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Isopentenyl pyrophosphate
Isopentenyl pyrophosphate
Isopentenyl pyrophosphate
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Isopentenyl pyrophosphate
Skeletal formula of IPP
Skeletal formula of IPP
Ball-and-stick model of IPP
Ball-and-stick model of IPP
Names
IUPAC name
(Hydroxy-(3-methylbut-3-enoxy) phosphoryl)oxyphosphonic acid
Identifiers
3D model (JSmol)
ChEBI
ChemSpider
MeSH isopentenyl+pyrophosphate
  • InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8) checkY[Pubchem]
    Key: NUHSROFQTUXZQQ-UHFFFAOYSA-N checkY[Pubchem]
  • CC(=C)CCOP(=O)(O)OP(=O)(O)O
Properties
C5H12O7P2
Molar mass 246.092 g·mol−1
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
checkY verify (what is checkY☒N ?)

Isopentenyl pyrophosphate (IPP, isopentenyl diphosphate, or IDP)[1] is an isoprenoid precursor. IPP is an intermediate in the classical, HMG-CoA reductase pathway (commonly called the mevalonate pathway) and in the non-mevalonate MEP pathway of isoprenoid precursor biosynthesis. Isoprenoid precursors such as IPP, and its isomer DMAPP, are used by organisms in the biosynthesis of terpenes and terpenoids.

Biosynthesis

[edit]

IPP is formed from acetyl-CoA via the mevalonate pathway (the "upstream" part), and then is isomerized to dimethylallyl pyrophosphate by the enzyme isopentenyl pyrophosphate isomerase.[2]

Mevalonate pathway
Simplified version of the steroid synthesis pathway with the intermediates isopentenyl pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP), geranyl pyrophosphate (GPP) and squalene. Some intermediates are omitted. The color scheme does not correctly represent the origins of the isoprene units of GPP.

IPP can be synthesised via an alternative non-mevalonate pathway of isoprenoid precursor biosynthesis, the MEP pathway, where it is formed from (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP) by the enzyme HMB-PP reductase (LytB, IspH). The MEP pathway is present in many bacteria, apicomplexan protozoa such as malaria parasites, and in the plastids of higher plants.[3]

See also

[edit]

References

[edit]
Revisions and contributorsEdit on WikipediaRead on Wikipedia

Isopentenyl pyrophosphate

View on Grokipedia
from Grokipedia
Isopentenyl pyrophosphate (IPP), chemically known as 3-methylbut-3-en-1-yl diphosphate, is an with the molecular formula C₅H₁₂O₇P₂ that serves as the universal five-carbon building block and key precursor in the of all isoprenoids in living organisms. This allylic pyrophosphate features a branched chain attached to a diphosphate group, enabling its reactivity in condensation reactions to form longer isoprenoid chains. IPP is produced through two independent metabolic pathways: the mevalonate (MVA) pathway and the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, which are compartmentalized differently across organisms and cell types. The MVA pathway, active in the of eukaryotes (including animals, fungi, and ) and in , begins with the condensation of three molecules to form , which is then reduced by the rate-limiting enzyme to mevalonate, followed by sequential phosphorylations and to yield IPP. In contrast, the MEP pathway (also called the non-mevalonate or DOXP pathway), predominant in , plastids, and certain , synthesizes IPP from pyruvate and via intermediates like 1-deoxy-D-xylulose 5-phosphate (DXP) and 2-C-methyl-D-erythritol 4-phosphate, without producing mevalonate. Once formed, IPP isomerizes to (DMAPP) via IPP isomerase, allowing head-to-tail condensations catalyzed by prenyltransferases to build diverse isoprenoid structures ranging from C10 monoterpenes to C>40 polyprenols. Isoprenoids derived from IPP fulfill essential biological roles, including the formation of sterols for , carotenoids for and pigmentation, ubiquinones for electron transport, and prenyl groups for protein anchoring, with alone producing over 50,000 such compounds vital for growth, defense, and stress response.

