Last Updated May 5, 2023
Introduction to Branched-Chain Amino Acid Metabolism Disorders
The branched-chain amino acids are leucine, isoleucine, and valine. The catabolism of all three branched-chain amino acids (BCAA) occurs in most cells but the highest rates of catabolism take place in skeletal muscle. BCAA catabolism yields both NADH and FADH2 which can be utilized for ATP generation which is a primary reason for their high rates of catabolism in skeletal muscle.
The catabolism of all three of these amino acids uses the same enzymes in the first two steps. The first step in branched-chain amino acid catabolism is a transamination using a pyridoxal phosphate-dependent BCAA aminotransferase (termed a branched-chain aminotransferase, BCAT), with 2-oxoglutarate (α-ketoglutarate) as amine acceptor. Humans express two genes that encode BCAT activity. These two genes are identified as BCAT1 and BCAT2. The primary protein encoded by the BCAT1 gene is a cytosolic version of the enzyme and the protein is identified as BCATc. The primary protein encoded by the BCAT2 gene is a mitochondrial version of the enzyme and this protein is designated BCATm.
The BCAT1 gene is located on chromosome 12p12.1 and is composed of 14 exons that generate five alternatively spliced mRNAs, each of which encode a distinct protein isoform. BCAT1 isoform 1 is a 386 amino acid protein. BCAT1 isoform 2 is a 349 amino acid protein. BCAT1 isoform 3 is a 325 amino acid protein. BCAT1 isoform 4 is a 398 amino acid protein. BCAT1 isoform 5 is a 385 amino acid protein. Expression of the BCAT1 gene occurs in a number of tissues with highest levels in the pancreas and brain. The BCAT1 gene represents the primary BCAT expressing gene in the brain.
The BCAT2 gene is located on chromosome 19q13.33 and is composed of 12 exons that generate three alternatively spliced mRNAs that encode three different isoforms. BCAT2 isoform a is a 392 amino acid protein which is also referred to as PP18a. BCAT2 isoform b is a 300 amino acid protein which is referred to as PP18b. The isoform b protein is found in the cytosol. BCAT2 isoform c is a 352 amino acid protein. Expression of BCAT2 is widely distributed among numerous tissues. Although detectable in the fetal liver, the adult liver does not express either BCAT gene.
The second step in BCAA catabolism involves an oxidation catalyzed by the branched-chain keto acid dehydrogenase (BCKD) complex. The BCKD complex is a multimeric enzyme composed of three catalytic subunits. The E1 portion of the complex is a thiamine pyrophosphate (TPP)-dependent decarboxylase with a subunit structure of α2β2. The E2 portion is a dihydrolipoamide branched-chain transacylase composed of 24 lipoic acid-containing polypeptides. The E3 portion is a homodimeric flavoprotein identified as dihydrolipoamide dehydrogenase, DLD.
The E1α gene (symbol: BCKDHA) is located on chromosome 19q13.2 and contains 9 exons that generate two alternatively spliced mRNAs that encode alpha subunit isoform 1 (445 amino acids) and alpha subunit isoform 2 (444 amino acids).
The E1β gene (symbol: BCKDHB) is located on chromosome 6q14.1 and is composed of 20 exons that generate three alternatively spliced mRNAs that collectively encode a 392 amino acid protein (isoform 1 ) and a 322 amino acid protein (isoform 2).
The E2 gene (symbol: DBT) is located on chromosome 1p21.2 and contains 15 exons that that generate three alternatively spliced mRNAs that collectively encode a 482 amino acid precursor protein (isoform 1 ) and a 3301 amino acid protein (isoform 2).
The E3 gene (symbol: DLD) is located on chromosome 7q31.1 contains 14 exons that generate four alternatively spliced mRNAs, each of which encode a distinct protein isoform. The DLD gene encodes the same dihydrolipoamide dehydrogenase subunits found in the PDHc and the 2-oxoglutarate dehydrogenase complexes.
