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Multienzyme complex

A multienzyme complex is a stable assembly of multiple enzymes that catalyze a series of sequential biochemical reactions, typically linked by shared metabolic intermediates and often involving the direct transfer of substrates between active sites without diffusion into the surrounding solution, a phenomenon known as substrate channeling.^[1]^[2] These complexes enable efficient coordination of metabolic pathways by maintaining high local concentrations of intermediates, protecting unstable or reactive molecules from degradation, and minimizing competition from other cellular processes.^[3]^[4] Multienzyme complexes play crucial roles in core cellular metabolism, including energy production and biosynthesis, and are found across all domains of life, from bacteria to eukaryotes.^[2] Prominent examples include the pyruvate dehydrogenase complex, which oxidatively decarboxylates pyruvate to form acetyl-CoA for entry into the citric acid cycle, and the α-ketoglutarate dehydrogenase complex, which performs a similar decarboxylation step within the cycle itself.^[5]^[6] Other well-studied complexes include fatty acid synthase, which iteratively builds lipid chains in a single multifunctional unit.^[2] These structures often incorporate cofactors like thiamine pyrophosphate, lipoic acid, and flavins to facilitate multi-step catalysis.^[6] The formation of multienzyme complexes confers significant kinetic advantages, such as accelerated reaction rates through reduced lag times for intermediate diffusion and enhanced overall pathway flux, which can be up to several orders of magnitude faster than unorganized enzyme systems.^[7] Additionally, they allow for precise regulation via allosteric mechanisms and compartmentalization, preventing the buildup of toxic byproducts while optimizing resource use in dynamic cellular environments.^[3] Dysregulation of these complexes has been implicated in metabolic disorders, underscoring their importance in health and disease.^[8]

Fundamentals

Definition

A multienzyme complex is a stable, non-covalent assembly of multiple enzymes that catalyze sequential reactions within a metabolic pathway, allowing for the direct transfer of reaction intermediates between active sites without release into the surrounding cellular environment.^[9] These complexes form through interactions such as hydrogen bonding, electrostatic forces, and hydrophobic effects, enabling coordinated catalysis that enhances metabolic efficiency.^[10] In biological systems, enzymes generally function as individual catalysts to accelerate specific reactions, but in multienzyme complexes, this modularity gives way to integrated units that process substrates in a streamlined manner.^[11] The defining feature of multienzyme complexes is their physical organization, which supports substrate channeling—a process where intermediates are efficiently passed from one enzyme to the next, minimizing diffusion losses and potential side reactions.^[12] This contrasts with related concepts in metabolic organization: metabolons represent dynamic, transient supramolecular assemblies of sequential enzymes, often regulated by substrate availability or cellular conditions, as originally proposed by Srere for supra-molecular complexes involving structural elements. Similarly, enzyme cascades describe sequential enzymatic actions in a pathway but lack the stable physical associations characteristic of multienzyme complexes, relying instead on diffusible intermediates.^[13] Examples of multienzyme complexes occur in key biosynthetic processes, such as fatty acid synthesis, where the assembly ensures rapid and regulated progression through multi-step reactions.^[11]

Historical Background

The concept of multienzyme complexes emerged in the mid-20th century as biochemists began to recognize that metabolic pathways involved not just isolated enzymes but organized assemblies facilitating coordinated catalysis. Early hints appeared in the 1930s through Hans A. Krebs's formulation of the citric acid cycle, which implied sequential enzymatic actions without free intermediate accumulation, suggesting potential structural integration.^[14] However, the modern notion crystallized in 1947 with David E. Green's pioneering studies on enzyme organization in oxidative metabolism, laying the groundwork for viewing enzymes as interactive units rather than solitary actors.^[15] By the 1950s, specific examples gained traction, with Green's 1951 description of the cyclophorase complex—a mitochondrial assembly implementing the citric acid cycle and fatty acid oxidation—marking a key milestone in isolating and characterizing such structures via differential centrifugation at low temperatures.^[16] The pyruvate dehydrogenase complex (PDC) was first characterized as a paradigmatic multienzyme system in the early 1960s by Lester J. Reed and colleagues, who resolved its components (E1, E2, E3) and demonstrated their stoichiometric assembly, revealing a molecular weight exceeding 4 MDa in bacterial forms.^[17] Green's group at the University of Wisconsin advanced this in the 1960s by resolving and reassembling complexes like PDC and α-ketoglutarate dehydrogenase, using techniques such as ultracentrifugation to assess sedimentation coefficients and early electron microscopy to visualize particulate morphologies.^[18]^[19] The 1970s and 1980s witnessed a paradigm shift toward integrated enzyme units, emphasizing spatiotemporal organization in cellular metabolism over isolated catalysis. This era saw structural elucidation via X-ray crystallography, such as the 1985 crystallization of the tryptophan synthase α₂β₂ complex, providing atomic insights into subunit interfaces and active site coordination. Post-2000 advancements in cryo-electron microscopy (cryo-EM) revolutionized the field, enabling near-atomic resolution of intact complexes like the PDC core (∼3.8 Å in 2021 studies) and revealing dynamic oligomeric states previously inaccessible.^[20] These milestones underscored multienzyme complexes as evolutionarily conserved hubs for metabolic efficiency.

