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Mevalonate Diphosphate Decarboxylase

Template:STRUCTURE 2hk3

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^[4]. Each polypeptide chain has ^[4]. 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].

Reaction

The mevalonate pathway encompasses 3 different enzymes that convert mevalonate to isopentenyl pyrophosphate, which is an important building block for all isoprenoids ^[5]. Mevalonate diphosphate decarboxylase is the last enzyme in this pathway, and it converts mevalonate diphosphate to IPP (Fig 2) ^[5]. 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 2)^[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 2) ^[1][2]. The IPP molecules can be joined together to make cholesterol or other isoprenoids.

Image:Protopedia figure.png

Fig. 2 Phosphorylation of mevalonate diphosphate, followed by dephosphorylation and decarboxylation of the unstable intermeditae, yeilding isopentyl pyrophosphate, inorganic phosphate, carbon dioxide and ADP,catalyzed by mevalonate diphosphate decarboxylase.

Significance

Mevalonate diphosphate decarboxylase is a necessary enzyme in the cholesterol and isoprenoid biosynthesis pathway ^{[1][6] [2] [3]}. Without this enzyme, the cholesterol synthesis production decreases ^[6], which can be detrimental to many organisms that rely on the formation of IPP for cholesterol, electron transport, membrane structures and anchors, and signaling pathways ^[3]. One such organism that requires MDD, is the Trypanosoma bruceii, a parasite that is transmitted to the human bloodstream through the bite of the tsetse fly, that causes African Sleeping sickness ^[3]. 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 ^[3]. 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} 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. ↑ ^{2.0 2.1 2.2 2.3 2.4 2.5} 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
3. ↑ ^{3.0 3.1 3.2 3.3 3.4 3.5} 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
4. ↑ ^{4.0 4.1} Kabsch W., Sander C. "Sequence/Structure details of Crystal Structure of mevalonate diphosphate decarboxylase from Staphylococcus aureus" RCSB Protein Databank, http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=2HK3
5. ↑ ^{5.0 5.1} 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
6. ↑ ^{6.0 6.1} 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