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MetaCyc Enzyme: dihydrolipoyl dehydrogenase

Gene: DLD Accession Number: HS01727 (MetaCyc)

Synonyms: GCSL, PHE3, DLDH, LAD, E3, dihydrolipoamide dehydrogenase, glycine cleavage system L protein

Species: Homo sapiens

Component of:
pyruvate dehydrogenase complex (extended summary available)
branched-chain α-keto acid dehydrogenase complex (extended summary available)
2-ketoglutarate dehydrogenase complex (extended summary available)

Subunit composition of dihydrolipoyl dehydrogenase = [DLD]2
         dihydrolipoyl dehydrogenase monomer = DLD

Summary:
Dihydrolipoyl dehydrogenase is a component of the mitochondrial pyruvate dehydrogenase complex, the 2-ketoglutarate dehydrogenase complex, the branched-chain α-keto acid dehydrogenase complex, and glycine cleavage. It is often referred to as the E3 component, and its role is to catalyze the transfer of electrons from dihydrolipoamide to NAD+.

This protein has 4 different domains: the FAD-binding domain, the NAD-binding domain, the center domain, and the interface domain. The protein forms a homodimer, with the FAD-binding and NAD binding domain of one subunit and the interface domain of the other subunit forming the active center [Wang07c]. The full complex contains six dimers [Reed01].

The cDNAs encoding the polypeptide have been isolated and sequenced [Pons88, Otulakowski87]. The DLD gene was localized to chromosome 7q31- q32 [Scherer91]. The gene is approximately 20 kb long and contains 14 exons [Feigenbaum93].

Defects in the enzyme cause pyruvate dehydrogenase deficiency, resulting in congenital lactic acidosis, α-ketoglutaric aciduria and a variant form of maple syrup urine disease [Brown02a, Liu93a, Munnich82].

Locations: mitochondrial lumen

Map Position: [106,015,310 -> 106,044,108]

Molecular Weight of Polypeptide: 54.15 kD (from nucleotide sequence)

Unification Links: ArrayExpress:P09622 , Ensembl:ENSG00000091140 , Entrez-gene:1738 , Entrez-Nucleotide:J03490 , Entrez-Nucleotide:J03620 , Entrez-Nucleotide:L13761 , GeneCards:DLD , MOPED:P09622 , OMIM:238331 , OMIM:246900 , OMIM:600065 , RefSeq:NM_000108 , RefSeq:NP_000099 , UCSC Human Genome:NM_000108 , UniGene:74635 , UniProt:P09622

Gene-Reaction Schematic: ?

GO Terms:

Cellular Component: GO:0005759 - mitochondrial matrix

Credits:
Created 15-Jun-2009 by Caspi R , SRI International
Revised 16-Jun-2009 by Caspi R , SRI International


Enzymatic reaction of: dihydrolipoyl dehydrogenase

a [pyruvate dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine + NAD+ <=> a [pyruvate dehydrogenase E2 protein] N6-lipoyl-L-lysine + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

This reaction is reversible.

In Pathways: pyruvate decarboxylation to acetyl CoA

Credits:
Imported from HumanCyc 03-Nov-2011 by Caspi R , SRI International


Enzymatic reaction of: dihydrolipoyl dehydrogenase

a [glycine-cleavage complex H protein] N6-dihydrolipoyl-L-lysine + NAD+ <=> a [glycine-cleavage complex H protein] N6-lipoyl-L-lysine + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

This reaction is reversible.

In Pathways: glycine biosynthesis II , glycine cleavage

Credits:
Imported from HumanCyc 03-Nov-2011 by Caspi R , SRI International


Enzymatic reaction of: dihydrolipoyl dehydrogenase

a [2-oxoglutarate dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine + NAD+ <=> a [2-oxoglutarate dehydrogenase E2 protein] N6-lipoyl-L-lysine + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Wang07c]

In Pathways: 2-oxoglutarate decarboxylation to succinyl-CoA

Cofactors or Prosthetic Groups: FAD [Wang07c]

Kinetic Parameters:

Substrate
Km (μM)
Citations
NADH
220.0
[Wang07c]
a [2-oxoglutarate dehydrogenase E2 protein] N6-lipoyl-L-lysine
380.0
[Wang07c]
NAD+
40.0
[Wang07c]
a [2-oxoglutarate dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine
560.0
[Wang07c]


Enzymatic reaction of: dihydrolipoyl dehydrogenase

an [apo BCAA dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine + NAD+ <=> an [apo BCAA dehydrogenase E2 protein] N6-lipoyl-L-lysine + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Wang07c]