Structural Features

Physical Organization

Multienzyme complexes display a variety of architectural organizations that facilitate the spatial arrangement of their constituent enzymes. Symmetrical configurations, such as those exhibiting icosahedral or octahedral symmetry, provide a highly ordered scaffold with repeating structural units for efficient subunit assembly.^[21] These assemblies typically range in molecular weight from 1 to 10 MDa, accommodating dozens to hundreds of polypeptide chains within a single macromolecular entity. The quaternary structure's stability relies on diverse non-covalent interactions, including hydrophobic contacts that bury nonpolar residues at interfaces, hydrogen bonds that form precise directional links between polar groups, and salt bridges that contribute electrostatic reinforcement between oppositely charged residues.^[22] These interactions collectively minimize dissociation and maintain the complex's integrity across varying cellular environments.^[23] Visualization of multienzyme complex architectures has advanced significantly through cryo-electron microscopy (cryo-EM) and X-ray crystallography. Cryo-EM captures native-like states of large complexes at resolutions of 3–4 Å, revealing overall morphologies and subunit distributions without requiring crystallization.^[24] X-ray crystallography complements this by delineating atomic-level details of rigid domains and interfaces within ordered regions of the assembly. Although structurally stable, multienzyme complexes exhibit inherent flexibility via dynamic conformational shifts that reposition subunits during operation, as evidenced by multiple structural snapshots in cryo-EM datasets. This adaptability arises from flexible linkers and hinges in the polypeptide chains, preserving the core architecture while permitting transient rearrangements.^[11]^[24]

Component Interactions

In multienzyme complexes, binding motifs such as lipoyl domains facilitate dynamic interactions between components through swinging-arm mechanisms, where a covalently attached lipoyl prosthetic group acts as a flexible linker to shuttle substrates and intermediates between active sites of different enzymes.^[25] These domains, typically comprising a β-sheet structure with a flexible linker, enable the lipoyl group to swing between catalytic centers, ensuring efficient transfer without diffusion into the bulk solvent.^[26] Inter-subunit communication in these complexes relies on precise molecular interfaces characterized by electrostatic complementarity, where electropositive regions on one subunit pair with electronegative patches on another to form stable salt bridges, often described as a "charge zipper" mechanism.^[22] Induced fit may occur at some interfaces to optimize binding, though certain interactions, like those in pyruvate dehydrogenase complexes, exhibit a lock-and-key fit with minimal conformational changes upon association.^[22] Cofactors such as lipoic acid and thiamine pyrophosphate (TPP) play crucial roles in linking enzymes; lipoic acid, attached to lysine residues in lipoyl domains, serves as a carrier for acyl groups across subunits, while TPP in decarboxylase components stabilizes intermediates and coordinates with lipoic acid for transfer.^[27] Stoichiometry in multienzyme complexes varies, with heterooligomers often featuring defined ratios of catalytic to regulatory subunits to balance activity and control; for instance, the human pyruvate dehydrogenase complex assembles with 48 catalytic E2 subunits, 12 regulatory E3-binding protein subunits in the core, plus 48 E1 heterotetramers (each with 4 subunits) and 12 E3 dimers, totaling over 200 subunits.^[28] Smaller heterooligomers, such as E1 (α₂β₂ tetramer with 4 subunits) or E3 (homodimer with 2 subunits), integrate into larger assemblies, while ratios can adjust based on cellular needs, ranging from 2 to more than 20 subunits per complex.^[28] Disruption of these interactions by environmental factors like pH shifts or increased ionic strength can lead to subunit dissociation and loss of function; for example, in the Neurospora crassa arom complex, variations in pH and ionic strength cause breakdown into subassemblies of 20,000–80,000 Da, impairing coordinated catalysis.^[29] Mutations at interface residues, such as those altering salt bridges in lipoamide dehydrogenase binding to core components, further promote dissociation by weakening electrostatic interactions, resulting in reduced complex stability and enzymatic efficiency.