Maple Syrup Urine Disease, MSUD
There are a number of genetic diseases associated with faulty catabolism of the branched-chain amino acids. The most common disorder results from defects in the function of the branched-chain keto acid dehydrogenase (BCKD) complex. Since there is only one dehydrogenase enzyme for all three BCAA, all three α-keto acids accumulate and are excreted in the urine. The keto acids are α-keto-β-methylvalerate (from isoleucine), α-ketoisocaproate (from leucine), and α-ketoisovalerate (from valine).
The details of maple syrup urine disease (MSUD) are covered in a separate page. The disease is so-called because of the characteristic odor of the urine in afflicted individuals. Intellectual impairment in MSUD can be extensive. Unfortunately, since these are essential amino acids, they cannot be heavily restricted in the diet. The main neurological problems are due to poor formation of myelin in the CNS. Although the outcomes for afflicted individuals used to be quite severe with abnormal development and a short life-span, many advances in the treatment of MSUD in recent years have improved the clinical picture. Liver transplantation can result in a relatively normal life for MSUD patients.
Isovaleric Acidemia
One of the additional disorders associated with defects in the catabolism of the α-ketoisocaproate derived from leucine is isovaleric acidemia. The details of isovaleric acidemia are covered in a separate page. Isovaleric acidemia results from mutations in the gene encoding the enzyme isovaleryl-CoA dehydrogenase (IVD) which converts isovaleryl-CoA to 3-methylcrotonyl-CoA. Isovaleryl-CoA dehydrogenase is a member of a family of acyl-CoA dehydrogenases (ACAD), several of which are involved in the process of mitochondrial fatty acid β-oxidation. As such isovaleryl-CoA dehydrogenase is also known as acyl-CoA dehydrogenase 2 (ACAD2).
3-Methylcrotonylglycinuria
The other major leucine metabolic defect is 3-methylcrotonylglycinuria which results from defects in either of the two subunits of the biotin-requiring enzyme, 3-methylcrotonyl-CoA carboxylase (3MCC). 3-Methylcrotonylglycinuria is also referred to as 3-methylcrotonyl-CoA carboxylase deficiency (3-MCCD). The function of 3-methylcrotonyl-CoA carboxylase is to catalyze the carboxylation of 3-methylcrotonyl-CoA to 3-methylglutaconyl-CoA during the catabolism of leucine. The 3-methylcrotonyl-CoA is the product of isovaleryl-CoA dehydrogenase which catalyzes the previous reaction in leucine catabolism.
As indicated 3MCC is composed of two subunits in a heterododecameric configuration composed of six α-subunits and six β-subunits (α6β6). The activity of 3MCC is dependent on biotin. The α-subunit covalently binds biotin while the carboxyltransferase activity is encoded by the β-subunit. The structure of 3MCC and its dependence on biotin make it highly similar in structure and catalytic activity to propionyl-CoA carboxylase, PCC. The α-subunit of 3MCC is encoded by the MCCC1 gene and the β-subunit is encoded by the MCCC2 gene. Mutations in the MCCC1 gene cause 3-methylcrotonylglycinuria type I, while mutations in the MCCC2 gene cause 3-methylcrotonylglycinuria type II.
The MCCC1 gene is located on chromosome 3q27.1 and is composed of 23 exons that generate three alternatively spliced mRNAs, two of which are known to encode functional protein. MCCC1 isoform 1 is a precursor protein of 725 amino acids and isoform 2 is a precursor protein of 608 amino acids. Mutations in the MCC1 gene are the cause of 3-methylcrotonylglycinuria type I.
The MCCC2 gene is located on chromosome 5q13.2 and is composed of 19 exons that generate two alternatively spliced mRNAs encoding precursor proteins of 563 amino acids (isoform 1) and 525 amino acids (isoform 2).
Inheritance of 3-methylcrotonylglycinuria (also referred to as 3MCC deficiency) occurs in an autosomal recessive manner. The symptoms that result from defects in either of the two genes encoding 3MCC can range from benign to profound metabolic acidosis and early death. In the more severe forms of 3MCC deficiency infants appear normal at birth but will develop symptoms during the first year of life or possibly not until early childhood. The characteristic features of the severe forms of 3MCC deficiency include difficulty feeding, recurrent episodes of vomiting and diarrhea, lethargy, and hypotonia. If left undiagnosed or untreated, 3MCC deficiency can lead to delayed development, seizures, coma, and ultimately death.
