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MetaCyc Pathway: lipoate biosynthesis and incorporation I

Pathway diagram: lipoate biosynthesis and incorporation I

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Biosynthesis Cofactors, Prosthetic Groups, Electron Carriers Biosynthesis Lipoate Biosynthesis

Some taxa known to possess this pathway include ? : Escherichia coli K-12 substr. MG1655

Expected Taxonomic Range: Bacteria , Eukaryota , Viridiplantae

Summary:
General Background

Lipoate is an organosulfur compound that contains a ditholane ring, which is a cyclic disulfide. Lipoate is used as an essential cofactor by many enzyme complexes involved in oxidative metabolism, including the pyruvate dehydrogenase complex [Herbert75, Stepp81, Reed93], the 2-oxoglutarate decarboxylation to succinyl-CoA [Herbert75, Stepp81, Reed93], the 2-oxoisovalerate decarboxylation to isobutanoyl-CoA [Reed90], and the glycine cleavage [Vanden91, Reed93].

Each of these enzyme complexes is composed of multiple copies of three enzymes: a substrate-specific decarboxylase-dehydrogenase (E1), a dihydrolipoamide acyltransferase (E2) specific for each type of complex, and a dihydrolipoamide dehydrogenase (E3). The (E2) proteins have a dedicated lipoyl domain. In order for the complex to be active, lipoate must be attached to the lipoyl domain by an amide linkage between its carboxylate moiety and a specific lysine residue in the enzyme [Reed93].

E1 catalyzes a reaction in which the substrate is attached to the lipoate cofactor and decarboxylated. During this reaction, the lipoate cofactor is reduced to dihydriolipoate. E2 then catalyzes an acyl transfer step, in which the product of the reaction is released. Finally, E3 catalyzes the oxidation of the dihydrolipoyl cofactor back to lipoyl form, with NAD being the ultimate electron acceptor [Reed90].

About This Pathway

The biosynthesis of lipoate is unusual, and shares the same mechanism as the biosynthesis of biotin. The precursor octanoate molecule is first attached to a specific L-lysine residue within the lipoyl domain, and is then converted to lipoate.

The first enzyme in this pathway, lipoyl(octanoyl) transferase, transfers the octanoate moiety from octanoate-[acp] molecule to a specific lysyl residue in lipoate-dependent enzymes, resulting in a [lipoyl-carrier protein] N6-octanoyl-L-lysine, and regenerating the acyl-carrier protein in the process [Morris95, Zhao03]. lipoyl(octanoyl) transferase-mediated attachment of octanoate to the apo-domain probably does not occur unless the octanoate is bound to an acyl-carrier protein.

The next enzyme in the pathway, lipoyl synthase, catalyzes the conversion of the octanoyl side chain to an active lipoyl, generating a fully active lipoylated domain. The enzyme is an iron-sulfur protein that requires S-adenosyl-L-methionine (AdoMet) [Reed93, Miller00a]. An electron which originates from the [4Fe-4S] cluster of the enzyme serves to split at least two molecules of AdoMet into a 5'-deoxyadenosyl radical and methionine [Ollagnierde02]. The radical then abstracts a hydrogen from a C-H bond of thew octanoyl side chain, becoming 5'-adenosine in the process. The newly-formed unstable octanoyl radical then reacts directly with the Fe-S center of the enzyme. Two sulfur atoms from the center enter the structure of the octanoyl side chain, producing lipoyl, which dissociates from the enzyme along with excess iron, leaving it with a [2Fe-2S] center. Thus, in this unusual reaction, the iron-sulfur center of the enzyme is not just a catalytic accelerator, but also a substrate, donating the two sulfur atoms [Marquet01]. It should be noted that although this process has been well documented in vitro [Miller00a], there is still a possibility that there exists another sulfur donor in vivo, and that the Fe-S center acts as sulfur donor only in the absence of this natural donor [Frey01].

It has been suggested that the conversion of octanoylated-domains to lipoylated ones described in this pathway may be a type of a repair pathway, activated only if the other lipoate biosynthetic pathways are malfunctioning [Zhao03].

Other routes for lipoate incorporation involve the lipoyl-protein ligase LplA, which utilizes either lipoate or octanoate imported from outside the cell (see lipoate salvage I and lipoate biosynthesis and incorporation II).

