Abstract:The pyruvate dehydrogenase multienzyme complex (PDHc) connects glycolysis to the tricarboxylic acid cycle by producing acetyl-CoA via the decarboxylation of pyruvate. Because of its pivotal role in glucose metabolism, this complex is closely regulated in mammals by reversible phosphorylation, the modulation of which is of interest in treating cancer, diabetes, and obesity. Mutations such as that leading to the αV138M variant in pyruvate dehydrogenase, the pyruvate-decarboxylating PDHc E1 component, can result … Show more
“…3 ) is likely to contribute to a more disordered loop and consequently lower enzymatic activity. Notably, the degree of disorder in P-loop A has been negatively correlated with E1 enzymatic activity, since an ordered loop favors TPP binding, which itself promotes P-loop A order [ 21 ]. Fig.…”
Section: Resultsmentioning
confidence: 99%
“…To better establish genotype–phenotype correlations regarding the missense mutations in PDHA1 , we undertook an in silico analysis of protein variants resulting from the described mutations. Besides evaluating the potential pathogenicity of the mutations using the PolyPhen-2 server [ 19 ], we sought to obtain structural models of the protein variants through two complementary strategies, previously described for the p.R253G, p.R378C, p.R378H, and p.F205L variants [ 20 ], and herein extended to p.R302H: i) submitting the sequence of the amino acid substituted variant to the SwissModel server and retrieving the corresponding model; and ii) using the Mutagenesis tool in Pymol (version 1.7) [ 43 ] employing the structure of WT PDC-E1 (PDB entry 3EXE) as template [ 21 ].…”
Background
The pyruvate dehydrogenase complex (PDC) catalyzes the irreversible decarboxylation of pyruvate into acetyl-CoA. PDC deficiency can be caused by alterations in any of the genes encoding its several subunits. The resulting phenotype, though very heterogeneous, mainly affects the central nervous system. The aim of this study is to describe and discuss the clinical, biochemical and genotypic information from thirteen PDC deficient patients, thus seeking to establish possible genotype–phenotype correlations.
Results
The mutational spectrum showed that seven patients carry mutations in the PDHA1 gene encoding the E1α subunit, five patients carry mutations in the PDHX gene encoding the E3 binding protein, and the remaining patient carries mutations in the DLD gene encoding the E3 subunit. These data corroborate earlier reports describing PDHA1 mutations as the predominant cause of PDC deficiency but also reveal a notable prevalence of PDHX mutations among Portuguese patients, most of them carrying what seems to be a private mutation (p.R284X). The biochemical analyses revealed high lactate and pyruvate plasma levels whereas the lactate/pyruvate ratio was below 16; enzymatic activities, when compared to control values, indicated to be independent from the genotype and ranged from 8.5% to 30%, the latter being considered a cut-off value for primary PDC deficiency. Concerning the clinical features, all patients displayed psychomotor retardation/developmental delay, the severity of which seems to correlate with the type and localization of the mutation carried by the patient. The therapeutic options essentially include the administration of a ketogenic diet and supplementation with thiamine, although arginine aspartate intake revealed to be beneficial in some patients. Moreover, in silico analysis of the missense mutations present in this PDC deficient population allowed to envisage the molecular mechanism underlying these pathogenic variants.
Conclusion
The identification of the disease-causing mutations, together with the functional and structural characterization of the mutant protein variants, allow to obtain an insight on the severity of the clinical phenotype and the selection of the most appropriate therapy.
“…3 ) is likely to contribute to a more disordered loop and consequently lower enzymatic activity. Notably, the degree of disorder in P-loop A has been negatively correlated with E1 enzymatic activity, since an ordered loop favors TPP binding, which itself promotes P-loop A order [ 21 ]. Fig.…”
Section: Resultsmentioning
confidence: 99%
“…To better establish genotype–phenotype correlations regarding the missense mutations in PDHA1 , we undertook an in silico analysis of protein variants resulting from the described mutations. Besides evaluating the potential pathogenicity of the mutations using the PolyPhen-2 server [ 19 ], we sought to obtain structural models of the protein variants through two complementary strategies, previously described for the p.R253G, p.R378C, p.R378H, and p.F205L variants [ 20 ], and herein extended to p.R302H: i) submitting the sequence of the amino acid substituted variant to the SwissModel server and retrieving the corresponding model; and ii) using the Mutagenesis tool in Pymol (version 1.7) [ 43 ] employing the structure of WT PDC-E1 (PDB entry 3EXE) as template [ 21 ].…”
Background
The pyruvate dehydrogenase complex (PDC) catalyzes the irreversible decarboxylation of pyruvate into acetyl-CoA. PDC deficiency can be caused by alterations in any of the genes encoding its several subunits. The resulting phenotype, though very heterogeneous, mainly affects the central nervous system. The aim of this study is to describe and discuss the clinical, biochemical and genotypic information from thirteen PDC deficient patients, thus seeking to establish possible genotype–phenotype correlations.