Chemical Structure and Properties

Molecular Formula and Structure

Isopentenyl (IPP), also known as isopentenyl diphosphate, has the molecular formula C5H12O7P2 in its neutral form, though it commonly exists as the dianionic species C5H10O7P22- under physiological conditions due to of the groups. This formula reflects a five-carbon skeleton combined with a moiety, where the consists of two groups linked by a phosphoanhydride bond. The core structure of IPP is based on a 3-methylbut-3-en-1-yl , featuring a at position 1 that is esterified to the group. The carbon includes a terminal between carbons 3 and 4, with a attached to carbon 3, giving the arrangement OP(O)(O)O-OP(O)(O)-O-CH2(1)-CH2(2)-C(3)(CH3)=CH2(4). This configuration positions the double bond in a 1,1-disubstituted , characteristic of the unit. The IUPAC name is (3-methylbut-3-en-1-yl) diphosphate, and the canonical SMILES notation is CC(=C)CCOP(=O)(O)OP(=O)(O)O. IPP is achiral, as its structure contains no tetrahedral stereocenters or other elements of ; the double bond geometry is fixed as the E/Z isomerism does not apply to this . This lack of stereoisomers simplifies its role as a universal building block in biochemical pathways.

Physical and Chemical Properties

Isopentenyl pyrophosphate (IPP) is typically obtained as a colorless, hygroscopic solid in its salt forms, such as the triammonium or trilithium salts, due to the polar nature of its groups. The molecular weight of the free acid form is 246.09 g/mol. IPP exhibits high solubility in water, exceeding 10 mg/mL in aqueous buffers for the triammonium salt, attributed to the ionic moieties that facilitate hydration and dissolution. However, it is unstable in aqueous solutions at neutral , where it undergoes of the pyrophosphate linkage, leading to degradation products like isopentenol and inorganic . Chemically, IPP features a high-energy pyrophosphate bond, rendering it susceptible to cleavage, particularly by enzymes in biological systems. This bond enables the allylic pyrophosphate (typically , the of IPP) to generate a that is attacked by the of IPP in condensation reactions catalyzed by prenyltransferases. The phosphate groups have multiple pKa values that influence its ionization and reactivity across ranges. IPP is sensitive to metal ions such as Mg²⁺ or Ca²⁺, which can catalyze non-enzymatic hydrolysis. For long-term storage, it requires conditions like pH 11.5 and -100°C to prevent degradation.

Biosynthesis Pathways

Mevalonate Pathway

The mevalonate pathway, also known as the classical mevalonate route, is the primary biosynthetic route for producing isopentenyl pyrophosphate (IPP) in eukaryotes, archaea, and some bacteria, beginning with the condensation of acetyl-CoA units and proceeding through a series of enzymatic steps in the cytosol. This pathway generates IPP, the universal five-carbon building block for isoprenoids, via key intermediates including acetoacetyl-CoA, 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA), mevalonate, 5-phosphomevalonate, and 5-diphosphomevalonate. In animals, the pathway operates mainly in the cytosol with HMG-CoA reductase localized to the endoplasmic reticulum, while in plants, the initial steps occur in the cytosol and the final phosphorylation and decarboxylation steps take place in peroxisomes. The pathway consists of six committed enzymatic reactions:
  1. Two molecules of are condensed to form acetoacetyl-CoA by acetoacetyl-CoA (EC 2.3.1.9), a reversible that does not require additional cofactors beyond the substrates.
  2. Acetoacetyl-CoA then reacts with a third to produce , catalyzed by HMG-CoA synthase (EC 2.3.3.10), an irreversible also occurring without external cofactors.
  3. HMG-CoA is reduced to mevalonate by (HMGR; EC 1.1.1.34), the rate-limiting and highly regulated step that consumes two molecules of NADPH and two protons.
  4. Mevalonate is phosphorylated to 5-phosphomevalonate by mevalonate kinase (EC 2.7.1.36), utilizing one molecule of ATP.
  5. 5-Phosphomevalonate is further phosphorylated to 5-diphosphomevalonate by phosphomevalonate kinase (EC 2.7.4.2), requiring another ATP molecule.
  6. Finally, 5-diphosphomevalonate undergoes ATP-dependent to yield IPP, catalyzed by mevalonate diphosphate decarboxylase (EC 4.1.1.33), which involves a concerted elimination of CO₂ and proton loss facilitated by a Mg²⁺-ATP complex.
Regulation of the primarily occurs at the step through multiple mechanisms to maintain cellular . In mammals, and oxysterols trigger feedback inhibition by binding to Insig proteins in the , which recruit the gp78 to promote HMGR ubiquitination and proteasomal degradation, reducing its half-life from over 12 hours in sterol-depleted conditions to less than 1 hour in sterol-replete states. Transcriptional control involves sterol regulatory element-binding proteins (SREBPs), which, when levels are low, are cleaved and translocated to the nucleus to upregulate HMGR ; high sterols retain SREBP precursors in the ER via Insig-Scap interaction, suppressing transcription. Additionally, statins such as act as competitive inhibitors of HMGR by mimicking the substrate in the , thereby reducing mevalonate production and downstream isoprenoid synthesis. Downstream isoprenoids like and also exert allosteric inhibition on mevalonate kinase, providing further feedback control. In contrast to the methylerythritol phosphate (MEP) pathway, which predominates in prokaryotes and plant plastids, the relies on as its carbon source and is the dominant route in eukaryotic .

