Dihydrolipoamide dehydrogenase explained

Dihydrolipoamide dehydrogenase (DLD), also known as dihydrolipoyl dehydrogenase, mitochondrial, is an enzyme that in humans is encoded by the DLD gene.^{[1] [2] [3] [4]} DLD is a flavoprotein enzyme that oxidizes dihydrolipoamide to lipoamide.

Dihydrolipoamide dehydrogenase (DLD) is a mitochondrial enzyme that plays a vital role in energy metabolism in eukaryotes. This enzyme is required for the complete reaction of at least five different multi-enzyme complexes.^[5] Additionally, DLD is a flavoenzyme oxidoreductase that contains a reactive disulfide bridge and a FAD cofactor that are directly involved in catalysis. The enzyme associates into tightly bound homodimers required for its enzymatic activity.^[6]

Structure

The protein encoded by the DLD gene comes together with another protein to form a dimer in the central metabolic pathway. Several amino acids within the catalytic pocket have been identified as important to DLD function, including R281 and N473.^{[7] [8]} Although the overall fold of the human enzyme is similar to that of yeast, the human structure is different in that it has two loops that extend from the general protein structure and into the FAD binding sites when bound the NAD+ molecule, required for catalysis, is not close to the FAD moiety. However, when NADH is bound instead, it is stacked directly op top of the FAD central structure. The current hE3 structures show directly that the disease-causing mutations occur at three locations in the human enzyme: the dimer interface, the active site, and the FAD and NAD(+)-binding sites.^[9]

Function

The DLD homodimer functions as the E3 component of the pyruvate, α-ketoglutarate, α-adipate and branched-chain amino acid-dehydrogenase complexes and the glycine cleavage system, all in the mitochondrial matrix. In these complexes, DLD converts dihydrolipoic acid and NAD+ into lipoic acid and NADH.^[10] DLD also has diaphorase activity, being able to catalyze the oxidation of NADH to NAD+ by using different electron acceptors such as O₂, labile ferric iron, nitric oxide, and ubiquinone. DLD is thought to have a pro-oxidant role by reducing oxygen to a superoxide or ferric to ferrous iron, which then catalyzes production of hydroxyl radicals.^{[11] [12]} Diaphorase activity of DLD may have an antioxidant role through its ability to scavenge nitric oxide and to reduce ubiquinone to ubiquinol.^{[13] [14] [15]} The dihyrolipamide dehydrogenase gene is known to have multiple splice variants.

Moonlighting function

Certain DLD mutations can simultaneously induce the loss of a primary metabolic activity and the gain of a moonlighting proteolytic activity. The moonlighting proteolytic activity of DLD is revealed by conditions that destabilize the DLD homodimer and decrease its DLD activity. Acidification of the mitochondrial matrix, as a result of ischemia-reperfusion injury, can disrupt the quaternary structure of DLD leading to decreased dehydrogenase activity and increased diaphorase activity.^[16] The moonlighting proteolytic activity of DLD could also arise under pathological conditions. Proteolytic activity can further complicate the reduction in energy metabolism and an increase in oxidative damage as a result of decreased DLD activity and an increase in diaphorase activity respectively. With its proteolytic function, DLD removes a functionally vital domain from the N-terminus of frataxin, a mitochondrial protein involved in iron metabolism and antioxidant protection.^{[17] [18]}

Clinical significance

In humans, mutations in DLD are linked to a severe disorder of infancy with failure to thrive, hypotonia, and metabolic acidosis.^[19] DLD deficiency manifests itself in a great degree of variability, which has been attributed to varying effects of different DLD mutations on the stability of the protein and its ability to dimerize or interact with other components of the three α-ketoacid dehydrogenase complexes.With its proteolytic function, DLD causes a deficiency in frataxin, which leads to the neurodegenerative and cardiac disease, Friedreich's ataxia.^[20]

Interactive pathway map

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Enzyme regulation

This protein may use the morpheein model of allosteric regulation.^[21]