In Pathways: 2-oxoisovalerate decarboxylation to isobutanoyl-CoA

Cofactors or Prosthetic Groups: FAD [Kim02h, Wang07c]

Kinetic Parameters:

Substrate
Km (μM)
Citations
an [apo BCAA dehydrogenase E2 protein] N6-dihydrolipoyl-L-lysine
380.0
[Wang07c]
an [apo BCAA dehydrogenase E2 protein] N6-lipoyl-L-lysine
560.0
[Wang07c]
NADH
40.0
[Wang07c]
NAD+
220.0
[Wang07c]


Subunit of: pyruvate dehydrogenase complex

Species: Homo sapiens

Subunit composition of pyruvate dehydrogenase complex = [(PDHB)2(PDHA1)2]30[DLAT]60[(PDHX)][(DLD)2]6
         pyruvate dehydrogenase E1 component (somatic) = (PDHB)2(PDHA1)2 (summary available)
                 pyruvate dehydrogenase E1 component β subunit = PDHB (summary available)
                 pyruvate dehydrogenase E1 component α subunit (somatic) = PDHA1 (summary available)
         pyruvate dehydrogenase E2 component = DLAT (extended summary available)
         pyruvate dehydrogenase E3-binding protein = (PDHX)
                 pyruvate dehydrogenase protein E3 component, mitochondrial = PDHX
         dihydrolipoyl dehydrogenase = (DLD)2 (extended summary available)
                 dihydrolipoyl dehydrogenase monomer = DLD

Summary:
The pyruvate dehydrogenase complex (PDH) is a large enzyme complex made up of multiple copies of three enzymes: E1 (20-30 copies of pyruvate dehydrogenase, an α2β2 heterotetramer), 60 copies of E2 (dihydrolipoamide acetyltransferase), and six homodimers of E3 (dihydrolipoamide dehydrogenase), together with the E3 binding protein, which is involved in the interaction between the E2 and E3 subunits.

Within the PDH complex, the E2 subunit forms the structural core and accepts acetyl groups from E1 and transfers them to coenzyme A. The irreversible decarboxylation of pyruvate and its conversion to acetyl-CoA by the PDH complex precedes the entry of glucose carbon into the tricarboxylic acid (TCA) cycle. This process is fundamental to the aerobic oxidation of glucose and is of particular importance in the brain where it is the obligatory pathway for energy generation under normal conditions [McWilliam10].

The mitochondrial pyruvate dehydrogenase complex (PDC) plays a critical fuel selection role in determining whether glucose-linked substrates are converted to acetyl-CoA. When carbohydrate stores are reduced, mammalian PDC activity is down-regulated and limits the oxidative utilization of glucose in most non-neural tissues.

Four pyruvate dehydrogenase kinase (PDK) isozymes and two pyruvate dehydrogenase phosphatase (PDP) isoforms control the activity state of PDC by determining the proportion of the pyruvate dehydrogenase (E1) component that is in the active, nonphosphorylated state [Roche03].

Credits:
Created in HumanCyc 04-Nov-2011 by Caspi R , SRI International
Imported from HumanCyc 04-Nov-2011 by Caspi R , SRI International


Enzymatic reaction of: pyruvate dehydrogenase

EC Number: 1.2.1.-

pyruvate + coenzyme A + NAD+ <=> acetyl-CoA + CO2 + NADH

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

This reaction is reversible.

In Pathways: pyruvate decarboxylation to acetyl CoA


Subunit of: branched-chain α-keto acid dehydrogenase complex

Species: Homo sapiens

Subunit composition of branched-chain α-keto acid dehydrogenase complex = [(BCKDHA)2(BCKDHB)2]12[(DBT)24][(DLD)2]6
         branched-chain α-keto acid dehydrogenase E1 component = (BCKDHA)2(BCKDHB)2 (summary available)
                 branched-chain α-keto acid dehydrogenase E1 component α subunit = BCKDHA
                 branched-chain α-keto acid dehydrogenase E1 component β subunit = BCKDHB
         branched-chain α-keto acid dehydrogenase complex E2 component = (DBT)24 (summary available)
                 branched-chain α-keto acid dehydrogenase complex E2 component subunit = DBT
         dihydrolipoyl dehydrogenase = (DLD)2 (extended summary available)
                 dihydrolipoyl dehydrogenase monomer = DLD

Summary:
The mammalian mitochondrial branched-chain α-keto acid dehydrogenase complex (BCDHC) is a heterotetramer that catalyzes the oxidative decarboxylation of branched-chain α -keto acids derived from L-leucine, L-isoleucine, and L-valine to branched-chain acyl-CoAs [Nobukuni90]. The reaction products are indirectly channeled into the TCA cycle III (animals) or linked to lipid and cholesterol biosynthesis.