Methylerythritol Phosphate (MEP) Pathway

The methylerythritol phosphate (MEP) pathway represents a distinct biosynthetic route for producing isopentenyl pyrophosphate (IPP) and its isomer dimethylallyl pyrophosphate (DMAPP), essential precursors for isoprenoid compounds, and is the primary pathway in many , the plastids of and , and apicomplexan parasites such as species. This pathway, also known as the non-mevalonate or 1-deoxy-D-xylulose 5-phosphate (DXP) pathway, begins with the C3 sugar precursors (G3P) and pyruvate, derived from central carbon metabolism, and proceeds through a series of seven enzyme-catalyzed transformations without involving mevalonate as an intermediate. Key intermediates include DXP, 2-C-methyl-D-erythritol 4-phosphate (MEP), 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (CDP-ME), 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (CDP-MEP), 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEcPP), and (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP). The pathway's elucidation in the 1990s, through isotope-labeling studies in and , revealed its operation parallel to the mevalonate pathway but confined to prokaryotic and plastid compartments. The pathway initiates with the condensation of pyruvate and G3P to form DXP and , catalyzed by 1-deoxy-D-xylulose 5-phosphate synthase (DXS), a (TPP)-dependent that represents the committed step. Next, DXP is isomerized and reduced to MEP by 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR or IspC), utilizing NADPH and a divalent metal ion such as Mn²⁺ as cofactors; this is a major target, inhibited by antibiotics like fosmidomycin. Subsequent activation involves MEP cytidylylation by 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (MCT or IspD) using (CTP) to yield CDP-ME and (PPi). This is followed by phosphorylation of CDP-ME at the 2-position by 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (CMK or IspE), which requires ATP and Mg²⁺ to produce CDP-MEP. The cyclization to MEcPP then occurs via 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (MCS or IspF), releasing (CMP) without additional cofactors. The final stages involve reduction and rearrangement: MEcPP is converted to HMBPP by (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase (HDS or IspG), an iron-sulfur [4Fe-4S] cluster enzyme that uses flavodoxin or ferredoxin as a reductant source. Lastly, (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR or IspH), another [4Fe-4S] cluster protein requiring a reductant like flavodoxin and Mg²⁺, reduces HMBPP to IPP and DMAPP in a branching reaction that typically yields IPP as the major product. These terminal enzymes, IspG and IspH, are critical for the pathway's completion and have been structurally characterized, revealing mechanisms involving radical chemistry facilitated by the iron-sulfur clusters. The MEP pathway's absence in animals, fungi, and —organisms that rely solely on the —highlights its evolutionary divergence and makes it an attractive target for selective inhibitors, such as antibiotics against bacterial pathogens and herbicides targeting plant plastids, as well as antimalarials against apicomplexans. This prokaryotic/plastid-specific distribution stems from ancient endosymbiotic events, with the pathway likely originating in bacterial ancestors of chloroplasts and retained in modern eubacteria. Seminal studies, including those identifying DXP as an early intermediate in the mid-1990s, underscored the pathway's role in essential isoprenoid production for synthesis, , and parasite survival.