Functional Mechanisms

Substrate Channeling

Substrate channeling refers to the direct transfer of reaction intermediates between the active sites of sequential enzymes within a multienzyme complex, minimizing their exposure to the bulk solvent and thereby enhancing overall catalytic efficiency.^[30] This process is facilitated by the physical organization of enzymes in close proximity, which positions active sites optimally for intermediate handover.^[31] Several mechanisms enable this direct transfer. Electrostatic guidance involves charged residues on enzyme surfaces that create pathways, such as positively charged grooves attracting negatively charged intermediates, directing them from one active site to the next.^[31] Hydrophobic tunnels, often lined with nonpolar residues, form enclosed channels within the complex that shield and transport intermediates over distances of tens to hundreds of angstroms.^[30] Swinging arms, consisting of covalently attached prosthetic groups tethered by flexible linkers, undergo conformational rotations to carry intermediates between distant active sites, ensuring protected delivery without solvent intervention.^[32] Substrate channeling confers significant efficiency advantages, including reductions in the apparent Michaelis constant (Km) for intermediates due to their localized high concentrations at downstream sites.^[30] It also prevents side reactions and degradation of unstable or reactive intermediates, leading to overall rate enhancements of 10- to 1000-fold in flux through the pathway.^[31] Evidence for substrate channeling derives from isotope labeling experiments, which demonstrate negligible release of labeled intermediates into the bulk phase, as indicated by minimal dilution in isotope dilution assays.^[31] Computational modeling, including Brownian dynamics simulations, further supports this by revealing favorable tunnel geometries and electrostatic fields that promote efficient intermediate trajectories.^[30] Despite these benefits, substrate channeling is not always absolute; many complexes exhibit imperfect channeling with some intermediate leakage, particularly under cellular stress conditions that disrupt enzyme associations or increase solvent accessibility.^[33]

Catalytic Coordination

In multienzyme complexes, catalytic coordination ensures the synchronized operation of constituent enzymes, enabling seamless progression through sequential reaction steps while optimizing overall metabolic flux. This synchronization minimizes delays in intermediate processing and enhances reaction efficiency compared to dissociated enzymes. Such coordination arises from the spatial proximity and dynamic interactions among enzymes, allowing the output of one catalytic event to directly influence the input of the next.^[34] Sequential catalysis in these complexes typically follows either ordered or random mechanisms. Ordered mechanisms impose a strict sequence of enzymatic actions, where the completion of one step is required before the next begins, often enforced by the complex's architecture. In contrast, random mechanisms permit flexible ordering of substrate binding and product release across enzymes. A critical feature is conformational coupling, whereby the catalytic activity of one enzyme induces structural changes in neighboring enzymes, thereby activating or orienting them for the subsequent reaction and ensuring temporal alignment.^[35]^[36]^[34] Cofactor sharing further supports this coordination through mobile carriers like NAD⁺/NADH, which transfer electrons or hydride ions between active sites in redox-dependent steps. These cofactors undergo regeneration cycles within the complex, where reduction by one enzyme is rapidly followed by oxidation at another, maintaining a balanced pool and preventing rate-limiting accumulation. This intra-complex shuttling reduces diffusion barriers and sustains high turnover rates.^[37]^[38] Kinetic modeling of catalytic coordination extends the Michaelis-Menten paradigm to multi-enzyme systems by incorporating coupled rate equations that account for shared intermediates and interdependent enzyme states. These models describe how the apparent affinities and velocities of individual enzymes are modulated by the complex's overall dynamics, including ping-pong bi-bi mechanisms in which enzymes cycle through modified and unmodified forms without stable multi-substrate complexes. Such frameworks reveal how coordination amplifies catalytic efficiency beyond additive single-enzyme kinetics. Experimental evidence for this synchronization is provided by stopped-flow spectroscopy, which captures transient kinetics and demonstrates coupled rate constants across enzymes, indicating minimal lag phases and direct influence of upstream activities on downstream ones.^[34]

