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| isovaleryl-CoA |
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| CHEBI:15487 |
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| A methylbutanoyl-CoA is the S-isovaleryl derivative of coenzyme A. |
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This entity has been manually annotated by the ChEBI Team.
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CHEBI:11856, CHEBI:1598, CHEBI:14481, CHEBI:20126
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| No supplier information found for this compound. |
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Molfile
XML
SDF
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more structures >>
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call loadScript javascripts\jsmol\core\package.js call loadScript javascripts\jsmol\core\core.z.js -- required by ClazzNode call loadScript javascripts\jsmol\J\awtjs2d\WebOutputChannel.js
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InChI=1S/C26H44N7O17P3S/c1- 14(2)9-17(35)54-8-7-28-16(34)5-6-29-24(38)21(37)26(3,4)11-47-53(44,45)50-52(42,43)46-10-15-20(49-51(39,40)41)19(36)25(48-15)33-13-32-18-22(27)30-12-31-23(18)33/h12-15,19-21,25,36-37H,5-11H2,1-4H3,(H,28,34)(H,29,38)(H,42,43)(H,44,45)(H2,27,30,31)(H2,39,40,41)/t15-,19-,20-,21+,25-/m1/s1 |
| UYVZIWWBJMYRCD-ZMHDXICWSA-N |
| CC(C)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N |
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Mus musculus
(NCBI:txid10090)
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Source: BioModels - MODEL1507180067
See:
PubMed
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Bacillus methanolicus
(NCBI:txid1471)
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From MetaboLights
See:
MetaboLights Study
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acyl donor
Any donor that can transfer acyl groups between molecular entities.
(via acyl-CoA )
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mouse metabolite
Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus).
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View more via ChEBI Ontology
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3'-phosphoadenosine 5'-{3-[(3R)-3-hydroxy-2,2-dimethyl-4-{[3-({2-[(3-methylbutanoyl)sulfanyl]ethyl}amino)-3-oxopropyl]amino}-4-oxobutyl] dihydrogen diphosphate}
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3-Methylbutanoyl-CoA
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KEGG COMPOUND
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3-methylbutanoyl-coenzyme A
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ChEBI
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3-methylbutyryl-CoA
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ChEBI
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3-methylbutyryl-coenzyme A
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ChEBI
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β-methylbutanoyl-CoA
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ChEBI
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β-methylbutanoyl-coenzyme A
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ChEBI
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β-methylbutyryl-CoA
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ChEBI
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β-methylbutyryl-coenzyme A
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ChEBI
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Isovaleryl-CoA
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KEGG COMPOUND
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isovaleryl-coenzyme A
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ChemIDplus
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S-(3-methylbutanoyl)-coenzyme A
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ChemIDplus
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6244-91-3
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CAS Registry Number
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ChemIDplus
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78268
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Reaxys Registry Number
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Reaxys
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Bock T, Volz C, Hering V, Scrima A, Müller R, Blankenfeldt W (2017)
The AibR-isovaleryl coenzyme A regulator and its DNA binding site - a model for the regulation of alternative de novo isovaleryl coenzyme A biosynthesis in Myxococcus xanthus.
Nucleic acids research 45, 2166-2178 [PubMed:27940564]
[show Abstract]
Isovaleryl coenzyme A (IV-CoA) is an important building block of iso-fatty acids. In myxobacteria, IV-CoA is essential for the formation of signaling molecules involved in fruiting body formation. Leucine degradation is the common source of IV-CoA, but a second, de novo biosynthetic route to IV-CoA termed AIB (alternative IV-CoA biosynthesis) was recently discovered in M. xanthus. The AIB-operon contains the TetR-like transcriptional regulator AibR, which we characterize in this study. We demonstrate that IV-CoA binds AibR with micromolar affinity and show by gelshift experiments that AibR interacts with the promoter region of the AIB-operon once IV-CoA is present. We identify an 18-bp near-perfect palindromic repeat as containing the AibR operator and provide evidence that AibR also controls an additional genomic locus coding for a putative acetyl-CoA acetyltransferase. To elucidate atomic details, we determined crystal structures of AibR in the apo, the IV-CoA- and the IV-CoA-DNA-bound state to 1.7 Å, 2.35 Å and 2.92 Å, respectively. IV-CoA induces partial unfolding of an α-helix, which allows sequence-specific interactions between AibR and its operator. This study provides insights into AibR-mediated regulation and shows that AibR functions in an unusual TetR-like manner by blocking transcription not in the ligand-free but in the effector-bound state. | Dong SH, Frane ND, Christensen QH, Greenberg EP, Nagarajan R, Nair SK (2017)
Molecular basis for the substrate specificity of quorum signal synthases.
