3-hydroxy-3-methylglutaryl-coenzyme A lyase deficiency: review of 18 reported patients

HMG-CoA lyase (HMGCL 4 ; EC 4.1.3.4) catalyzes a cationdependent cleavage of substrate into acetyl-CoA and acetoacetate (Scheme 1) (1). This reaction is a key step in ketogenesis, the products of which support anaplerotic metabolism in bacteria (2) and energy production in nonhepatic animal tissues (3). Ketogenesis is particularly important to human metabolism during the prenatal period and during fasting or starvation. In accordance with these physiological roles, it is not surprising that gene knock-out in mice results in embryonic lethality (4). The physiological importance of the enzyme in humans is underscored by the observation that mutations that diminish HMGCL activity correlate with inherited metabolic disease that can be lethal if uncontrolled (5).A variety of human mutations, including many point mutations in protein-coding exons of the gene, have been documented (6). A computational modeling approach was used to explain the molecular basis for some mutations linked to inherited disease (7). This led to the prediction that HMGCL adopts a ␤/␣-barrel fold and a proposal that the acyl-S-pantetheine moiety of the bound substrate passes through the barrel lumen. Initial structural work on human HMGCL liganded to cation and hydroxyglutarate (8) demonstrated that the folding prediction was reasonable but that the substrate binding proposal was unlikely to be correct. The positions of bound cation and hydroxyglutarate (from hydrolyzed hydroxyglutaryl-CoA) indicated the catalytic site to be positioned at the C-terminal end of the barrel, but the absence of a full acyl-CoA molecule in the experimentally determined structure limited detailed insight into the substrate-binding site.To more fully address questions regarding the conformation of bound substrate, activator cation liganding, details concerning reaction chemistry and specificity, as well as the molecular basis for certain inherited HMGCL deficiencies, new structural information on enzyme bound to an intact acyl-CoA molecule is required. To remedy this need, complexes of the WT enzyme with the competitive inhibitor 3-hydroxyglutaryl-CoA and also of catalytically deficient R41M enzyme with the authentic substrate HMG-CoA have been supplemented with the activator cation Mg 2ϩ , and crystallization of the desired ternary complexes has been accomplished. Diffraction quality crystals have been produced, supporting three-dimensional structural determinations for ternary complexes of enzyme, cation, and either the acyl-CoA substrate or inhibitory analog. These findings are

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confidence: 99%

Functional Insights into Human HMG-CoA Lyase from Structures of Acyl-CoA-containing Ternary Complexes

Runquist

Montgomery

et al. 2010

“…This set of compounds represents an alternative metabolic energy source for brain, heart, and kidneys and plays an important role in diabetes and some forms of epilepsy (3,4). Ketone bodies are essential to maintain physiological viability during hypoglycemia because cells die due to energy deprivation when both glucose and ketone body concentrations fall below critical threshold levels.…”

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confidence: 99%

Crystal Structures of Two Bacterial 3-Hydroxy-3-methylglutaryl-CoA Lyases Suggest a Common Catalytic Mechanism among a Family of TIM Barrel Metalloenzymes Cleaving Carbon-Carbon Bonds

Forouhar

Hussain

Farid

et al. 2006

The enzyme 3-hydroxy-3-methylglutaryl-coenzyme A (HMGCoA) lyase catalyzes the terminal steps in ketone body generation and leucine degradation. Mutations in this enzyme cause a human autosomal recessive disorder called primary metabolic aciduria, which typically kills victims because of an inability to tolerate hypoglycemia. Here we present crystal structures of the HMG-CoA lyases from Bacillus subtilis and Brucella melitensis at 2.7 and 2.3 Å resolution, respectively. These enzymes share greater than 45% sequence identity with the human orthologue. Although the enzyme has the anticipated triose-phosphate isomerase (TIM) barrel fold, the catalytic center contains a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel, contrary to the predictions of homology models. Surprisingly, the residues forming this cation-binding site and most of their interaction partners are shared with three other TIM barrel enzymes that catalyze diverse carbon-carbon bond cleavage reactions believed to proceed through enolate intermediates (4-hydroxy-2-ketovalerate aldolase, 2-isopropylmalate synthase, and transcarboxylase 5S). We propose the name "DRE-TIM metallolyases" for this newly identified enzyme family likely to employ a common catalytic reaction mechanism involving an invariant AspArg-Glu (DRE) triplet. The Asp ligates the divalent cation, while the Arg probably stabilizes charge accumulation in the enolate intermediate, and the Glu maintains the precise structural alignment of the Asp and Arg. We propose a detailed model for the catalytic reaction mechanism of HMG-CoA lyase based on the examination of previously reported product complexes of other DRE-TIM metallolyases and induced fit substrate docking studies conducted using the crystal structure of human HMG-CoA lyase (reported in the accompanying paper by Fu, et al.