Biological Roles and Functions

Role in Isoprenoid Biosynthesis

Isopentenyl pyrophosphate (IPP) serves as the fundamental five-carbon building block for the of all isoprenoids, a diverse class of natural products essential for cellular functions across organisms. In this pathway, IPP undergoes to (DMAPP) catalyzed by isopentenyl diphosphate isomerase (IDI), a that generates the allylic starter unit required for subsequent chain elongation. This proceeds via a protonation-deprotonation mechanism involving a intermediate and is magnesium-dependent, enabling the interconversion between the saturated IPP and the unsaturated DMAPP. The core assembly of isoprenoid chains occurs through head-to-tail condensations mediated by prenyltransferase enzymes, such as synthase (FPPS), where DMAPP acts as the initial allylic substrate and IPP as the elongating unit. FPPS first catalyzes the condensation of DMAPP with one IPP molecule to yield (GPP, C10), followed by the addition of a second IPP to produce (FPP, C15). These reactions involve a carbocationic in a single-step mechanism, with the release of (PPi) and dependence on Mg2+ ions for stabilization of the intermediates. The general condensation can be represented as: Allyl-PP+IPP→(n+5)-isoprenyl-PP+PPi\text{Allyl-PP} + \text{IPP} \rightarrow \text{(n+5)-isoprenyl-PP} + \text{PP}_\text{i} where Allyl-PP denotes DMAPP or longer allylic pyrophosphates, and n refers to the carbon chain length of the allylic substrate. This modular elongation process generates a wide array of isoprenoids, including monoterpenes (C10, from GPP), sesquiterpenes (C15, from FPP), and diterpenes (C20, from , GGPP). For instance, are derived from GGPP in the plastids, while steroids arise from the head-to-head dimerization of FPP to form , a precursor to sterols. In , IPP from the methylerythritol phosphate (MEP) pathway is primarily utilized in plastids for the synthesis of chlorophylls, whereas IPP from the in the supports production. This compartmentalization ensures targeted allocation of precursors to specific metabolic needs.

Involvement in Protein Prenylation and Other Processes

Isopentenyl (IPP) serves as the foundational building block for (FPP) and (GGPP), which are covalently attached to specific proteins through a known as . This process is catalyzed by farnesyltransferase (FTase) and geranylgeranyltransferase type I (GGTase-I), which transfer the 15-carbon farnesyl group from FPP or the 20-carbon geranylgeranyl group from GGPP to the group of a residue near the of target proteins, typically in a CAAX motif where C is , A is an aliphatic , and X is variable. The mechanism involves coordination of the protein substrate's cysteine to a ion in the , enhancing its nucleophilicity for an SN1-like attack on the allylic carbon of FPP or GGPP, resulting in the formation of a thioether bond and release of (PPi). Prenylation anchors proteins to cellular membranes, facilitating their proper localization and function in key signaling pathways. For instance, of Ras and Rho family enables their association with the plasma membrane, where they regulate , migration, and survival; dysregulation of Ras prenylation is implicated in oncogenic signaling and cancer progression. Similarly, geranylgeranylation of Rab is essential for their membrane targeting, supporting vesicular trafficking, , and processes critical for cellular logistics. Beyond , IPP contributes to the of ubiquinone (coenzyme ), where it is condensed into the polyisoprenoid that enhances the molecule's in the mitochondrial inner and supports electron transport in respiration. In the , the MEP pathway analog (E)-4-hydroxy-3-methyl-but-2-enyl (HMBPP), structurally similar to IPP, acts as a potent phosphoantigen that activates Vγ9Vδ2 T cells during bacterial infections, triggering release and cytotoxic responses to eliminate infected cells. Pharmacological inhibition of has therapeutic implications, as statins block 3-hydroxy-3-methylglutaryl-coenzyme A reductase in the , reducing IPP production and thereby depleting FPP and GGPP levels to impair prenylation of . Nitrogen-containing bisphosphonates, such as zoledronate, inhibit synthase (FPPS), leading to intracellular accumulation of IPP and upstream intermediates while diminishing FPP availability, which indirectly disrupts prenylation and has applications in cancer and bone disorders.