Key Examples

Pyruvate Dehydrogenase Complex

The pyruvate dehydrogenase complex (PDC) is a multienzyme assembly primarily found in the mitochondrial matrix of eukaryotic cells, where it catalyzes the irreversible oxidative decarboxylation of pyruvate derived from glycolysis. This process generates acetyl-CoA, which serves as the primary substrate for the tricarboxylic acid (TCA) cycle, thereby linking carbohydrate catabolism to aerobic respiration and ATP production. The complex's abundance in mitochondria underscores its central role in energy metabolism, with each mammalian cell containing multiple PDC units to handle high flux rates of pyruvate oxidation.^[39]^[40] The PDC consists of three main catalytic subunits: E1 (pyruvate dehydrogenase, a heterotetramer of two α and two β subunits), E2 (dihydrolipoyl transacetylase), and E3 (dihydrolipoyl dehydrogenase, a homodimer). In mammalian systems, the core is formed by 48 copies of E2, arranged with 12 copies of the E3-binding protein (E3BP) to create a stable scaffold of approximately 9 MDa; 48 copies of peripheral E1 and 12 copies of E3 bind dynamically to this core via subunit-binding domains. This oligomeric composition enables efficient catalysis, with the subunits working in concert to process substrates without dissociation of intermediates.^[39]^[41]^[42] Structurally, the PDC features a central core of E2 and E3BP subunits organized in pseudoicosahedral symmetry with dodecahedral organization, providing binding sites for the peripheral E1 and E3 enzymes at its edges. Each E2 subunit includes flexible lipoyl domains attached to swinging arms via hinge regions, which facilitate the transfer of acetyl groups between active sites through substrate channeling, minimizing diffusion losses and enhancing reaction efficiency. These lipoyl arms, numbering 144 per complex (three per E2), oscillate to interact sequentially with E1, the E2 catalytic center, and E3, ensuring coordinated multistep catalysis.^[25]^[43]^[39]^[42] The catalytic pathway proceeds in three coordinated steps. First, E1 uses thiamine pyrophosphate (TPP) as a cofactor to decarboxylate pyruvate, forming hydroxyethyl-TPP and releasing CO₂. Second, the hydroxyethyl group is transferred to the lipoamide cofactor on E2's swinging arm, forming acetyl-dihydrolipoamide, which then reacts with coenzyme A (CoA) to produce acetyl-CoA. Third, E3 reoxidizes the reduced dihydrolipoamide using flavin adenine dinucleotide (FAD), transferring electrons to NAD⁺ to generate NADH. The overall reaction is:

\text{Pyruvate} + \text{[CoA](/page/COA)} + \text{NAD}^{+} \rightarrow \text{[Acetyl-CoA](/page/Acetyl-CoA)} + \text{CO}_{2} + \text{NADH} + \text{H}^{+}

^[39]^[40]

Fatty Acid Synthase Complex

The fatty acid synthase (FAS) complex exemplifies a type I multienzyme system dedicated to de novo fatty acid biosynthesis in eukaryotes. It catalyzes the iterative assembly of saturated fatty acids, primarily palmitate, from simple precursors in a coordinated manner within a single polypeptide chain. This anabolic process occurs in the cytosol and is essential for lipid production in response to nutritional abundance.^[44] In eukaryotes, the FAS complex is composed of a large homodimeric polypeptide, approximately 540 kDa in mammals, where each monomer integrates seven catalytic domains: β-ketoacyl synthase (KS), acetyl/malonyl transacylase (AT or MAT), β-ketoacyl reductase (KR), dehydratase (DH), enoyl reductase (ER), acyl carrier protein (ACP), and thioesterase (TE). These domains are covalently linked by flexible linker regions, enabling intramolecular interactions. In contrast, prokaryotes and plants employ a type II FAS system, consisting of dissociated, individual enzymes that perform analogous functions but lack the fused multidomain architecture.^[45]^[44] The biosynthetic pathway involves the iterative elongation of acyl chains by two-carbon units, starting from acetyl-CoA and malonyl-CoA. The process includes condensation, reduction, dehydration, and further reduction steps, repeated seven times to yield the 16-carbon palmitate. The overall reaction for palmitate synthesis is:

$8 \text{ Acetyl-CoA} + 14 \text{ NADPH} + 7 \text{ ATP} \rightarrow \text{Palmitate} + 14 \text{ NADP}^+ + 8 \text{ CoA} + 7 \text{ ADP} + 7 \text{ P}_i + 6 \text{ H}_2\text{O}

