Sandbox Reserved 333

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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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Mevalonate Diphosphate Decarboxylase

Contents

Fig 1 Mevalonate diphosphate decarboxylase in the homodimeric form

Drag the structure with the mouse to rotate

Introduction

Mevalonate diphosphate decarboxylase (MDD) is an important enzyme required by every cell for the biosynthesis of cholesterol and other isoprenoids in mammals, bacteria, yeast and fungi [1] [2]. 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 (IPP) with the help of 1 ATP molecule[1] [3]. 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] [4]. 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].

See also Mevalonate pathway

Structure

Mevalonate diphosphate decarboxylase exists as a symmetrical dimer[1] [3] [4] . 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 each monomer, and also through salt bridge interactions, tyrosine stacking, 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 [3]. This small interface between monomers is a characteristic of GHMP kinases [3]. Each monomer consists of a single polypeptide chain with 331 amino acid residues [5]. Each polypeptide chain has and [5]. The active site on each monomer is a deep, highly charged cleft made up seven segments of polypeptide chain [1] . The active sites are located away from the solvent filled channel, and they are unaffected by dimerization [1]. The amino acid residues Tyr19, Trp20, Trp158 and Met203 form a that is important in the active site for helping to orient the mevalonate diphosphate properly [1]. One important animo acid in the active site is Tyrosine 19 (Fig 2) because it is strategically placed to interact with the terminal phosphate group of mevalonate diphosphate when it is bound in the active site [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].
Fig 2 Tyrosine 19 in the active site of mevalonate diphosphate decarboxylase.
Fig 2 Tyrosine 19 in the active site of mevalonate diphosphate decarboxylase.


Reaction

The mevalonate pathway encompasses 3 different enzymes that convert mevalonate to isopentenyl pyrophosphate (IPP), which is an important building block for all isoprenoids [6]. Mevalonate diphosphate decarboxylase is the last enzyme in this pathway and it converts mevalonate diphosphate to IPP (Fig 3) [6]. The conversion of mevalonate diphosphate to isopentenyl pyrophosphate is a two-stage reaction [1]. First, MDD binds an ATP molecule to the P loop near the active site and the mevalonate diphosphate in the active site [1]. 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 [1]. The phosphorylation of the C3 carbon creates an unstable intermediate and a good leaving group on C3 (Fig 3)[1]. The second stage of the reaction is when MDD dephosphorylates and decarboxylates the substrate, releasing isopentenyl pyrophosphate, inorganic phosphate, ADP and a CO2 molecule (Fig 3) [1] [3]. The IPP molecules can react together to make cholesterol or other isoprenoids.
Fig. 3 Showing the phosphorylation of mevalonate diphosphate, followed by dephosphorylation and decarboxylation of the unstable intermediate, yielding isopentyl pyrophosphate, inorganic phosphate, carbon dioxide and ADP, all catalyzed by mevalonate diphosphate decarboxylase
Fig. 3 Showing the phosphorylation of mevalonate diphosphate, followed by dephosphorylation and decarboxylation of the unstable intermediate, yielding isopentyl pyrophosphate, inorganic phosphate, carbon dioxide and ADP, all catalyzed by mevalonate diphosphate decarboxylase


Significance

Mevalonate diphosphate decarboxylase is a necessary enzyme in the cholesterol and isoprenoid biosynthesis pathway [1] [7] [3] [4]. Without this enzyme isoprenoid biosynthesis decreases [7], which can be detrimental to many organisms that rely on the formation of IPP for cholesterol, electron transport, membrane structures, membrane anchors, and signaling pathways [4]. One such organism that requires MDD is Trypanosoma bruceii, a parasite that causes African Sleeping sickness after being transmitted to the human bloodstream through the bite of a tsetse fly [4]. MDD was thought to be a potential target enzyme for an inhibitor that would disable the catalytic activity of MDD, thereby stopping IPP production and effectively killing the parasite [4]. It is believed now that the MDD found in Trypanosoma bruceii resembles human MDD too closely, and so it would be difficult to make a species specific inhibitor for MDD [1].



References

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 Byres E, Alphey MS, Smith TK, Hunter WN. Crystal structures of Trypanosoma brucei and Staphylococcus aureus mevalonate diphosphate decarboxylase inform on the determinants of specificity and reactivity. J Mol Biol. 2007 Aug 10;371(2):540-53. Epub 2007 Jun 4. PMID:17583736 doi:http://dx.doi.org/10.1016/j.jmb.2007.05.094
  2. ↑ Nelson, D.L. and Cox, M.M. 2008. Lehninger Principles of Biochemistry, Fifth ed. W.H. Freeman and Company. pp 831
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 Voynova NE, Fu Z, Battaile KP, Herdendorf TJ, Kim JJ, Miziorko HM. Human mevalonate diphosphate decarboxylase: characterization, investigation of the mevalonate diphosphate binding site, and crystal structure. Arch Biochem Biophys. 2008 Dec 1;480(1):58-67. Epub 2008 Sep 18. PMID:18823933 doi:S0003-9861(08)00414-1
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 Byres E, Martin DM, Hunter WN. A preliminary crystallographic analysis of the putative mevalonate diphosphate decarboxylase from Trypanosoma brucei. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jun 1;61(Pt, 6):581-4. Epub 2005 Jun 1. PMID:16511101 doi:10.1107/S1744309105014594
  5. ↑ 5.0 5.1 Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577-637. PMID:6667333 doi:http://dx.doi.org/10.1002/bip.360221211
  6. ↑ 6.0 6.1 Andreassi JL 2nd, Vetting MW, Bilder PW, Roderick SL, Leyh TS. Structure of the ternary complex of phosphomevalonate kinase: the enzyme and its family. Biochemistry. 2009 Jul 14;48(27):6461-8. PMID:19485344 doi:10.1021/bi900537u
  7. ↑ 7.0 7.1 Krepkiy D, Miziorko HM. Identification of active site residues in mevalonate diphosphate decarboxylase: implications for a family of phosphotransferases. Protein Sci. 2004 Jul;13(7):1875-81. Epub 2004 May 28. PMID:15169949 doi:10.1110/ps.04725204
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