Proceedings of the National Academy of Sciences of the United States of America 114, 9092-9097 [PubMed:28784791]
[show Abstract]
In several Proteobacteria, LuxI-type enzymes catalyze the biosynthesis of acyl-homoserine lactones (AHL) signals using S-adenosyl-l-methionine and either cellular acyl carrier protein (ACP)-coupled fatty acids or CoA-aryl/acyl moieties as progenitors. Little is known about the molecular mechanism of signal biosynthesis, the basis for substrate specificity, or the rationale for donor specificity for any LuxI member. Here, we present several cocrystal structures of BjaI, a CoA-dependent LuxI homolog that represent views of enzyme complexes that exist along the reaction coordinate of signal synthesis. Complementary biophysical, structure-function, and kinetic analysis define the features that facilitate the unusual acyl conjugation with S-adenosylmethionine (SAM). We also identify the determinant that establishes specificity for the acyl donor and identify residues that are critical for acyl/aryl specificity. These results highlight how a prevalent scaffold has evolved to catalyze quorum signal synthesis and provide a framework for the design of small-molecule antagonists of quorum signaling. | Bock T, Reichelt J, Müller R, Blankenfeldt W (2016)
The Structure of LiuC, a 3-Hydroxy-3-Methylglutaconyl CoA Dehydratase Involved in Isovaleryl-CoA Biosynthesis in Myxococcus xanthus, Reveals Insights into Specificity and Catalysis.
Chembiochem : a European journal of chemical biology 17, 1658-1664 [PubMed:27271456]
[show Abstract]
Myxobacteria are able to produce the important metabolite isovaleryl coenzyme A by a route other than leucine degradation. The first step into this pathway is mediated by LiuC, a member of the 3-methylglutaconyl CoA hydratases (MGCH). Here we present crystal structures refined to 2.05 and 1.1 Å of LiuC in the apo form and bound to coenzyme A, respectively. By using simulated annealing we modeled the enzyme substrate complex and identified residues potentially involved in substrate binding, specificity, and catalysis. The dehydration of 3-hydroxy-3-methylglutaconyl CoA to 3-methylglutaconyl CoA catalyzed by LiuC involves Glu112 and Glu132 and likely employs the typical crotonase acid-base mechanism. In this, Tyr231 and Arg69 are key players in positioning the substrate to enable catalysis. Surprisingly, LiuC shows higher sequence and structural similarity to human MGCH than to bacterial forms, although they convert the same substrate. This study provides structural insights into the alternative isovaleryl coenzyme A biosynthesis pathway and might open a path for biofuel research, as isovaleryl-CoA is a source for isobutene, a precursor for renewable fuels and chemicals. | Mohsen AW, Vockley J (2015)
Kinetic and spectral properties of isovaleryl-CoA dehydrogenase and interaction with ligands.
Biochimie 108, 108-119 [PubMed:25450250]
[show Abstract]
Isovaleryl-CoA dehydrogenase (IVD) catalyzes the conversion of isovaleryl-CoA to 3-methylcrotonyl-CoA and the transfer of electrons to the electron transfer flavoprotein (ETF). Recombinant human IVD purifies with bound CoA-persulfide. A modified purification protocol was developed to isolate IVD without bound CoA-persulfide and to protect the protein thiols from oxidation. The CoA-persulfide-free IVD specific activity was 112.5 μmol porcine ETF min(-)(1) mg(-)(1), which was ∼20-fold higher than that of its CoA-persulfide bound form. The Km and catalytic efficiency (kcat/Km) for isovaleryl-CoA were 1.0 μM and 4.3 × 10(6) M(-1) s(-1) per monomer, respectively, and its Km for ETF was 2.0 μM. Anaerobic titration of isovaleryl-CoA into an IVD solution resulted in a stable blue complex with increased absorbance at 310 nm, decreased absorbance at 373 and 447 nm, and the appearance of the charge transfer complex band at 584 nm. The apparent dissociation constant (KDapp) determined spectrally for isovaleryl-CoA was 0.54 μM. Isovaleryl-CoA, acetoacetyl-CoA, methylenecyclopropyl-acetyl-CoA, and ETF induced CD spectral changes at the 250-500 nm region while isobutyryl-CoA did not, suggesting conformational changes occur at the flavin ring that are ligand specific. Replacement of the IVD Trp166 with a Phe did not block IVD interaction with ETF, indicating that its indole ring is not essential for electron transfer to ETF. A twelve amino acid synthetic peptide that matches the sequence of the ETF docking peptide competitively inhibited the enzyme reaction when ETF was used as the electron acceptor with a Ki of 1.5 mM. | Kitanishi K, Cracan V, Banerjee R (2015)
Engineered and Native Coenzyme B12-dependent Isovaleryl-CoA/Pivalyl-CoA Mutase.
