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Branched-chain alpha-keto acid dehydrogenase complex

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The branched-chain α-ketoacid dehydrogenase complex (BCKDC or BCKDH complex) is a multi-subunit complex of enzymes that is found on the mitochondrial inner membrane.[1] This enzyme complex catalyzes the oxidative decarboxylation of branched, short-chain alpha-ketoacids. BCKDC is a member of the mitochondrial α-ketoacid dehydrogenase complex family, which also includes pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase, key enzymes that function in the Krebs cycle.

Biological function

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In animal tissue, BCKDC catalyzes an irreversible step[2] in the catabolism of the branched-chain amino acids L-isoleucine, L-valine, and L-leucine, acting on their deaminated derivatives (L-alpha-keto-beta-methylvalerate, alpha-ketoisovalerate, and alpha-ketoisocaproate, respectively) and converting them[3] to α-Methylbutyryl-CoA, Isobutyryl-CoA and Isovaleryl-CoA respectively.[4][5][6] In bacteria, this enzyme participates in the synthesis of branched, long-chain fatty acids.[7] In plants, this enzyme is involved in the synthesis of branched, long-chain hydrocarbons.

The overall catabolic reaction catalyzed by the BCKDC is shown in Figure 1.

Figure 1: This is the overall reaction catalyzed by the branched-chain alpha-ketoacid dehydrogenase complex.

Structure

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The mechanism of enzymatic catalysis by the BCKDC draws largely upon the elaborate structure of this large enzyme complex. This enzyme complex is composed of three catalytic components:

Unit EC number Name Gene Cofactor
E1 EC 1.2.4.4 alpha-ketoacid dehydrogenase BCKDHA thiamine pyrophosphate (TPP)
E2 EC 2.3.1.168 dihydrolipoyl transacylase DBT lipoic acid, coenzyme A
E3 EC 1.8.1.4 dihydrolipoamide dehydrogenase DLD FAD, NAD

In humans, 24 copies of E2 arranged in octahedral symmetry form the core of the BCKDC.[8] Non-covalently linked to this polymer of 24 E2 subunits are 12 E1 α2β2 tetramers and 6 E3 homodimers. In addition to the E1/E3-binding domain, there are 2 other important structural domains in the E2 subunit: (i) a lipoyl-bearing domain in the amino-terminal portion of the protein and (ii) an inner-core domain in the carboxy-terminal portion. The inner-core domain is linked to the other two domains of the E2 subunit by two interdomain segments (linkers).[9] The inner-core domain is necessary to form the oligomeric core of the enzyme complex and catalyzes the acyltransferase reaction (shown in the "Mechanism" section below).[10] The lipoyl domain of E2 is free to swing between the active sites of the E1, E2, and E3 subunits on the assembled BCKDC by virtue of the conformational flexibility of the aforementioned linkers (see Figure 2).[11][12] Thus, in terms of function as well as structure, the E2 component plays a central role in the overall reaction catalyzed by the BCKDC.

Figure 2:This is a schematic of the "swinging" lipoyl domain. Note that this lipoyl domain is covalently attached to the E2 subunit of the BCKDC, but is free to swing between the E1, E2, and E3 subunits. As is described in the "Mechanism" section, the ability of the lipoyl group to freely swing between the active sites on each of the three subunits of the BCKDC plays a large and important role in the catalytic activity of this enzyme complex.[13]

The role of each subunit is as follows:

E1 subunit

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E1 uses thiamine pyrophosphate (TPP) as a catalytic cofactor. E1 catalyzes both the decarboxylation of the α-ketoacid and the subsequent reductive acylation of the lipoyl moiety (another catalytic cofactor) that is covalently bound to E2.

E2 subunit

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E2 catalyzes a transfer of the acyl group from the lipoyl moiety to coenzyme A (a stoichiometric cofactor).[14]

E3 subunit

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The E3 component is a flavoprotein, and it re-oxidizes the reduced lipoyl sulfur residues of E2 using FAD (a catalytic cofactor) as the oxidant. FAD then transfers these protons and electrons to NAD+ (a stoichiometric cofactor) to complete the reaction cycle.

Mechanism

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As previously mentioned, BCKDC's primary function in mammals is to catalyze an irreversible step in the catabolism of branched-chain amino acids. However BCKDC has a relatively broad specificity, also oxidizing 4-methylthio-2-oxobutyrate and 2-oxobutyrate at comparable rates and with similar Km values as for its branched-chain amino acid substrates.[15] The BCKDC will also oxidize pyruvate, but at such a slow rate this side reaction has very little physiological significance.[16][17]

The reaction mechanism is as follows.[18] Please note that any of several branched-chain α-ketoacids could have been used as a starting material; for this example, α-ketoisovalerate was arbitrarily chosen as the BCKDC substrate.