This equation encompasses the coupled activities of acetyl-CoA carboxylase (for malonyl-CoA production) and the FAS complex itself.^[46] Structurally, the eukaryotic FAS forms a flexible X-shaped homodimer featuring two independent reaction chambers, one per monomer, that house the catalytic machinery. The ACP domain, bearing a phosphopantetheine prosthetic group, shuttles growing acyl intermediates between active sites within these chambers, facilitating efficient substrate channeling over distances up to 50 Å in mammalian FAS. Cryo-EM and X-ray studies reveal conformational dynamics that allow domain rearrangements for sequential catalysis.^[47]^[48] Physiologically, the FAS complex drives de novo lipogenesis primarily in the liver and adipose tissue, converting excess carbohydrates into fatty acids for triglyceride storage, membrane lipid synthesis, and energy homeostasis. In mammals, type I FAS predominates in these tissues, differing from the type II system in bacteria, which supports essential membrane lipid production in a more modular fashion.^[49]^[50]

Regulation and Dynamics

Allosteric and Covalent Regulation

Multienzyme complexes are subject to allosteric regulation, where effector molecules bind to sites distinct from the active site, inducing conformational changes that propagate across subunits to modulate catalytic activity. This heterotropic regulation allows for coordinated responses between components, enhancing or inhibiting overall flux based on cellular needs. For instance, product inhibition occurs when end products bind to regulatory sites; in the pyruvate dehydrogenase complex (PDC), NADH binds to the E3 subunit (dihydrolipoyl dehydrogenase), increasing the Km for NAD+ and reducing electron transfer efficiency, thereby slowing the complex's decarboxylation of pyruvate.^[51] Similarly, in the fatty acid synthase (FAS) complex, long-chain acyl-CoAs like palmitoyl-CoA act as allosteric inhibitors, binding to induce conformational shifts that decrease Vmax for substrate condensation steps and prevent excessive lipid accumulation.^[52] Substrate activation provides a counterbalance, as seen in PDC where pyruvate binds allosterically to inhibit pyruvate dehydrogenase kinase (PDK), indirectly promoting complex activity by reducing phosphorylation; this lowers the apparent Km for pyruvate and fine-tunes entry into the TCA cycle.^[39] Feedback loops integrate allosteric signals with cellular energy status, ensuring metabolic homeostasis. High ratios of ATP/ADP, NADH/NAD+, or acetyl-CoA/CoA signal energy abundance, triggering inhibition across the complex; for example, in PDC, elevated acetyl-CoA and NADH synergistically bind to E2 and E3 subunits, respectively, causing a 50-70% reduction in overall activity under physiological conditions.^[53] These heterotropic effects extend to inter-subunit communication, as in the shikimate pathway's multi-enzyme assemblies where aromatic amino acids like phenylalanine inhibit 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) allosterically, altering downstream enzyme conformations in the complex to balance aromatic compound biosynthesis.^[54] Such regulation impacts kinetics by shifting enzyme conformations between high- and low-affinity states, often decreasing Vmax during inhibition or increasing it via activation, without dissociating the complex structure. Covalent modifications provide reversible, long-term control over multienzyme complex activity, often in response to hormonal or nutritional cues. Phosphorylation and dephosphorylation are prominent, particularly in PDC where PDK phosphorylates serine residues (e.g., Ser-264) on the E1 subunit, inducing a conformational change that blocks the active site and inactivates the complex, reducing Vmax by over 90%; conversely, pyruvate dehydrogenase phosphatase (PDP) removes these phosphates to restore activity, with Ca2+ enhancing PDP efficiency during energy demand.^[39] In other complexes, acetylation modifies lysine residues; for instance, reversible acetylation of PDC's E2 subunit modulates complex activity, with deacetylation by sirtuins such as SIRT3.^[55] ADP-ribosylation, though less common in metabolic complexes, occurs in certain bacterial assemblies like those involved in toxin regulation, where it adds ADP-ribose to arginine or diphthamide residues, sterically hindering subunit interactions and decreasing activity until hydrolases reverse the modification.^[56] These modifications integrate with allosteric cues, such as high acetyl-CoA promoting phosphorylation in PDC, to align complex function with broader metabolic dynamics like energy status.