Dimethylallyl Pyrophosphate (DMAPP)

, with the molecular formula C₅H₁₂O₇P₂, is the allylic isomer of and serves as a critical building block in isoprenoid biosynthesis. Its systematic name is 3-methylbut-2-en-1-yl diphosphate, featuring a branched five-carbon chain where the diphosphate group is esterified to the at C1, a between C2 and C3, and a methyl substituent at C3. This structural arrangement contrasts with IPP by positioning the double bond internally, eliminating the terminal =CH₂ group and creating an allylic system that enhances reactivity. The interconversion between IPP and DMAPP is reversible and catalyzed by isopentenyl diphosphate isomerase (IDI; EC 5.3.3.2), referred to as IspA in bacteria. There are two types of IDI: type I (metal-dependent, in eukaryotes and some bacteria) and type II (flavin-dependent, in many bacteria and plant plastids). The mechanism of type I IDI involves protonation of the C3=C4 double bond at C4 of IPP, generating a tertiary carbocation at C3, followed by deprotonation at C2 to form DMAPP. Type II IDI employs a radical mechanism involving reduced FMN. In vivo, the equilibrium strongly favors DMAPP, with ratios typically around 87% DMAPP to 13% IPP depending on the organism and conditions. DMAPP exhibits heightened electrophilicity at the C1 position owing to conjugation between the C2-C3 and the electron-withdrawing , rendering it an ideal for nucleophilic attack in reactions. This property enables DMAPP to initiate the head-to-tail with IPP units during isoprenoid chain elongation. In the methylerythritol phosphate (MEP) pathway, prevalent in plastids and many , DMAPP is co-produced with IPP in the final reductive step catalyzed by (E)-4-hydroxy-3-methylbut-2-enyl diphosphate reductase (IspH or HDR), which converts (E)-4-hydroxy-3-methylbut-2-enyl diphosphate to both isomers. The two isomers remain interconvertible through IDI activity in both the MEP and mevalonate pathways, ensuring a balanced pool for downstream . Beyond isoprenoid elongation, DMAPP acts as a precursor to farnesyl pyrophosphate (FPP), which mediates protein prenylation processes essential for cellular signaling.

Geranyl Pyrophosphate and Higher Isoprenoids

Geranyl pyrophosphate (GPP), also known as geranyl diphosphate, is a C10 linear isoprenoid intermediate synthesized through the head-to-tail condensation of one molecule of dimethylallyl pyrophosphate (DMAPP) with one molecule of isopentenyl pyrophosphate (IPP). This reaction is catalyzed by geranyl pyrophosphate synthase (GPPS), a short-chain prenyltransferase enzyme that facilitates the stereospecific addition, releasing pyrophosphate (PPi) as a byproduct. The resulting GPP features an (E)-configured double bond at the C2-C3 position, contributing to its extended linear structure essential for further chain elongation. Farnesyl pyrophosphate (FPP), a C15 isoprenoid, is produced by the subsequent condensation of GPP with an additional IPP unit, again releasing PPi. This step is mediated by synthase (FPPS), another member of the prenyltransferase family, which exhibits high specificity for GPP as the allylic substrate. FPP adopts an all-trans configuration across its configured double bonds, providing a stable scaffold for higher-order isoprenoids. FPPS operates through a sequential mechanism where the allylic substrate binds first, followed by IPP, ensuring efficient chain extension. Geranylgeranyl pyrophosphate (GGPP), the C20 extension, arises from the condensation of FPP with yet another IPP, catalyzed by geranylgeranyl pyrophosphate synthase (GGPPS). GGPPS, like its predecessors, promotes head-to-tail linkage with PPi release and maintains an all-trans stereochemistry throughout the configured bonds of the chain, making GGPP a key precursor for biosynthesis. These synthases belong to a class of multimeric prenyltransferases, often forming homodimers or heterodimers, with active sites featuring distinct binding pockets: one for the allylic substrate and another for IPP, accommodating the growing hydrophobic chain to control product length and specificity. The general mechanism across these condensations involves ionization of the allylic pyrophosphate to form a resonance-stabilized allylic , followed by nucleophilic attack from the C4 of IPP's double bond, and to yield the new trans (E)-double bond. This arises from the enzyme's geometry, which orients substrates to favor E-configuration over cis, ensuring the linear, non-branched architecture of these higher isoprenoids. Prenyltransferases' binding pockets evolve in size and hydrophobicity with chain length, preventing premature release and enabling iterative elongation.

References

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