Results
The mutational spectrum showed that seven patients carry mutations in the PDHA1 gene encoding the E1α subunit, five patients carry mutations in the PDHX gene encoding the E3 binding protein, and the remaining patient carries mutations in the DLD gene encoding the E3 subunit. These data corroborate earlier reports describing PDHA1 mutations as the predominant cause of PDC deficiency but also reveal a notable prevalence of PDHX mutations among Portuguese patients, most of them carrying what seems to be a private mutation (p.R284X). The biochemical analyses revealed high lactate and pyruvate plasma levels whereas the lactate/pyruvate ratio was below 16; enzymatic activities, when compared to control values, indicated to be independent from the genotype and ranged from 8.5% to 30%, the latter being considered a cut-off value for primary PDC deficiency. Concerning the clinical features, all patients displayed psychomotor retardation/developmental delay, the severity of which seems to correlate with the type and localization of the mutation carried by the patient. The therapeutic options essentially include the administration of a ketogenic diet and supplementation with thiamine, although arginine aspartate intake revealed to be beneficial in some patients. Moreover, in silico analysis of the missense mutations present in this PDC deficient population allowed to envisage the molecular mechanism underlying these pathogenic variants.
Conclusion
The identification of the disease-causing mutations, together with the functional and structural characterization of the mutant protein variants, allow to obtain an insight on the severity of the clinical phenotype and the selection of the most appropriate therapy.
“…Therefore, in the p.R302H E1α variant, the net loss of four possible side chain interactions with other P-loop A residues ( Figure 3) is likely to contribute to a more disordered loop and consequently lower enzymatic activity. Notably, the degree of disorder in P-loop A has been negatively correlated with E1 enzymatic activity, since an ordered loop favors TPP binding, which itself promotes P-loop A order (19).…”
Background : Pyruvate dehydrogenase complex (PDC) catalyzes the irreversible decarboxylation of pyruvate into acetyl-CoA which ultimately generates ATP. PDC deficiency can be caused by alterations in any of the genes encoding its several subunits, and the resulting phenotype, though very heterogeneous, mainly affects the neuro-encephalic system. The aim of this study is to describe and discuss the clinic, metabolic and genotypic profiles of thirteen PDC deficient patients, thus seeking to establish possible genotype-phenotype correlations. Results : The mutational spectrum revealed that seven patients (54 %) carry mutations in the PDHA1 gene , encoding the E1α subunit, five patients (38 %) carry mutations in the PDHX gene, encoding the E3 binding protein, and the remaining patient (8 %) harbors mutations in the DLD gene, encoding the E3 subunit. These data corroborate PDHA1 mutations as the predominant cause of PDC deficiency, though revealing a notable prevalence of PDHX mutations among Portuguese patients, most of them carrying a seemingly private mutation (p.R284X). The biochemical analyses revealed high lactate and pyruvate plasma levels whereas de ratio L/P was under 16; enzymatic activities, when compared to control values, revealed to be independent from the genotype and ranged from 8.5% to 30% which may be considered a cut-off value for primary PDC deficiency. Concerning the clinical features, all patients displayed developmental delay/psychomotor retardation, the severity of which seems to correlate with the type and localization of the mutation carried by the patient. The therapeutic options essentially go through the administration of a ketogenic diet and supplementation with thiamine, although arginine aspartate intake revealed to be beneficial in some patients. Moreover, the in silico analysis of the missense mutations present in this PDC deficient population allowed to understand the molecular mechanism underlying these pathogenic variants. Conclusion : The identification of the disease-causing mutations, together with the functional and structural characterization of the mutant protein variants, allows to get insight on the severity of the clinical phenotype and the selection of the most appropriate therapy.
“…The phosphorylation of loop A plays an integral role in channeling and anchoring thiamine diphosphate to the active site of E1p, whereas the phosphorylation of loop B coordinates a Mg 2+ ion that is chelated by the diphosphate group of the cofactor [ 36 ]. The disorder of these phosphorylation loops was well-defined by the authors, who interpreted the absence of electron density in the crystallographic structures as characteristic of disorder [ 36 , 80 ]. The phosphorylation of the E1p loops causes a steric clash between introduced phosphoryl groups and nearby residues, abolishing the hydrogen-bonding network essential for maintaining ordered loop conformations [ 36 ].…”
Section: Introductionmentioning
confidence: 99%
“…The phosphorylation of the E1p loops causes a steric clash between introduced phosphoryl groups and nearby residues, abolishing the hydrogen-bonding network essential for maintaining ordered loop conformations [ 36 ]. Surprisingly, the increased regulatory loop disorder is associated with the loss of E1p catalytic efficiency, a molecular cause of PDHc deficiency (PDCD) [ 80 ]. Other modifications are also important, e.g.…”
Metabolites produced via traditional biochemical processes affect intracellular communication, inflammation, and malignancy. Unexpectedly, acetyl-CoA, α-ketoglutarate and palmitic acid, which are chemical species of reactions catalyzed by highly abundant, gigantic enzymatic complexes, dubbed as “metabolons”, have broad “nonmetabolic” signaling functions. Conserved unstructured regions within metabolons determine the yield of these metabolites. Unstructured regions tether functional protein domains, act as spatial constraints to confine constituent enzyme communication, and, in the case of acetyl-CoA production, tend to be regulated by intricate phosphorylation patterns. This review presents the multifaceted roles of these three significant metabolites and describes how their perturbation leads to altered or transformed cellular function. Their dedicated enzymatic systems are then introduced, namely, the pyruvate dehydrogenase (PDH) and oxoglutarate dehydrogenase (OGDH) complexes, and the fatty acid synthase (FAS), with a particular focus on their structural characterization and the localization of unstructured regions. Finally, upstream metabolite regulation, in which spatial occupancy of unstructured regions within dedicated metabolons may affect metabolite availability and subsequently alter cell functions, is discussed.
Graphical abstract
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