“…Uncontrolled HMG-CoA lyase deficiency is lethal in about 20% of cases and can result in mental retardation, episodes of seizure, and coma (5). Several mutations in the HMG-CoA lyase gene correlating with deficiency have been identified (5), including the following missense mutations: H233R (6), R41Q, D42E, D42H, D42G (7), and recently E279K (8). These mutations have been studied by using our recombinant human lyase protein expression system, providing a more detailed biochemical explanation for the significant consequences of such mutations.…”

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confidence: 99%

Crystal Structure of Human 3-Hydroxy-3-methylglutaryl-CoA Lyase

Runquist

Forouhar

et al. 2006

3-Hydroxy-3-methylglutaryl-CoA (HMG-CoA) lyase is a key enzyme in the ketogenic pathway that supplies metabolic fuel to extrahepatic tissues. Enzyme deficiency may be due to a variety of human mutations and can be fatal. Diminished activity has been explained based on analyses of recombinant human mutant proteins or, more recently, in the context of structural models for the enzyme. We report the experimental determination of a crystal structure at 2.1 Å resolution of the recombinant human mitochondrial HMG-CoA lyase containing a bound activator cation and the dicarboxylic acid 3-hydroxyglutarate. The enzyme adopts a (␤␣) 8 barrel fold, and the N-terminal barrel end is occluded. The structure of a physiologically relevant dimer suggests that substrate access to the active site involves binding across the cavity located at the C-terminal end of the barrel. An alternative hypothesis that involves substrate insertion through a pore proposed to extend through the barrel is not compatible with the observed structure. The activator cation ligands included Asn 235; the latter three residues had been implicated previously as contributing to metal binding or enzyme activity. Arg 41, previously shown to have a major effect on catalytic efficiency, is also located at the active site. In the observed structure, this residue interacts with a carboxyl group of 3-hydroxyglutarate, the hydrolysis product of the competitive inhibitor 3-hydroxyglutaryl-CoA required for crystallization of human enzyme. The structure provides a rationale for the decrease in enzyme activity due to clinical mutations, including H233R, R41Q, D42H, and D204N, that compromise active site function or enzyme stability.3-Hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) 2 lyase (EC 4.1.3.4) catalyzes the cleavage of HMG-CoA into acetyl-CoA and acetoacetate (1). Scheme 1 is a key step in ketogenesis (2), which maintains the energy requirements of nonhepatic tissues especially during fasting or starvation. The reaction is also an important step in leucine catabolism (3). Homologous C-C bond cleavage or condensation reactions are catalyzed by various members of the HMG-CoA lyase family of enzymes, which includes homocitrate synthase, isopropylmalate synthase, and 4-hydroxy-2-ketovalerate aldolase (4).The importance of the ketogenic cycle is underscored in hereditary HMG-CoA lyase deficiency, which can result in hypoketotic hypoglycemia and a marked increase in serum levels of several organic acids. Uncontrolled HMG-CoA lyase deficiency is lethal in about 20% of cases and can result in mental retardation, episodes of seizure, and coma (5). Several mutations in the HMG-CoA lyase gene correlating with deficiency have been identified (5), including the following missense mutations: H233R (6), R41Q, D42E, D42H, D42G (7), and recently E279K (8). These mutations have been studied by using our recombinant human lyase protein expression system, providing a more detailed biochemical explanation for the significant consequences of such mutations.The cleavage of HMG-CoA req...