Lipoate Biosynthesis in Other Organisms

Genes encoding LipA and LipB have been identified in mammalian genomes and it has been shown that mammalian cells are capable of synthesizing (R)-lipoate in mitochondria [Morikawa01]. However, their significance is not fully understood because it is generally believed that mammals primarily rely on salvaged (R)-lipoate (see lipoate salvage I). Lipoate biosynthesis has also been demonstrated in plants [Gueguen00].

It is not clear whether Archaea utilize lipoate. No clear evidence is available, although the genes encoding a putative 2-oxoacid dehydrogenase complex have been reported in Haloferax volcanii [Jolley00].

Variants: lipoate biosynthesis and incorporation (glycine cleavage system, yeast) , lipoate biosynthesis and incorporation (pyruvate dehydrogenase and oxoglutarate dehydrogenase, yeast) , lipoate biosynthesis and incorporation II , lipoate biosynthesis and incorporation III (Bacillus) , lipoate salvage I , lipoate salvage II

Unification Links: EcoCyc:PWY0-501

Credits:
Created 26-Mar-2003 by Arnaud M , SRI International
Revised 08-May-2006 by Caspi R , SRI International


References

Frey01: Frey PA (2001). "Radical mechanisms of enzymatic catalysis." Annu Rev Biochem 70;121-48. PMID: 11395404

Gueguen00: Gueguen V, Macherel D, Jaquinod M, Douce R, Bourguignon J (2000). "Fatty acid and lipoic acid biosynthesis in higher plant mitochondria." J Biol Chem 275(7);5016-25. PMID: 10671542

Herbert75: Herbert AA, Guest JR (1975). "Lipoic acid content of Escherichia coli and other microorganisms." Arch Microbiol 106(3);259-66. PMID: 814874

Jolley00: Jolley KA, Maddocks DG, Gyles SL, Mullan Z, Tang SL, Dyall-Smith ML, Hough DW, Danson MJ (2000). "2-Oxoacid dehydrogenase multienzyme complexes in the halophilic Archaea? Gene sequences and protein structural predictions." Microbiology 146 ( Pt 5);1061-9. PMID: 10832633

Marquet01: Marquet A, Bui BT, Florentin D (2001). "Biosynthesis of biotin and lipoic acid." Vitam Horm 61;51-101. PMID: 11153271

Miller00a: Miller JR, Busby RW, Jordan SW, Cheek J, Henshaw TF, Ashley GW, Broderick JB, Cronan JE, Marletta MA (2000). "Escherichia coli LipA is a lipoyl synthase: in vitro biosynthesis of lipoylated pyruvate dehydrogenase complex from octanoyl-acyl carrier protein." Biochemistry 39(49);15166-78. PMID: 11106496

Morikawa01: Morikawa T, Yasuno R, Wada H (2001). "Do mammalian cells synthesize lipoic acid? Identification of a mouse cDNA encoding a lipoic acid synthase located in mitochondria." FEBS Lett 498(1);16-21. PMID: 11389890

Morris95: Morris TW, Reed KE, Cronan JE (1995). "Lipoic acid metabolism in Escherichia coli: the lplA and lipB genes define redundant pathways for ligation of lipoyl groups to apoprotein." J Bacteriol 177(1);1-10. PMID: 8002607

Ollagnierde02: Ollagnier-de Choudens S, Sanakis Y, Hewitson KS, Roach P, Munck E, Fontecave M (2002). "Reductive cleavage of S-adenosylmethionine by biotin synthase from Escherichia coli." J Biol Chem 277(16);13449-54. PMID: 11834738

Reed90: Reed LJ, Hackert ML (1990). "Structure-function relationships in dihydrolipoamide acyltransferases." J Biol Chem 265(16);8971-4. PMID: 2188967

Reed93: Reed KE, Cronan JE (1993). "Lipoic acid metabolism in Escherichia coli: sequencing and functional characterization of the lipA and lipB genes." J Bacteriol 175(5);1325-36. PMID: 8444795

Stepp81: Stepp LR, Bleile DM, McRorie DK, Pettit FH, Reed LJ (1981). "Use of trypsin and lipoamidase to study the role of lipoic acid moieties in the pyruvate and alpha-ketoglutarate dehydrogenase complexes of Escherichia coli." Biochemistry 20(16);4555-60. PMID: 6794598