NOTE: Steps 1 and 2 occur in the E1 domain

STEP 1: α-ketoisovalerate combines with TPP and is then decarboxylated. The proper arrow-pushing mechanism is shown in Figure 3.

Figure 3: α-ketoisovalerate combines with TPP and is then decarboxylated

STEP 2: The 2-methylpropanol-TPP is oxidized to form an acyl group while being simultaneously transferred to the lipoyl cofactor on E2. Note that TPP is regenerated. The proper arrow-pushing mechanism is shown in Figure 4.

Figure 4: The 2-methylpropanol-TPP is oxidized to form an acyl group while being simultaneously transferred to the lipoyl cofactor on E2. Note that TPP is regenerated.
NOTE: The acylated lipoyl arm now leaves E1 and swings into the E2 active site, where Step 3 occurs.

STEP 3: Acyl group transfer to CoA. The proper arrow-pushing mechanism is shown in Figure 5.

Figure 5: Acyl group transfer to CoA
*NOTE: The reduced lipoyl arm now swings into the E3 active site, where Steps 4 and 5 occur.

STEP 4: Oxidation of the lipoyl moiety by the FAD coenzyme, as shown in Figure 6.

Figure 6: Oxidation of the lipoyl moiety by the FAD coenzyme.

STEP 5: Reoxidation of FADH2 to FAD, producing NADH:

FADH2 + NAD+ → FAD + NADH + H+

Disease relevance

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A deficiency in any of the enzymes of this complex as well as an inhibition of the complex as a whole leads to a buildup of branched-chain amino acids and their harmful derivatives in the body. These accumulations lend a sweet smell to bodily excretions (such as ear wax and urine), leading to a pathology known as maple syrup urine disease.[19]

This enzyme is an autoantigen recognized in primary biliary cirrhosis, a form of acute liver failure. These antibodies appear to recognize oxidized protein that has resulted from inflammatory immune responses. Some of these inflammatory responses are explained by gluten sensitivity.[20] Other mitochondrial autoantigens include pyruvate dehydrogenase and branched-chain oxoglutarate dehydrogenase, which are antigens recognized by anti-mitochondrial antibodies.

Mutations of the BCKDK gene, whose protein product controls the activity of the complex, may result in over-activation of the complex and excessive catabolism of the three amino acids. This leads to branched-chain keto acid dehydrogenase kinase deficiency, a rare disease first described in humans in 2012.[21]