Assembly and Stability

The assembly of multienzyme complexes typically involves the coordinated folding and docking of individual enzyme subunits, often facilitated by molecular chaperones such as Hsp70 and Hsp90 families, which prevent misfolding and aggregation of nascent polypeptides during subunit maturation.^[57] These chaperones act as holdases to maintain subunits in competent states for interaction, with Hsp70 binding exposed hydrophobic regions on nascent chains emerging from the ribosome.^[58] In eukaryotic cells, co-translational assembly is a common mechanism, where pre-synthesized stable subunits dock onto a nascent polypeptide as its interaction domains exit the ribosomal exit tunnel, typically after 24-37 amino acids, thereby enhancing docking efficiency and reducing off-pathway aggregation.^[58] This process relies on specific non-covalent interactions between subunit interfaces, as established in component interactions. The stability of multienzyme complexes is highly dependent on cellular conditions, including pH, temperature, ionic strength, and metabolite concentrations, which can modulate subunit affinities and prevent dissociation.^[59] Stabilizing factors such as scaffolding proteins or electrostatic interactions further reinforce complex integrity, particularly for transient assemblies that form metabolons.^[60] Half-lives of these complexes vary widely, ranging from hours for loosely associated transient forms to days for more rigid structures, reflecting their dynamic equilibrium under physiological conditions.^[61] Disassembly of multienzyme complexes is triggered by cellular stress, such as elevated temperatures or oxidative conditions, leading to subunit dissociation and aggregate formation.^[62] Proteolytic degradation via the ubiquitin-proteasome pathway serves as a primary mechanism for complex turnover, where ubiquitination targets individual subunits or entire assemblies for proteolysis, ensuring cellular homeostasis.^[63] In vitro reconstitution of multienzyme complexes enables detailed study of assembly dynamics and has been achieved through methods like heterologous co-expression of subunits in bacterial or yeast systems, followed by affinity purification to isolate functional assemblies.^[64] Scaffold-based approaches, using protein domains such as cohesin-dockerin pairs or DNA nanostructures, facilitate controlled docking of purified enzymes to mimic native geometries and assess stability under defined conditions.^[65] These techniques often incorporate chaperone co-expression to replicate in vivo folding assistance, allowing quantification of assembly yields and kinetic parameters.^[66]

Biological and Evolutionary Significance

Metabolic Advantages

Multienzyme complexes provide significant metabolic advantages by enhancing the efficiency of sequential enzymatic reactions through physical proximity and substrate channeling, which minimizes diffusion times for intermediates and can increase overall pathway flux by orders of magnitude. For instance, in diffusion-limited steps, enzyme clustering can elevate effective local concentrations, leading to rate enhancements of up to 1000-fold compared to free enzymes, as demonstrated in models of metabolic pathways where intermediate transfer is direct rather than diffusive. This proximity also conserves cellular resources by reducing the need for large pools of unstable or reactive intermediates, preventing their accumulation and potential side reactions that would otherwise dilute metabolic flux. A key benefit arises from compartmentalization, where multienzyme complexes shield intermediates from competing cellular pathways or dilution in the crowded cytosolic environment, thereby exerting tighter control over flux in linear metabolic routes. In the tricarboxylic acid (TCA) cycle, for example, the association of malate dehydrogenase and citrate synthase facilitates rapid oxaloacetate transfer, curtailing interference from enzymes like aspartate aminotransferase and maintaining directional flow. Such organization enhances the committed steps of metabolism, such as the production of acetyl-CoA from pyruvate via the pyruvate dehydrogenase complex (PDC), which is localized in the mitochondrial matrix to optimize oxidative metabolism while isolating it from cytosolic glycolysis.^[67] At the cellular level, these complexes contribute to metabolic zoning by partitioning reactions between organelles, ensuring efficient energy partitioning—such as directing glycolytic flux toward mitochondrial oxidation—and supporting high-throughput processes like fatty acid synthesis in the cytosol. Dysfunctions in these systems underscore their advantages; for example, PDC deficiency impairs substrate channeling and acetyl-CoA flux, resulting in lactic acidosis due to pyruvate accumulation and inefficient carbohydrate metabolism.^[68]