This enzyme belongs to the 2-oxo acid dehydrogenase complex family, which also includes the pyruvate dehydrogenase complex, 2-ketoglutarate dehydrogenase complex and glycine cleavage. All of these proteins function at strategic points in catabolic pathways and are subject to stringent control [deKok98].

With the exception of the glycine cleavage, the 2-oxo acid dehydrogenase complexes share a common structure. They consist of three main components, namely a 2-oxo acid dehydrogenase (E1), a dihydrolipoamide acyltransferase (E2), and dihydrolipoamide dehydrogenase (E3).

The E1 component is either a heterotetramer composed of two types of subunits, or a homodimer, made up of a single type of subunit. In all cases described so far many copies of each subunit assemble to form the full complex.

The core is made of either 24 or 60 E2 units, which contain the lipoyl active site in the form of lipoyllysine, as well as binding sites for the other two subunits (60 subunits cores are found in the PDH complexes from mammalian and avian tissues, fungi, and the Gram positive bacterium Geobacillus stearothermophilus [Reed01].

Cryoelectron microscopy of PDHC from ox kidney has revealed that the E2 inner core is surrounded by an outer shell of E1 and E3 components, with the lipoyl domains confined to the annular space between them where they must make successive journeys between the three types of active sites (E1-E3), which are physically far apart [Zhou01][Fries03].

E1, which contains a thiamin diphosphate cofactor, catalyzes the binding of the 2-oxo acid to the lipoyl group of E2, which then transfers an acyl group (the nature of the acyl group depends on the particular enzyme) to coenzyme A, forming an acyl-CoA, while reducing the lipoyl group to dihydrolipoyl. E3 then transfers the protons to NAD, forming NADH and restoring the dihydrolipoyllysine group back to lipoyllysine.

In the case of the mammalian branched-chain α-keto acid dehydrogenase complex, the E1 component is a heterotetrameric α2β2 subcomplex [Pettit78]. The complex also contains two regulatory enzymes, the BCD kinase and the BCD phosphatase that regulate its activity by phosphorylation (inactivation) and dephosphorylation (activation) cycles [Harris97].

Mutations in components of the branched-chain α-keto acid dehydrogenase complex cause serious metabolic disorders in humans, including maple syrup urine disease, where the body cannot break down the branched chain amino acids [AEvarsson00].

Credits:
Created 08-Mar-2006 by Caspi R , SRI International


Enzymatic reaction of: 4-methyl-2-oxopentanoate dehydrogenase (branched-chain α-keto acid dehydrogenase complex)

EC Number: 1.2.1.-

4-methyl-2-oxopentanoate + coenzyme A + NAD+ <=> isovaleryl-CoA + CO2 + NADH

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.

In Pathways: 2-oxoisovalerate decarboxylation to isobutanoyl-CoA , leucine degradation I

Credits:
Imported from HumanCyc 07-May-2014 by Weerasinghe D , SRI International


Enzymatic reaction of: 3-methyl-2-oxopentanoate dehydrogenase (branched-chain α-keto acid dehydrogenase complex)

EC Number: 1.2.1.-

(S)-3-methyl-2-oxopentanoate + coenzyme A + NAD+ <=> 2-methylbutanoyl-CoA + CO2 + NADH

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

This reaction is reversible.

In Pathways: 2-oxoisovalerate decarboxylation to isobutanoyl-CoA , isoleucine degradation I


Enzymatic reaction of: 2-oxobutanoate dehydrogenase (branched-chain α-keto acid dehydrogenase complex)

2-oxobutanoate + coenzyme A + NAD+ <=> propanoyl-CoA + CO2 + NADH

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.

In Pathways: superpathway of methionine salvage and degradation , 2-oxobutanoate degradation I , threonine degradation


Enzymatic reaction of: 3-methyl-2-oxobutanoate dehydrogenase (branched-chain α-keto acid dehydrogenase complex)

EC Number: 1.2.1.25

3-methyl-2-oxobutanoate + coenzyme A + NAD+ <=> isobutanoyl-CoA + CO2 + NADH

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

In Pathways: 2-oxoisovalerate decarboxylation to isobutanoyl-CoA , valine degradation I