References

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  1. ^ Indo I, Kitano A, Endo F, Akaboshi I, Matsuda I (1987). "Altered Kinetic Properties of the Branched-Chain Alpha-Keto Acid Dehydrogenase Complex Due to Mutation of the Beta-Subunit of the Branched-Chain Alpha-Keto Acid Decarboxylase (E1) Component in Lymphoblastoid Cells Derived from Patients with Maple Syrup Urine Disease". J Clin Invest. 80 (1): 63–70. doi:10.1172/JCI113064. PMC 442202. PMID 3597778.
  2. ^ Yeaman SJ (1989). "The 2-oxo acid dehydrogenase complexes: recent advances". Biochem. J. 257 (3): 625–632. doi:10.1042/bj2570625. PMC 1135633. PMID 2649080.
  3. ^ Rodwell, Vector (2015). "29". Harper's illustrated biochemistry. USA: McGraw Hill. p. 310. ISBN 978-0-07-182537-5.
  4. ^ Broquist HP, Trupin JS (1966). "Amino Acid Metabolism". Annual Review of Biochemistry. 35: 231–247. doi:10.1146/annurev.bi.35.070166.001311.
  5. ^ Harris RA, Paxton R, Powell SM, Goodwin GW, Kuntz MJ, Han AC (1986). "Regulation of branched-chain alpha-ketoacid dehydrogenase complex by covalent modification". Adv Enzyme Regul. 25: 219–237. doi:10.1016/0065-2571(86)90016-6. PMID 3028049.
  6. ^ Namba Y, Yoshizawa K, Ejima A, Hayashi T, Kaneda T (1969). "Coenzyme A- and nicotinamide adenine dinucleotide-dependent branched chain alpha-keto acid dehydrogenase. I. Purification and properties of the enzyme from Bacillus subtilis". J Biol Chem. 244 (16): 4437–4447. doi:10.1016/S0021-9258(18)94337-1. PMID 4308861.
  7. ^ Lennarz WJ; et al. (1961). "The role of isoleucine in the biosynthesis of branched-chain fatty acids by micrococcus lysodeikticus". Biochemical and Biophysical Research Communications. 6 (2): 1112–116. doi:10.1016/0006-291X(61)90395-3. PMID 14463994.
  8. ^ Aevarsson A, Chuang JL, Wynn RM, Turley S, Chuang DT, Hol WGJ (2000). "Crystal structure of human branched-chain α-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease". Structure. 8 (3): 277–291. doi:10.1016/S0969-2126(00)00105-2. PMID 10745006.
  9. ^ Chuang DT. (1989). "Molecular studies of mammalian branched-chain alpha-keto acid dehydrogenase complexes: domain structures, expression, and inborn errors". Annals of the New York Academy of Sciences. 573: 137–154. doi:10.1111/j.1749-6632.1989.tb14992.x. PMID 2699394. S2CID 33210101.
  10. ^ Chuang DT, Hu CW, Ku LS, Markovitz PJ, Cox RP (1985). "Subunit structure of the dihydrolipoyl transacylase component of branched-chain alpha-keto acid dehydrogenase complex from bovine liver. Characterization of the inner transacylase core". J Biol Chem. 260 (25): 13779–86. doi:10.1016/S0021-9258(17)38793-8. PMID 4055756.
  11. ^ Reed LJ, Hackert ML (1990). "Structure-function relationships in dihydrolipoamide acyltransferases". J Biol Chem. 265 (16): 8971–8974. doi:10.1016/S0021-9258(19)38795-2. PMID 2188967.
  12. ^ Perham RN. (1991). "Domains, motifs, and linkers in 2-oxo acid dehydrogenase multienzyme complexes: a paradigm in the design of a multifunctional protein". Biochemistry. 30 (35): 8501–8512. doi:10.1021/bi00099a001. PMID 1888719.
  13. ^ Berg, Jeremy M., John L. Tymoczko, Lubert Stryer, and Lubert Stryer. Biochemistry. 6th ed. New York: W.H. Freeman, 2007. 481. Print.
  14. ^ Heffelfinger SC, Sewell ET, Danner DJ (1983). "Identification of specific subunits of highly purified bovine liver branched-chain ketoacid dehydrogenase". Biochemistry. 22 (24): 5519–5522. doi:10.1021/bi00293a011. PMID 6652074.
  15. ^ Jones SM, Yeaman SJ (1986). "Oxidative decarboxylation of 4-methylthio-2-oxobutyrate by branched-chain 2-oxo acid dehydrogenase complex". Biochemical Journal. 237 (2): 621–623. doi:10.1042/bj2370621. PMC 1147032. PMID 3800905.
  16. ^ Pettit FH, Yeaman SJ, Reed LJ (1978). "Purification and characterization of branched chain alpha-keto acid dehydrogenase complex of bovine kidney". Proceedings of the National Academy of Sciences of the United States of America. 75 (10): 4881–4885. doi:10.1073/pnas.75.10.4881. PMC 336225. PMID 283398.
  17. ^ Damuni Z, Merryfield ML, Humphreys JS, Reed LJ (1984). "Purification and properties of branched-chain alpha-keto acid dehydrogenase phosphatase from bovine kidney". Proceedings of the National Academy of Sciences of the United States of America. 81 (14): 4335–4338. doi:10.1073/pnas.81.14.4335. PMC 345583. PMID 6589597.
  18. ^ Berg, Jeremy M., John L. Tymoczko, Lubert Stryer, and Lubert Stryer. Biochemistry. 6th ed. New York: W.H. Freeman, 2007. 478-79. Print.
  19. ^ Podebrad F, Heil M, Reichert S, Mosandl A, Sewell AC, Böhles H (April 1999). "4,5-dimethyl-3-hydroxy-25H-furanone (sotolone)--the odour of maple syrup urine disease". Journal of Inherited Metabolic Disease. 22 (2): 107–114. doi:10.1023/A:1005433516026. PMID 10234605. S2CID 6426166.
  20. ^ Leung PS, Rossaro L, Davis PA, et al. (2007). "Antimitochondrial antibodies in acute liver failure: Implications for primary biliary cirrhosis". Hepatology. 46 (5): 1436–42. doi:10.1002/hep.21828. PMC 3731127. PMID 17657817.
  21. ^ Novarino G, El-Fishawy P, Kayserili H, Meguid NA, Scott EM, Schroth J, Silhavy JL, Kara M, Khalil RO, Ben-Omran T, Ercan-Sencicek AG, Hashish AF, Sanders SJ, Gupta AR, Hashem HS, Matern D, Gabriel S, Sweetman L, Rahimi Y, Harris RA, State MW, Gleeson JG (October 2012). "Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy". Science. 338 (6105): 394–7. doi:10.1126/science.1224631. PMC 3704165. PMID 22956686.
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