Evolutionary Origins

Multienzyme complexes trace their origins to ancient prokaryotic ancestors, with core structures like the pyruvate dehydrogenase complex (PDC) exhibiting conserved designs across bacterial lineages that likely predate the divergence of major domains of life. The E2 component of PDC, which forms the structural core, derives from primordial acyltransferase enzymes and assembles into highly symmetric multimers—cubic in gram-negative bacteria and icosahedral in gram-positive bacteria and eukaryotes—reflecting a shared evolutionary blueprint that facilitated efficient substrate channeling in early metabolic pathways.^[27] Although direct evidence for PDC in the last universal common ancestor (LUCA) remains elusive due to its association with aerobic metabolism, comparative analyses of metabolic gene sets suggest that analogous dehydrogenase activities were present in LUCA's core network, evolving into modern complexes through prokaryotic innovations.^[69] A key mechanism in the evolution of multienzyme complexes involved gene fusion events, particularly evident in the fatty acid synthase (FAS) system, where dissociated monofunctional enzymes in bacterial type II FAS fused into large, multifunctional polypeptides characteristic of eukaryotic type I FAS. This transition, driven by domain shuffling and duplication, allowed for the integration of catalytic domains such as ketoacyl synthase, acyltransferase, and acyl carrier protein into single polypeptides, enhancing stability and coordination in more complex cellular environments. Phylogenetic reconstructions indicate that these fusions occurred after the prokaryote-eukaryote split, with modular architectures in bacterial polyketide synthases serving as precursors that were rearranged in eukaryotes.^[70] Selective pressures in fluctuating ancient environments favored the assembly of multienzyme complexes, promoting their retention and spread through horizontal gene transfer (HGT), as seen in modular systems like the Sox sulfur oxidation complex, which originated in thermophilic bacterial ancestors and disseminated via HGT among Aquificae and Epsilonproteobacteria. Such transfers enabled adaptation to variable redox conditions by bundling enzymes into efficient units, reducing diffusion losses in diverse niches. Comparative genomics further reveals broad conservation of multienzyme complexes across archaea, bacteria, and eukaryotes, with 2-oxoacid dehydrogenase complexes present in aerobic archaea and bacteria, underscoring their ancient utility. However, in minimal genomes like those of Mycoplasma species, reductive evolution led to losses of certain complexes, such as components of assimilative dehydrogenase pathways, reflecting parasitism-driven genome streamlining while retaining simplified versions for essential metabolism.^[71]^[72]^[73]