The Journal of biological chemistry 290, 20466-20476 [PubMed:26134562]
[show Abstract]
Adenosylcobalamin-dependent isomerases catalyze carbon skeleton rearrangements using radical chemistry. We have recently demonstrated that an isobutyryl-CoA mutase variant, IcmF, a member of this enzyme family that catalyzes the interconversion of isobutyryl-CoA and n-butyryl-CoA also catalyzes the interconversion between isovaleryl-CoA and pivalyl-CoA, albeit with low efficiency and high susceptibility to inactivation. Given the biotechnological potential of the isovaleryl-CoA/pivalyl-CoA mutase (PCM) reaction, we initially attempted to engineer IcmF to be a more proficient PCM by targeting two active site residues predicted based on sequence alignments and crystal structures, to be key to substrate selectivity. Of the eight mutants tested, the F598A mutation was the most robust, resulting in an ∼17-fold increase in the catalytic efficiency of the PCM activity and a concomitant ∼240-fold decrease in the isobutyryl-CoA mutase activity compared with wild-type IcmF. Hence, mutation of a single residue in IcmF tuned substrate specificity yielding an ∼4000-fold increase in the specificity for an unnatural substrate. However, the F598A mutant was even more susceptible to inactivation than wild-type IcmF. To circumvent this limitation, we used bioinformatics analysis to identify an authentic PCM in genomic databases. Cloning and expression of the putative AdoCbl-dependent PCM with an α2β2 heterotetrameric organization similar to that of isobutyryl-CoA mutase and a recently characterized archaeal methylmalonyl-CoA mutase, allowed demonstration of its robust PCM activity. To simplify kinetic analysis and handling, a variant PCM-F was generated in which the αβ subunits were fused into a single polypeptide via a short 11-amino acid linker. The fusion protein, PCM-F, retained high PCM activity and like PCM, was resistant to inactivation. Neither PCM nor PCM-F displayed detectable isobutyryl-CoA mutase activity, demonstrating that PCM represents a novel 5'-deoxyadenosylcobalamin-dependent acyl-CoA mutase. The newly discovered PCM and the derivative PCM-F, have potential applications in bioremediation of pivalic acid found in sludge, in stereospecific synthesis of C5 carboxylic acids and alcohols, and in the production of potential commodity and specialty chemicals. | Jost M, Born DA, Cracan V, Banerjee R, Drennan CL (2015)
Structural Basis for Substrate Specificity in Adenosylcobalamin-dependent Isobutyryl-CoA Mutase and Related Acyl-CoA Mutases.
The Journal of biological chemistry 290, 26882-26898 [PubMed:26318610]
[show Abstract]
Acyl-CoA mutases are a growing class of adenosylcobalamin-dependent radical enzymes that perform challenging carbon skeleton rearrangements in primary and secondary metabolism. Members of this class of enzymes must precisely control substrate positioning to prevent oxidative interception of radical intermediates during catalysis. Our understanding of substrate specificity and catalysis in acyl-CoA mutases, however, is incomplete. Here, we present crystal structures of IcmF, a natural fusion protein variant of isobutyryl-CoA mutase, in complex with the adenosylcobalamin cofactor and four different acyl-CoA substrates. These structures demonstrate how the active site is designed to accommodate the aliphatic acyl chains of each substrate. The structures suggest that a conformational change of the 5'-deoxyadenosyl group from C2'-endo to C3'-endo could contribute to initiation of catalysis. Furthermore, detailed bioinformatic analyses guided by our structural findings identify critical determinants of acyl-CoA mutase substrate specificity and predict new acyl-CoA mutase-catalyzed reactions. These results expand our understanding of the substrate specificity and the catalytic scope of acyl-CoA mutases and could benefit engineering efforts for biotechnological applications ranging from production of biofuels and commercial products to hydrocarbon remediation. | Bode HB, Ring MW, Schwär G, Altmeyer MO, Kegler C, Jose IR, Singer M, Müller R (2009)
Identification of additional players in the alternative biosynthesis pathway to isovaleryl-CoA in the myxobacterium Myxococcus xanthus.