See also

• Lipoic acid

Further reading

• Silverberg MS, Cho JH, Rioux JD, McGovern DP, Wu J, Annese V, Achkar JP, Goyette P, Scott R, Xu W, Barmada MM, Klei L, Daly MJ, Abraham C, Bayless TM, Bossa F, Griffiths AM, Ippoliti AF, Lahaie RG, Latiano A, Paré P, Proctor DD, Regueiro MD, Steinhart AH, Targan SR, Schumm LP, Kistner EO, Lee AT, Gregersen PK, Rotter JI, Brant SR, Taylor KD, Roeder K, Duerr RH . 6 . Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study . Nature Genetics . 41 . 2 . 216–20 . February 2009 . 19122664 . 2652837 . 10.1038/ng.275 .
• Brautigam CA, Chuang JL, Tomchick DR, Machius M, Chuang DT . Crystal structure of human dihydrolipoamide dehydrogenase: NAD+/NADH binding and the structural basis of disease-causing mutations . Journal of Molecular Biology . 350 . 3 . 543–52 . July 2005 . 15946682 . 10.1016/j.jmb.2005.05.014 .
• Reed LJ, Hackert ML . Structure-function relationships in dihydrolipoamide acyltransferases . The Journal of Biological Chemistry . 265 . 16 . 8971–4 . June 1990 . 2188967 . 10.1016/S0021-9258(19)38795-2 . free .
• Ciszak EM, Makal A, Hong YS, Vettaikkorumakankauv AK, Korotchkina LG, Patel MS . How dihydrolipoamide dehydrogenase-binding protein binds dihydrolipoamide dehydrogenase in the human pyruvate dehydrogenase complex . The Journal of Biological Chemistry . 281 . 1 . 648–55 . January 2006 . 16263718 . 10.1074/jbc.M507850200 . free .
• Asano K, Matsushita T, Umeno J, Hosono N, Takahashi A, Kawaguchi T, Matsumoto T, Matsui T, Kakuta Y, Kinouchi Y, Shimosegawa T, Hosokawa M, Arimura Y, Shinomura Y, Kiyohara Y, Tsunoda T, Kamatani N, Iida M, Nakamura Y, Kubo M . 6 . A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population . Nature Genetics . 41 . 12 . 1325–9 . December 2009 . 19915573 . 10.1038/ng.482 . 20507558 .
• Odièvre MH, Chretien D, Munnich A, Robinson BH, Dumoulin R, Masmoudi S, Kadhom N, Rötig A, Rustin P, Bonnefont JP . 6 . A novel mutation in the dihydrolipoamide dehydrogenase E3 subunit gene (DLD) resulting in an atypical form of alpha-ketoglutarate dehydrogenase deficiency . Human Mutation . 25 . 3 . 323–4 . March 2005 . 15712224 . 10.1002/humu.9319 . 19929944 .
• Brautigam CA, Wynn RM, Chuang JL, Machius M, Tomchick DR, Chuang DT . Structural insight into interactions between dihydrolipoamide dehydrogenase (E3) and E3 binding protein of human pyruvate dehydrogenase complex . Structure . 14 . 3 . 611–21 . March 2006 . 16442803 . 2879633 . 10.1016/j.str.2006.01.001 .
• Kim H . Activity of human dihydrolipoamide dehydrogenase is largely reduced by mutation at isoleucine-51 to alanine . Journal of Biochemistry and Molecular Biology . 39 . 2 . 223–7 . March 2006 . 16584639 . 10.5483/bmbrep.2006.39.2.223 . free .
• Sugden MC, Holness MJ . Recent advances in mechanisms regulating glucose oxidation at the level of the pyruvate dehydrogenase complex by PDKs . American Journal of Physiology. Endocrinology and Metabolism . 284 . 5 . E855-62 . May 2003 . 12676647 . 10.1152/ajpendo.00526.2002 .
• Wang YC, Wang ST, Li C, Chen LY, Liu WH, Chen PR, Chou MC, Liu TC . 6 . The role of amino acids T148 and R281 in human dihydrolipoamide dehydrogenase . Journal of Biomedical Science . 15 . 1 . 37–46 . January 2008 . 17960497 . 10.1007/s11373-007-9208-9 .
• Brown AM, Gordon D, Lee H, Caudy M, Hardy J, Haroutunian V, Blass JP . Association of the dihydrolipoamide dehydrogenase gene with Alzheimer's disease in an Ashkenazi Jewish population . American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics . 131B . 1 . 60–6 . November 2004 . 15389771 . 10.1002/ajmg.b.30008 . 26098296 .
• Wang YC, Wang ST, Li C, Liu WH, Chen PR, Chen LY, Liu TC . The role of N286 and D320 in the reaction mechanism of human dihydrolipoamide dehydrogenase (E3) center domain . Journal of Biomedical Science . 14 . 2 . 203–10 . March 2007 . 17171578 . 10.1007/s11373-006-9136-0 .
• Foster LJ, Rudich A, Talior I, Patel N, Huang X, Furtado LM, Bilan PJ, Mann M, Klip A . 6 . Insulin-dependent interactions of proteins with GLUT4 revealed through stable isotope labeling by amino acids in cell culture (SILAC) . Journal of Proteome Research . 5 . 1 . 64–75 . January 2006 . 16396496 . 10.1021/pr0502626 .
• Kim H . Asparagine-473 residue is important to the efficient function of human dihydrolipoamide dehydrogenase . Journal of Biochemistry and Molecular Biology . 38 . 2 . 248–52 . March 2005 . 15826505 . 10.5483/bmbrep.2005.38.2.248 . free .
• Hiromasa Y, Fujisawa T, Aso Y, Roche TE . Organization of the cores of the mammalian pyruvate dehydrogenase complex formed by E2 and E2 plus the E3-binding protein and their capacities to bind the E1 and E3 components . The Journal of Biological Chemistry . 279 . 8 . 6921–33 . February 2004 . 14638692 . 10.1074/jbc.M308172200 . free .
• Wynn RM, Kato M, Machius M, Chuang JL, Li J, Tomchick DR, Chuang DT . Molecular mechanism for regulation of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex by phosphorylation . Structure . 12 . 12 . 2185–96 . December 2004 . 15576032 . 10.1016/j.str.2004.09.013 . free .
• Martins-de-Souza D, Gattaz WF, Schmitt A, Novello JC, Marangoni S, Turck CW, Dias-Neto E . Proteome analysis of schizophrenia patients Wernicke's area reveals an energy metabolism dysregulation . BMC Psychiatry . 9 . 17 . April 2009 . 19405953 . 2684104 . 10.1186/1471-244X-9-17 . free .

