other monomer, and is unaffected by dimerization [1]. An ATP binding polypeptide segment called the P loop is also located near the active site [1]. A total of 19 amino acid residue side chains are involved with substrate binding in the active site [1].
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Reaction
- The mevalonate pathway encompasses 3 different enzymes that convert mevalonate to isopentenyl pyrophosphate, which is an important building block for all isoprenoids [4]