Vanden91: Vanden Boom TJ, Reed KE, Cronan JE (1991). "Lipoic acid metabolism in Escherichia coli: isolation of null mutants defective in lipoic acid biosynthesis, molecular cloning and characterization of the E. coli lip locus, and identification of the lipoylated protein of the glycine cleavage system." J Bacteriol 173(20);6411-20. PMID: 1655709

Zhao03: Zhao X, Miller JR, Jiang Y, Marletta MA, Cronan JE (2003). "Assembly of the covalent linkage between lipoic acid and its cognate enzymes." Chem Biol 10(12);1293-302. PMID: 14700636

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Booker04: Booker SJ (2004). "Unraveling the pathway of lipoic acid biosynthesis." Chem Biol 11(1);10-2. PMID: 15112987

Booker07: Booker SJ, Cicchillo RM, Grove TL (2007). "Self-sacrifice in radical S-adenosylmethionine proteins." Curr Opin Chem Biol 11(5);543-52. PMID: 17936058

Busby99: Busby RW, Schelvis JP M, Yu DS, Babcock GT, Marletta MA (1999). "Lipoic Acid Biosynthesis:  LipA Is an Iron−Sulfur Protein." Journal of the American Chemical Society 121(19);4706-4707.

Byers07: Byers DM, Gong H (2007). "Acyl carrier protein: structure-function relationships in a conserved multifunctional protein family." Biochem Cell Biol 85(6);649-62. PMID: 18059524

Chang91: Chang YY, Cronan JE, Li SJ, Reed K, Vanden Boom T, Wang AY (1991). "Locations of the lip, poxB, and ilvBN genes on the physical map of Escherichia coli." J Bacteriol 173(17);5258-9. PMID: 1832150

ChoiRhee05: Choi-Rhee E, Cronan JE (2005). "A nucleosidase required for in vivo function of the S-adenosyl-L-methionine radical enzyme, biotin synthase." Chem Biol 12(5);589-93. PMID: 15911379

Cicchillo04: Cicchillo RM, Lee KH, Baleanu-Gogonea C, Nesbitt NM, Krebs C, Booker SJ (2004). "Escherichia coli lipoyl synthase binds two distinct [4Fe-4S] clusters per polypeptide." Biochemistry 43(37);11770-81. PMID: 15362861

Cicchillo04a: Cicchillo RM, Iwig DF, Jones AD, Nesbitt NM, Baleanu-Gogonea C, Souder MG, Tu L, Booker SJ (2004). "Lipoyl synthase requires two equivalents of S-adenosyl-L-methionine to synthesize one equivalent of lipoic acid." Biochemistry 43(21);6378-86. PMID: 15157071

Cicchillo05: Cicchillo RM, Booker SJ (2005). "Mechanistic investigations of lipoic acid biosynthesis in Escherichia coli: both sulfur atoms in lipoic acid are contributed by the same lipoyl synthase polypeptide." J Am Chem Soc 127(9);2860-1. PMID: 15740115

Creaghan78: Creaghan IT, Guest JR (1978). "Succinate dehydrogenase-dependent nutritional requirement for succinate in mutants of Escherichia coli K12." J Gen Microbiol 107(1);1-13. PMID: 366070

Cronan05: Cronan JE, Zhao X, Jiang Y (2005). "Function, attachment and synthesis of lipoic acid in Escherichia coli." Adv Microb Physiol 50;103-46. PMID: 16221579

Cronan14: Cronan JE (2014). "The structure of lipoyl synthase, a remarkable enzyme that performs the last step of an extraordinary biosynthetic pathway." Biochem J 464(1);e1-3. PMID: 25341020

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Feng: Feng Y, Cronan JE "PdhR, the pyruvate dehydrogenase repressor, does not regulate lipoic acid synthesis." Res Microbiol 165(6);429-38. PMID: 24816490

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Gonidakis10: Gonidakis S, Finkel SE, Longo VD (2010). "Genome-wide screen identifies Escherichia coli TCA-cycle-related mutants with extended chronological lifespan dependent on acetate metabolism and the hypoxia-inducible transcription factor ArcA." Aging Cell 9(5);868-81. PMID: 20707865

Gonidakis10a: Gonidakis S, Finkel SE, Longo VD (2010). "E. coli hypoxia-inducible factor ArcA mediates lifespan extension in a lipoic acid synthase mutant by suppressing acetyl-CoA synthetase." Biol Chem 391(10);1139-47. PMID: 20707605

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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
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