Notes and References

1. Web site: Entrez Gene: dihydrolipoamide dehydrogenase.
2. Otulakowski G, Robinson BH . Isolation and sequence determination of cDNA clones for porcine and human lipoamide dehydrogenase. Homology to other disulfide oxidoreductases . The Journal of Biological Chemistry . 262 . 36 . 17313–8 . December 1987 . 3693355 . 10.1016/S0021-9258(18)45379-3 . free .
3. Pons G, Raefsky-Estrin C, Carothers DJ, Pepin RA, Javed AA, Jesse BW, Ganapathi MK, Samols D, Patel MS . 6 . Cloning and cDNA sequence of the dihydrolipoamide dehydrogenase component human alpha-ketoacid dehydrogenase complexes . Proceedings of the National Academy of Sciences of the United States of America . 85 . 5 . 1422–6 . March 1988 . 3278312 . 279783 . 10.1073/pnas.85.5.1422 . 1988PNAS...85.1422P . free .
4. Scherer SW, Otulakowski G, Robinson BH, Tsui LC . Localization of the human dihydrolipoamide dehydrogenase gene (DLD) to 7q31----q32 . Cytogenetics and Cell Genetics . 56 . 3–4 . 176–7 . 1991 . 2055113 . 10.1159/000133081 . free . 10722/42531 .
5. Babady NE, Pang YP, Elpeleg O, Isaya G . Cryptic proteolytic activity of dihydrolipoamide dehydrogenase . Proceedings of the National Academy of Sciences of the United States of America . 104 . 15 . 6158–63 . April 2007 . 17404228 . 1851069 . 10.1073/pnas.0610618104 . 2007PNAS..104.6158B . free .
6. Ciszak EM, Makal A, Hong YS, Vettaikkorumakankauv AK, Korotchkina LG, Patel MS . How dihydrolipoamide dehydrogenase-binding protein binds dihydrolipoamide dehydrogenase in the human pyruvate dehydrogenase complex . The Journal of Biological Chemistry . 281 . 1 . 648–55 . January 2006 . 16263718 . 10.1074/jbc.M507850200 . free .
7. Kim H . Asparagine-473 residue is important to the efficient function of human dihydrolipoamide dehydrogenase . Journal of Biochemistry and Molecular Biology . 38 . 2 . 248–52 . March 2005 . 15826505 . 10.5483/bmbrep.2005.38.2.248 . free .
8. Wang YC, Wang ST, Li C, Chen LY, Liu WH, Chen PR, Chou MC, Liu TC . 6 . The role of amino acids T148 and R281 in human dihydrolipoamide dehydrogenase . Journal of Biomedical Science . 15 . 1 . 37–46 . January 2008 . 17960497 . 10.1007/s11373-007-9208-9 .
9. Brautigam CA, Chuang JL, Tomchick DR, Machius M, Chuang DT . Crystal structure of human dihydrolipoamide dehydrogenase: NAD+/NADH binding and the structural basis of disease-causing mutations . Journal of Molecular Biology . 350 . 3 . 543–52 . July 2005 . 15946682 . 10.1016/j.jmb.2005.05.014 .
10. Carothers DJ, Pons G, Patel MS . Dihydrolipoamide dehydrogenase: functional similarities and divergent evolution of the pyridine nucleotide-disulfide oxidoreductases . Archives of Biochemistry and Biophysics . 268 . 2 . 409–25 . February 1989 . 2643922 . 10.1016/0003-9861(89)90309-3 .