Chembiochem : a European journal of chemical biology 10, 128-140 [PubMed:18846531]
[show Abstract]
Isovaleryl-CoA (IV-CoA) is usually derived from the degradation of leucine by using the Bkd (branched-chain keto acid dehydrogenase) complex. We have previously identified an alternative pathway for IV-CoA formation in myxobacteria that branches from the well-known mevalonate-dependent isoprenoid biosynthesis pathway. We identified 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) synthase (MvaS) to be involved in this pathway in Myxococcus xanthus, which is induced in mutants with impaired leucine degradation (e.g., bkd(-)) or during myxobacterial fruiting-body formation. Here, we show that the proteins required for leucine degradation are also involved in the alternative IV-CoA biosynthesis pathway through the efficient catalysis of the reverse reactions. Moreover, we conducted a global gene-expression experiment and compared vegetative wild-type cells with bkd mutants, and identified a five-gene operon that is highly up-regulated in bkd mutants and contains mvaS and other genes that are directly involved in the alternative pathway. Based on our experiments, we assigned roles to the genes required for the formation of IV-CoA from HMG-CoA. Additionally, several genes involved in outer-membrane biosynthesis and a plethora of genes encoding regulatory proteins were decreased in expression levels in the bkd(-) mutant; this explains the complex phenotype of bkd mutants including a lack of adhesion in developmental submerse culture. | Mahmud T, Wenzel SC, Wan E, Wen KW, Bode HB, Gaitatzis N, Müller R (2005)
A biosynthetic pathway to isovaleryl-CoA in myxobacteria: the involvement of the mevalonate pathway.
Chembiochem : a European journal of chemical biology 6, 322-330 [PubMed:15619721]
[show Abstract]
A biosynthetic shunt pathway branching from the mevalonate pathway and providing starter units for branched-chain fatty acid and secondary metabolite biosynthesis has been identified in strains of the myxobacterium Stigmatella aurantiaca. This pathway is upregulated when the branched-chain alpha-keto acid dehydrogenase gene (bkd) is inactivated, thus impairing the normal branched-chain amino acid degradation process. We previously proposed that, in this pathway, isovaleryl-CoA is derived from 3,3-dimethylacrylyl-CoA (DMA-CoA). Here we show that DMA-CoA is an isomerization product of 3-methylbut-3-enoyl-CoA (3MB-CoA). This compound is directly derived from 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) by a decarboxylation/ dehydration reaction resembling the conversion of mevalonate 5-diphosphate to isopentenyl diphosphate. Incubation of cell-free extracts of a bkd mutant with HMG-CoA gave product(s) with the molecular mass of 3MB-CoA or DMA-CoA. The shunt pathway most likely also operates reversibly and provides an alternative source for the monomers of isoprenoid biosynthesis in myxobacteria that utilize L-leucine as precursor. | Tajima G, Sakura N, Yofune H, Dwi Bahagia Febriani A, Nishimura Y, Sakamoto A, Ono H, Shigematsu Y, Kobayashi M (2005)
Establishment of a practical enzymatic assay method for determination of isovaleryl-CoA dehydrogenase activity using high-performance liquid chromatography.