3-Methylglutaconic Aciduria, Type 1
During the catabolism of leucine, the 3-methylglutaconyl-CoA is converted to 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) via the action of the bifunctional enzyme, 3-methylglutaconyl-CoA hydratase. The 3-methylglutaconyl-CoA hydratase enzyme possesses both RNA-binding and hydratase activities accounting for the official name of the gene encoding this enzyme, AU RNA-binding methylglutaconyl-CoA hydratase (AUH). The AUH gene is located on chromosome 9q22.31 and is composed of 20 exons that generate five alternatively spliced mRNAs that collectively encode four distinct protein isoforms.
Mutations in the AUH gene result in the extremely rare autosomal recessive disorder referred to as 3-methylglutaconic aciduria, type 1 (MGCA1). To date less than 20 cases of MGCA1 have been identified. MGCA1 is associated with urinary excretion of 3-methylglutaconic acid and its derivatives, 3-methylglutaric acid and 3-hydroxyisovaleric acid. Patients with MGCA1 manifest with two main phenotypic presentations, a childhood presentation and an adult presentation. The childhood onset form of the disorder is associated with the nonspecific finding of psychomotor impairment. The adult onset form is associated with progressive neurodegeneration characterized by ataxia, spasticity, and sometimes dementia. The adult onset patients also develop white matter lesions in the brain.
There are nine identified forms of 3-methylglutaconic aciduria (MGCA1 to MGCA9), but only MGCA1 is associated with direct deficiency in leucine catabolism. MGCA1 can be distinguished from the other forms of MGCA because the levels of 3-methylglutaconic acid are highly elevated, whereas levels of methylglutaric acid are usually only slightly elevated, and there is a high level of 3-hydroxyisovaleric acid excretion which is not seen in the other forms of MGCA.
3-Hydroxy-3-Methylglutaric Aciduria
Mutations in the HMGCL gene, that encodes 3-hydroxy-3-methylglutaryl-CoA lyase (HMG-CoA lyase), result in a disorder referred to as 3-hydroxy-3-methylglutaric aciduria. Inheritance of 3-hydroxy-3-methylglutaric aciduria occurs as an autosomal recessive disorder. The function of 3-hydroxy-3-methylglutaryl-CoA lyase is to catalyze the hydrolysis of 3-hydroxy-3-methylglutaryl-CoA to acetyl-CoA and acetoacetate during the catabolism of leucine.
Since the enzyme encoded by the HMGCL gene is also involved in ketone body synthesis, mutations in the HMGCL gene also result in defects in ketone synthesis. The reduced capacity to synthesize ketone bodies results in inefficient energy production by the brain during periods of fasting. Reduced HMG-CoA lyase activity is associated with episodes of hypoglycemia and metabolic acidosis.
The HMGCL gene is located on chromosome 1p36.11 and is composed of 9 exons that generate two alternatively spliced mRNAs. These two mRNAs encode mitochondrially localized proteins that are synthesized as precursor proteins of 325 amino acids (isoform 1) and 254 amino acids (isoform 2).
Characteristic findings in patients with mutations in the HMGCL gene are accumulation of leucine metabolites, 3-hydroxy-3-methylglutaric acid, 3-methylglutaconic acid, 3-methylglutaric acid, and 3-hydroxyisovaleric acid. HMG-CoA lyase deficiency is treatable by diet, particularly leucine restriction, and avoidance of prolonged fasting. Supplementary glucose is administered to prevent hypoglycemia. Without prompt and proper therapeutic intervention, death occurs early in life.
Beta-Ketothiolase Deficiency
Mutations in the ACAT1 (acetyl-CoA acetyltransferase 1) gene result in the autosomal recessive disorder somewhat inappropriately identified as β-ketothiolase (3-ketothiolase) deficiency. The function of the 3-ketothiolase enzyme in isoleucine catabolism is to hydrolyze 2-methylacetoacetyl-CoA into acetyl-CoA and propionyl-CoA.