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The pyruvate dehydrogenase complexes (PDCs) from all known living organisms comprise three principal catalytic components for their mission.<|control11|><|separator|>
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Pyruvate Dehydrogenase Complex and TCA Cycle
The Pyruvate Dehydrogenase and TCA cycle page details the pyruvate dehydrogenase (PDH) reaction and the pathway for oxidation of acetyl-CoA.<|separator|>
[42]
Structures of the Human Pyruvate Dehydrogenase Complex Cores
Among them, one E3BP and two of the four E2 subunits are likely to be bound by E3 and E1 molecules, respectively. The E3 molecule interacts with E1s to form ...
[43]
Fatty Acid Biosynthesis Revisited: Structure Elucidation and ...
An excellent current review by Grininger discusses type I structure and the evolution of these megasynthases.Fas Transport: Acp · Chain Initiation: Mcat · Enoyl Acp Reductase (er)
[44]
Current understanding of fatty acid biosynthesis and the acyl carrier ...
Jul 28, 2010 · FASs (FA synthases) can be divided into two classes, type I and II, which are primarily present in eukaryotes and bacteria/plants respectively.
[45]
Comparative Approach of the de novo Fatty Acid Synthesis ...
The biosynthesis of palmitate is catalyzed by the complex of fatty acid synthase (FAS). The overall reaction catalyzed by FAS can be summarized by the equation: ...
[46]
Architecture of mammalian fatty acid synthase at 4.5 A resolution
Mar 3, 2006 · We have calculated a 4.5 angstrom-resolution x-ray crystallographic map of porcine fatty acid synthase, highly homologous to the human multienzyme.Missing: type | Show results with:type
[47]
Snapshots of acyl carrier protein shuttling in human fatty acid synthase
Feb 20, 2025 · The dimer forms two reaction chambers that each contain the entire catalytic machinery for synthesizing palmitate (Extended Data Fig. 4). We ...
[48]
Regulation and Metabolic Significance of De Novo Lipogenesis in ...
De novo lipogenesis (DNL) is a complex and highly regulated process in which carbohydrates from circulation are converted into fatty acids.
[49]
The Human Fatty Acid Synthase Gene and De Novo Lipogenesis ...
Fatty acid synthase (FAS) is the central enzyme in DNL, catalyzing all of the enzymatic steps in the conversion of acetyl-CoA and malonyl-CoA to palmitate. FAS ...
[50]
Detailed evaluation of pyruvate dehydrogenase complex inhibition ...
Mar 2, 2021 · Our model reveals that PDC flux in physiological conditions is primarily inhibited by product inhibition (∼60%), mostly NADH inhibition (∼30-50%).
[51]
Detailed evaluation of pyruvate dehydrogenase complex inhibition ...
However, PDK and PDP activity are allosterically regulated by several effectors fully overlapping PDC substrates and products.
[52]
Multi-Enzyme Synergy and Allosteric Regulation in the Shikimate ...
This review explores how multi-enzyme synergy and allosteric regulation coordinate metabolic flux through this pathway by focusing on three key enzymes: 3-deoxy ...
[53]
Emerging roles of pyruvate dehydrogenase phosphatase 1 - Frontiers
May 25, 2025 · Within the mitochondria, the PDH converts the pyruvate to acetyl-CoA, feeding into the tricarboxylic acid (TCA) cycle for energy production.
[54]
ADP-ribosylation from molecular mechanisms to therapeutic ...
In basic molecular terms, ADP-ribosylation is an enzymatic modification reaction that proceeds via the transfer of the ADP-ribose moiety from NAD+ as a donor ...
[55]
Hsp70/Hsp90 chaperone machinery is involved in the assembly of ...
In this work, we provide evidence that the heat shock protein 90 (Hsp90)/heat shock protein 70 (Hsp70) chaperone machinery is involved in stabilization or ...
[56]
Cotranslational assembly of protein complexes in eukaryotes ... - NIH
We find nine complexes assemble cotranslationally; the three complexes that do not show cotranslational interactions are regulated by dedicated assembly ...
[57]
First evidence for a multienzyme complex of lipid biosynthesis ...
Feb 15, 2018 · We report here the first direct evidence of the existence of a lipogenic multienzyme complex (the lipid metabolon) involving ME, FAS, ATP: citrate lyase (ACL), ...
[58]
Stable and Temporary Enzyme Complexes and Metabolons ...
Methods of evaluating substrate channeling. (A) The isotope dilution experiment was used to test channeling of glycolysis. The isolated potato mitochondria was ...Multimeric Enzyme Complexes · Protein Complexes In... · The Tca Cycle
[59]
Lysosomal multienzyme complex: biochemistry, genetics ... - PubMed
The complex plays a protective role for all components, extending their half-life in the lysosome from several hours to several days; and for sialidase, the ...
[60]
Thermal Disassembly of Pyruvate Dehydrogenase Multienzyme ...
Jun 12, 2014 · The thermal denaturation of the enzymes resulted in disassembly of the complex. El was involved in a resulting aggregate of the complex. The ...
[61]
The ubiquitin-proteasome proteolytic pathway: destruction ... - PubMed
Degradation of a protein via the ubiquitin/proteasome pathway involves two successive steps: 1) conjugation of multiple ubiquitin moieties to the substrate and ...
[62]
Reconstitution of Multi-Protein Complexes through Ribozyme ...
Dec 13, 2022 · We developed a Ribozyme-Assisted Polycistronic co-expression system (pRAP) for heterologous co-production and in vivo assembly of multi-subunit complexes.
[63]
Research progress of multi-enzyme complexes based on the design ...
Oct 23, 2023 · ... and SH3–PDZ–GBD for enzyme cascade. Full size table. Scaffold ... and the biotechnological applications of multienzyme complex. Appl ...
[64]
DNA-Scaffolded Proximity Assembly and Confinement of ...
Apr 4, 2020 · In this review, we focus on recent progress in the field of DNA-scaffolded assembly and confinement of multienzyme reactions.<|separator|>
[65]
https://bioresourcesbioprocessing.springeropen.com/articles/10.1186/s40643-023-00695-8
[66]
Pyruvate Dehydrogenase Complex Deficiency: An Unusual Cause ...
Pyruvate dehydrogenase complex deficiency (PDCD) is a rare genetic, potentially life-threatening mitochondrial disorder commonly associated with lactic acidosis ...
[67]
The metabolic network of the last bacterial common ancestor - Nature
Mar 26, 2021 · We identified 146 protein families that trace to the last bacterial common ancestor, LBCA, and form the conserved predicted core of its metabolic network.
[68]
The type I fatty acid and polyketide synthases: a tale of two ...
Following a period of intense competition between David Green's group in Wisconsin and Feodor Lynen's group in Munich, the enzymological details of the ...
[69]
Origin of the Sox multienzyme complex system in ancient ... - PubMed
Jul 16, 2009 · ... originated in putatively common ancestors of Aquificae and Epsilonproteobacteria, and evolved through extensive horizontal gene transfer ...
[70]
Multienzyme Complexes in the Archaea: Predictions from Genome ...
Abstract. Aerobic Bacteria and Eukarya possess a family of 2-oxoacid dehydrogenase multienzyme complexes that catalyse the general reaction: EquationSource ...Missing: comparative | Show results with:comparative
[71]
Molecular Biology and Pathogenicity of Mycoplasmas - PMC
The supply of nutrients from their hosts apparently enabled mycoplasmas to lose, during evolution, the genes for many assimilative processes. During their ...