Clinica chimica acta; international journal of clinical chemistry 353, 193-199 [PubMed:15698607]
[show Abstract]
BackgroundIsovaleric acidemia (IVA) is one of the various target disorders for tandem mass spectrometry (MS/MS) newborn screening. In the diagnosis of IVA, no enzymatic assay method for isovaleryl-CoA dehydrogenase (IVD) activity has been reported whereby the production of enoyl-CoA species was directly detected. We established a direct assay method to detect 3-methylcrotonyl-CoA (MC-CoA) production using high-performance liquid chromatography (HPLC).MethodsIsovaleryl-CoA dehydrogenase crude enzyme was prepared by sonicating lymphocytes in peripheral blood. Aliquots were incubated with isovaleryl-CoA, flavin adenine dinucleotide, and phenazine methosulfate. 3-Methylcrotonyl-CoA produced in the samples was separated by HPLC and detected using an ultraviolet spectrophotometer.ResultsThe detection of MC-CoA was reproducible depending upon the concentration of the substrates, the incubation time, and the number of cells contained in the crude enzyme solution. We applied this assay to three patients diagnosed with IVA and showed that neither of them had detectable residual activity. Only a few hours were required from the initial blood sampling to the end of the assay.ConclusionsThese results demonstrate that this method for detecting MC-CoA production, using HPLC, is a practical assay for determining IVD activity. It can be a useful confirmatory test for IVA cases detected through MS/MS screening of newborns. | Däschner K, Couée I, Binder S (2001)
The mitochondrial isovaleryl-coenzyme a dehydrogenase of arabidopsis oxidizes intermediates of leucine and valine catabolism.
Plant physiology 126, 601-612 [PubMed:11402190]
[show Abstract]
We recently identified a cDNA encoding a putative isovaleryl-coenzyme A (CoA) dehydrogenase in Arabidopsis (AtIVD). In animals, this homotetrameric enzyme is located in mitochondria and catalyzes the conversion of isovaleryl-CoA to 3-methylcrotonyl-CoA as an intermediate step in the leucine (Leu) catabolic pathway. Expression of AtIVD:smGFP4 fusion proteins in tobacco (Nicotiana tabacum) protoplasts and biochemical studies now demonstrate the in vivo import of the plant isovaleryl-CoA dehydrogenase (IVD) into mitochondria and the enzyme in the matrix of these organelles. Two-dimensional separation of mitochondrial proteins by blue native and SDS-PAGE and size determination of the native and overexpressed proteins suggest homodimers to be the dominant form of the plant IVD. Northern-blot hybridization and studies in transgenic Arabidopsis plants expressing Ativd promoter:gus constructs reveal strong expression of this gene in seedlings and young plants grown in the absence of sucrose, whereas promoter activity in almost all tissues is strongly inhibited by exogeneously added sucrose. Substrate specificity tests with AtIVD expressed in Escherichia coli indicate a strong preference toward isovaleryl-CoA but surprisingly also show considerable activity with isobutyryl-CoA. This strongly indicates a commitment of the enzyme in Leu catabolism, but the activity observed with isobutyryl-CoA also suggests a parallel involvement of the enzyme in the dehydrogenation of intermediates of the valine degradation pathway. Such a dual activity has not been observed with the animal IVD and may suggest a novel connection of the Leu and valine catabolism in plants. | Rhead WJ, Tanaka K (1980)
Demonstration of a specific mitochondrial isovaleryl-CoA dehydrogenase deficiency in fibroblasts from patients with isovaleric acidemia.
Proceedings of the National Academy of Sciences of the United States of America 77, 580-583 [PubMed:6928646]
[show Abstract]
To study the enzymatic basis of isovaleric acidemia, we have developed assay methods for isovaleryl-CoA and butyryl-CoA dehydrogenases that measure the amount of tritium released from the respective [2,3-3H]acyl CoAs. Because assay of these enzymes in human fibroblast homogenates was subject to interference by nonspecific reactions, we have isolated mitochondria from cultured skin fibroblasts by protease treatment, homogenization, and differential centrifugation. By using this assay method with these isolated mitochondria, we have demonstrated a specific deficiency of isovaleryl-CoA dehydrogenase [isovaleryl-CoA: (acceptor) oxidoreductase, EC 1.3.99.10] activity in cultured skin fibroblasts from five patients with isovaleric acidemia. In contrast, mitochondrial butyryl-CoA dehydrogenase [butyryl-CoA: (acceptor) oxidoreductase, EC 1.3.99.2] activity in these cells was preserved at normal levels. These results have been reproduced by using the conventional dye reduction assays. These observations give further support to the hypothesis that isovaleryl CoA is dehydrogenated by a specific enzyme and that isovaleric acidemia is due to a deficiency of this enzyme. |
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