Due to the common usage of the term, β-ketothiolase, in the context of the final step in mitochondrial β-oxidation of long-chain fatty acids, this disorder is often misconstrued as a disorder of fatty acid oxidation. However, the thiolase activity of long-chain fatty acid β-oxidation is associated with the β-subunit (encoded by the HADHB gene) of the mitochondrial trifunctional protein, MTP. The oxidation of medium- and short-chain fatty acids, and the utilization of the ketone, acetoacetate, involves the mitochondrial matrix-associated β-ketothiolase encoded by the ACAA2 gene.
The ACAT1 gene is located on chromosome 11q22.3 and is composed of 17 exons that generate 13 alternatively spliced mRNAs, eight of which encode the same 337 amino acid protein (identified as isoform e). To date a total of 105 different mutations in the ACAT1 gene have been identified in β-ketothiolase deficient patients with the majority of mutations being missense mutations.
The signs and symptoms of β-ketothiolase (ACAT1) deficiency typically appear between 6 and 24 months of age. Affected children experience ketoacidotic attacks associated with vomiting, dehydration, difficulty breathing, lethargy, and, occasionally, seizures and coma. The ketoacidotic attacks in β-ketothiolase deficient patients are frequently triggered by infections or periods of fasting. Increased intake of protein-rich foods can also play a role in the onset of symptoms in β-ketothiolase deficient patients. Mutations in the ACAT1 gene are associated with accumulation and urinary excretion of 2-methyl-3-hydroxybutyric acid and as such β-ketothiolase deficiency is also referred to as 2-methyl-3-hydroxybutyric aciduria.
Isobutyryl-CoA Dehydrogenase Deficiency
Mutations in the gene (ACAD8) encoding isobutyryl-CoA dehydrogenase (IBD or IBDH) result in the very rare autosomal recessive disorder referred to as isobutyryl-CoA dehydrogenase deficiency and also as isobutyrylglycinuria. The ACAD8 gene is located on chromosome 11q25 and is composed of 15 exons that encode a 415 amino acid protein that localizes to the mitochondria.
Most individuals harboring mutations in the ACAD8 gene do not manifest with any serious symptoms aside from increased levels of valine and its catabolic byproducts up to isobutyrylglycine, the latter imparting the name of the disorder. Some infants, identified through newborn screening via detection of increased C4-carnitine, experience developmental delay, hypotonia, dilated cardiomyopathy, anemia, and reduced serum carnitine. Isobutyryl-CoA dehydrogenase deficiency has only been reported in 22 patients.
Short/Branched-Chain Acyl-CoA Dehydrogenase Deficiency
Short/branched-chain acyl-CoA dehydrogenase (SBCAD) is also identified as 2-methylbutyryl-CoA dehydrogenase. The SBCAD enzyme is involved in the catabolism of isoleucine where it is responsible for the conversion of 2-methylbutyryl-CoA (α-methylbutyryl-CoA) to tiglyl-CoA.
Mutations in the ACADSB gene that encodes SBCAD result in the rare autosomal recessive disorder commonly referred to as 2-methylbutyrylglycinuria. Due to defective activity of the ACADSB encoded enzyme 2-methylbutyryl carnitine accumulates in the blood and 2-methylbutyrylglycine accumulates in the urine, hence the common name (2-methylglycinuria) of this disorder.
The ACADSB gene is located on chromosome 10q26.13 and is composed of 11 exons that generate two alternatively spliced mRNAs, both of which encode distinct protein isoforms.
Most individuals harboring mutations in the ACADSB gene do not manifest with any pathology. A small percentage of individuals will develop symptoms, and if they do, the symptoms usually begin soon after birth or later in childhood. The initial symptoms often include poor feeding, lethargy, vomiting, and irritability. In some patients these symptoms progress to a more serious state and include difficulty breathing, seizures, and coma. Additional problems can include poor growth, vision impairment, learning disabilities, muscle weakness, and delays in motor skills such as standing and walking.