Subunit of: 2-ketoglutarate dehydrogenase complex

Synonyms: α-ketoglutarate dehydrogenase, 2-ketoglutarate dehydrogenase

Species: Homo sapiens

Subunit composition of 2-ketoglutarate dehydrogenase complex = [(DLD)2]6[(DLST)24][(OGDH)2]12
         dihydrolipoyl dehydrogenase = (DLD)2 (extended summary available)
                 dihydrolipoyl dehydrogenase monomer = DLD
         2-oxoglutarate dehydrogenase complex, (E2) inner core = (DLST)24 (extended summary available)
                 2-oxoglutarate dehydrogenase complex, dihydrolipoamide succinyltransferase component = DLST
         2-oxoglutarate dehydrogenase complex E1 dimer = (OGDH)2
                 2-oxoglutarate dehydrogenase E1 component = OGDH

Summary:
The 2-ketoglutarate dehydrogenase complex converts 2-oxoglutarate to succinyl-CoA and produces NADH and CO2 in a complicated series of irreversible reactions. These include oxidative decarboxylation, formation of CoA ester, and reoxidation of a lipoamide cofactor. Three different subunits, 2-oxo acid dehydrogenase (E1), a dihydrolipoamide acyltransferase (E2), and dihydrolipoamide dehydrogenase (E3) are required to perform the series of reactions which are driven by the decrease in free energy and the removal of CO2 generated in the first E1-catalyzed step. The enzyme complex belongs to the 2-oxo acid dehydrogenase family, which also includes the pyruvate dehydrogenase (PDHC), the branched-chain α-keto acid dehydrogenase complex (BCDHC), the glycine cleavage (GDHC), and the acetoin dehydrogenase complex (ADHC).

The E1 component is either a heterotetramer composed of two types of subunits, or a homodimer, made up of a single type of subunit. In all cases described so far many copies of each subunit assemble to form the full complex.

Cryoelectron microscopy of PDHC from ox kidney [Zhou01] has revealed that the E2 inner core is surrounded by an outer shell of E1 and E3 components, with the lipoyl domains confined to the annular space between them where they must make successive journeys between the three types of active sites (E1-E3), which are physically far apart [Fries03].

E1, which contains a thiamin diphosphate cofactor, catalyzes the binding of the 2-oxo acid to the lipoyl group of E2, which then transfers an acyl group (the nature of the acyl group depends on the particular enzyme) to coenzyme A, forming an acyl-CoA, while reducing the lipoyl group to dihydrolipoyl. E3 then transfers the protons to NAD, forming NADH and restoring the dihydrolipoyllysine group back to lipoyllysine.

Locations: mitochondrial lumen

GO Terms:

Cellular Component: GO:0005759 - mitochondrial matrix

Credits:
Revised 15-Jun-2009 by Caspi R , SRI International

Exons/Introns:


References

AEvarsson00: AEvarsson A, Chuang JL, Wynn RM, Turley S, Chuang DT, Hol WG (2000). "Crystal structure of human branched-chain alpha-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease." Structure 8(3);277-91. PMID: 10745006

Ambrus09: Ambrus A, Torocsik B, Adam-Vizi V (2009). "Periplasmic cold expression and one-step purification of human dihydrolipoamide dehydrogenase." Protein Expr Purif 63(1);50-7. PMID: 18845259

Brown02a: Brown RM, Head RA, Brown GK (2002). "Pyruvate dehydrogenase E3 binding protein deficiency." Hum Genet 110(2);187-91. PMID: 11935326

deKok98: de Kok A, Hengeveld AF, Martin A, Westphal AH (1998). "The pyruvate dehydrogenase multi-enzyme complex from Gram-negative bacteria." Biochim Biophys Acta 1385(2);353-66. PMID: 9655933

Feigenbaum93: Feigenbaum AS, Robinson BH (1993). "The structure of the human dihydrolipoamide dehydrogenase gene (DLD) and its upstream elements." Genomics 17(2);376-81. PMID: 8406489

Fries03: Fries M, Jung HI, Perham RN (2003). "Reaction mechanism of the heterotetrameric (alpha2beta2) E1 component of 2-oxo acid dehydrogenase multienzyme complexes." Biochemistry 42(23);6996-7002. PMID: 12795594

Harris97: Harris RA, Hawes JW, Popov KM, Zhao Y, Shimomura Y, Sato J, Jaskiewicz J, Hurley TD (1997). "Studies on the regulation of the mitochondrial alpha-ketoacid dehydrogenase complexes and their kinases." Adv Enzyme Regul 37;271-93. PMID: 9381974

Kim02h: Kim H (2002). "Activity of human dihydrolipoamide dehydrogenase is reduced by mutation at threonine-44 of FAD-binding region to valine." J Biochem Mol Biol 35(4);437-41. PMID: 12297006