11. Petrat F, Paluch S, Dogruöz E, Dörfler P, Kirsch M, Korth HG, Sustmann R, de Groot H . 6 . Reduction of Fe(III) ions complexed to physiological ligands by lipoyl dehydrogenase and other flavoenzymes in vitro: implications for an enzymatic reduction of Fe(III) ions of the labile iron pool . The Journal of Biological Chemistry . 278 . 47 . 46403–13 . November 2003 . 12963736 . 10.1074/jbc.M305291200 . free .
12. Yoneyama K, Shibata R, Igarashi A, Kojima S, Kodani Y, Nagata K, Kurose K, Kawase R, Takeshita T, Hattori S . 6 . Proteomic identification of dihydrolipoamide dehydrogenase as a target of autoantibodies in patients with endometrial cancer . Anticancer Research . 34 . 9 . 5021–7 . September 2014 . 25202086 .
13. Igamberdiev AU, Bykova NV, Ens W, Hill RD . Dihydrolipoamide dehydrogenase from porcine heart catalyzes NADH-dependent scavenging of nitric oxide . FEBS Letters . 568 . 1–3 . 146–50 . June 2004 . 15196936 . 10.1016/j.febslet.2004.05.024 . 20180110 . free . 2004FEBSL.568..146I .
14. Olsson JM, Xia L, Eriksson LC, Björnstedt M . Ubiquinone is reduced by lipoamide dehydrogenase and this reaction is potently stimulated by zinc . FEBS Letters . 448 . 1 . 190–2 . April 1999 . 10217438 . 10.1016/s0014-5793(99)00363-4 . 34370150 . free . 1999FEBSL.448..190O .
15. Xia L, Björnstedt M, Nordman T, Eriksson LC, Olsson JM . Reduction of ubiquinone by lipoamide dehydrogenase. An antioxidant regenerating pathway . European Journal of Biochemistry . 268 . 5 . 1486–90 . March 2001 . 11231302 . 10.1046/j.1432-1327.2001.02013.x . free .
16. Klyachko NL, Shchedrina VA, Efimov AV, Kazakov SV, Gazaryan IG, Kristal BS, Brown AM . pH-dependent substrate preference of pig heart lipoamide dehydrogenase varies with oligomeric state: response to mitochondrial matrix acidification . The Journal of Biological Chemistry . 280 . 16 . 16106–14 . April 2005 . 15710613 . 10.1074/jbc.M414285200 . free .
17. Al-Karadaghi S, Franco R, Hansson M, Shelnutt JA, Isaya G, Ferreira GC . Chelatases: distort to select? . Trends in Biochemical Sciences . 31 . 3 . 135–42 . March 2006 . 16469498 . 2997100 . 10.1016/j.tibs.2006.01.001 .
18. O'Neill HA, Gakh O, Park S, Cui J, Mooney SM, Sampson M, Ferreira GC, Isaya G . 6 . Assembly of human frataxin is a mechanism for detoxifying redox-active iron . Biochemistry . 44 . 2 . 537–45 . January 2005 . 15641778 . 10.1021/bi048459j .
19. Book: Quinonez SC, Thoene JG . Dihydrolipoamide Dehydrogenase Deficiency . Adam MP, Ardinger HH, Pagon RA, Wallace SE, Bean LJ, Mirzaa G, Amemiya A . GeneReviews . 9 July 2020 . University of Washington, Seattle . 25032271 .
20. Ambrus A, Adam-Vizi V . Human dihydrolipoamide dehydrogenase (E3) deficiency: Novel insights into the structural basis and molecular pathomechanism . Neurochemistry International . 117 . 5–14 . July 2018 . 28579060 . 10.1016/j.neuint.2017.05.018 . 38777180 .
21. Selwood T, Jaffe EK . Dynamic dissociating homo-oligomers and the control of protein function . Archives of Biochemistry and Biophysics . 519 . 2 . 131–43 . March 2012 . 22182754 . 3298769 . 10.1016/j.abb.2011.11.020 .