Liu93a: Liu TC, Kim H, Arizmendi C, Kitano A, Patel MS (1993). "Identification of two missense mutations in a dihydrolipoamide dehydrogenase-deficient patient." Proc Natl Acad Sci U S A 90(11);5186-90. PMID: 8506365

McWilliam10: McWilliam CA, Ridout CK, Brown RM, McWilliam RC, Tolmie J, Brown GK (2010). "Pyruvate dehydrogenase E2 deficiency: a potentially treatable cause of episodic dystonia." Eur J Paediatr Neurol 14(4);349-53. PMID: 20022530

Munnich82: Munnich A, Saudubray JM, Taylor J, Charpentier C, Marsac C, Rocchiccioli F, Amedee-Manesme O, Coude FX, Frezal J, Robinson BH (1982). "Congenital lactic acidosis, alpha-ketoglutaric aciduria and variant form of maple syrup urine disease due to a single enzyme defect: dihydrolipoyl dehydrogenase deficiency." Acta Paediatr Scand 71(1);167-71. PMID: 6897145

Nobukuni90: Nobukuni Y, Mitsubuchi H, Endo F, Akaboshi I, Asaka J, Matsuda I (1990). "Maple syrup urine disease. Complete primary structure of the E1 beta subunit of human branched chain alpha-ketoacid dehydrogenase complex deduced from the nucleotide sequence and a gene analysis of patients with this disease." J Clin Invest 86(1);242-7. PMID: 2365818

Otulakowski87: Otulakowski G, Robinson BH (1987). "Isolation and sequence determination of cDNA clones for porcine and human lipoamide dehydrogenase. Homology to other disulfide oxidoreductases." J Biol Chem 262(36);17313-8. PMID: 3693355

Paxton86: Paxton R, Scislowski PW, Davis EJ, Harris RA (1986). "Role of branched-chain 2-oxo acid dehydrogenase and pyruvate dehydrogenase in 2-oxobutyrate metabolism." Biochem J 234(2);295-303. PMID: 3718468

Pettit78: Pettit FH, Yeaman SJ, Reed LJ (1978). "Purification and characterization of branched chain alpha-keto acid dehydrogenase complex of bovine kidney." Proc Natl Acad Sci U S A 75(10);4881-5. PMID: 283398

Pons88: Pons G, Raefsky-Estrin C, Carothers DJ, Pepin RA, Javed AA, Jesse BW, Ganapathi MK, Samols D, Patel MS (1988). "Cloning and cDNA sequence of the dihydrolipoamide dehydrogenase component human alpha-ketoacid dehydrogenase complexes." Proc Natl Acad Sci U S A 85(5);1422-6. PMID: 3278312

Reed01: Reed LJ (2001). "A trail of research from lipoic acid to alpha-keto acid dehydrogenase complexes." J Biol Chem 276(42);38329-36. PMID: 11477096

Roche03: Roche TE, Hiromasa Y, Turkan A, Gong X, Peng T, Yan X, Kasten SA, Bao H, Dong J (2003). "Essential roles of lipoyl domains in the activated function and control of pyruvate dehydrogenase kinases and phosphatase isoform 1." Eur J Biochem 270(6);1050-6. PMID: 12631265

Scherer91: Scherer SW, Otulakowski G, Robinson BH, Tsui LC (1991). "Localization of the human dihydrolipoamide dehydrogenase gene (DLD) to 7q31----q32." Cytogenet Cell Genet 56(3-4);176-7. PMID: 2055113

Tsuruta98: Tsuruta M, Mitsubuchi H, Mardy S, Miura Y, Hayashida Y, Kinugasa A, Ishitsu T, Matsuda I, Indo Y (1998). "Molecular basis of intermittent maple syrup urine disease: novel mutations in the E2 gene of the branched-chain alpha-keto acid dehydrogenase complex." J Hum Genet 43(2);91-100. PMID: 9621512

Wang07c: Wang YC, Wang ST, Li C, Liu WH, Chen PR, Chen LY, Liu TC (2007). "The role of N286 and D320 in the reaction mechanism of human dihydrolipoamide dehydrogenase (E3) center domain." J Biomed Sci 14(2);203-10. PMID: 17171578

Zhou01: Zhou ZH, McCarthy DB, O'Connor CM, Reed LJ, Stoops JK (2001). "The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes." Proc Natl Acad Sci U S A 98(26);14802-7. PMID: 11752427


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Wed Nov 26, 2014, biocyc13.