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Escherichia coli K-12 substr. MG1655 Pathway: tetrahydrofolate biosynthesis

Note: a dashed line (without arrowheads) between two compound names is meant to imply that the two names are just different instantiations of the same compound -- i.e. one may be a specific name and the other a general name, or they may both represent the same compound in different stages of a polymerization-type pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Locations of Mapped Genes:

Genetic Regulation Schematic: ?

Synonyms: folic acid biosynthesis, folate biosynthesis, THF biosynthesis

Superclasses: Biosynthesis Cofactors, Prosthetic Groups, Electron Carriers Biosynthesis Vitamins Biosynthesis Folate Biosynthesis

Summary:
General Background

Tetrahydrofolate (vitamin B9, tetrahydropteroylmonoglutamate) and its derivatives are commonly termed folates. Folates are tripartite molecules made up of a pterin, 4-aminobenzoate, and L-glutamate moieties. The pterin is synthesized from GTP and 4-aminobenzoate is synthesized from chorismate as shown in the pathway links to 6-hydroxymethyl-dihydropterin diphosphate biosynthesis I and 4-aminobenzoate biosynthesis, respectively.

The product of this pathway, tetrahydrofolate, is merely the parent structure of this large family of coenzymes. Members of the family differ in the oxidation state of the pteridine ring, the character of the one-carbon substituent at the N5 and N10 positions, and the number of glutamate residues. The glutamate residues are conjugated one to another via a series of γ-glutamyl links to form an oligo-γ-glutamyl tail, as shown in the pathway link to folate polyglutamylation.

Folates are essential cofactors that facilitate the transfer of one-carbon units from donor molecules into important biosynthetic pathways. In E. coli folates lead to the biosynthesis of methionine, purines, thymidylate and pantothenate (see pathways methionine biosynthesis I, inosine-5'-phosphate biosynthesis I, superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli), and phosphopantothenate biosynthesis I). They also mediate the interconversion of serine and glycine (see pathway glycine biosynthesis I) and participate in the biosynthesis of N-formyl-L-methionyl-tRNAfmet. Folates are biosynthesized de novo by bacteria, fungi and plants. Vertebrates are dependent on nutritional sources of folate, making it a vitamin. In addition to the de novo pathway, many organisms also possess salvage pathways that are used to re-synthesize tetrahydrofolate from pre-existing derivatives of folates in the cell (see pathway tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate).

About This Pathway

Dihydropteroate synthase encoded by folP catalyzes the condensation of 4-aminobenzoate (p-aminobenzoate) with 6-hydroxymethyl-dihydropterin diphosphate to produce 7,8-dihydropteroate (dihydropteroate) [Richey69]. Sulfonamide derivatives (sulfa drugs) are structural analogs of 4-aminobenzoate that compete with this substrate for the enzyme. Several mechanisms of sulfonamide resistance can develop, including mutations in folP [Vedantam98, Swedberg93].

Dihydrofolate synthetase encoded by folC then catalyzes the synthesis of dihydrofolate from dihydropteroate, L-glutamate and ATP [Griffin64]. In E. coli FolC is a bifunctional enzyme that also catalyzes subsequent additions of L-glutamate to tetrahydrofolate (folylpoly-γ-glutamate synthetase activity) [Bognar85] (see pathway folate polyglutamylation). The folC gene has been shown to be essential in E. coli [Pyne92].

Dihydrofolate reductase encoded by folA is the major enzyme responsible for reducing 7,8-dihydrofolate monoglutamate (dihydrofolate) to physiologically active tetrahydrofolate. Its substrate dihydrofolate is also a product of thymidylate synthase encoded by thyA during de novo pyrimidine biosynthesis (a 5,10-methylene-tetrahydrofolate + dUMP → dTMP + a 7,8-dihydrofolate). Because thymidylate synthase utilizes both the tetrahydrofolate derivative 5,10-methylenetetrahydrofolate and dUMP as substrates, dihydrofolate reductase must quickly reduce dihydrofolate to tetrahydrofolate when thymidylate is being synthesized in order to maintain cellular stores of tetrahydrofolate derivatives.

Strains containing a deletion of folA have been isolated from thyA strains, suggesting the existence of another enzyme with dihydrofolate reductase activity. FolM is considered to be a candidate for this [Giladi03], although its physiological role is incompletely understood. Another candidate was suggested to be NAD(P)H nitroreductase NfsB encoded by nfsB which was reported to have dihydrofolate reductase activity [Vasudevan92], although more studies are needed to support this.

Review: Green, J.M. and R.G. Matthews (2007) "Folate Biosynthesis, Reduction, and Polyglutamylation and the Interconversion of Folate Derivatives" EcoSal 3.6.3.6 [ECOSAL]

Superpathways: superpathway of tetrahydrofolate biosynthesis , superpathway of chorismate metabolism

Variants: 4-aminobenzoate biosynthesis , folate polyglutamylation , N10-formyl-tetrahydrofolate biosynthesis

Credits:
Created 22-Sep-2010 by Caspi R , SRI International
Last-Curated ? 30-May-2012 by Fulcher C , SRI International


References

Bognar85: Bognar AL, Osborne C, Shane B, Singer SC, Ferone R (1985). "Folylpoly-gamma-glutamate synthetase-dihydrofolate synthetase. Cloning and high expression of the Escherichia coli folC gene and purification and properties of the gene product." J Biol Chem 1985;260(9);5625-30. PMID: 2985605

ECOSAL: "Escherichia coli and Salmonella: Cellular and Molecular Biology." Online edition.

Giladi03: Giladi M, Altman-Price N, Levin I, Levy L, Mevarech M (2003). "FolM, a new chromosomally encoded dihydrofolate reductase in Escherichia coli." J Bacteriol 185(23);7015-8. PMID: 14617668

Griffin64: Griffin MJ, Brown GM (1964). "The biosynthesis of folic acid. III. Enzymatic formation of dihydrofolic acid from dihydropteroic acid and of tetrahydropteroylpolyglutamic acid compounds from tetrahydrofolic acid." J Biol Chem 239;310-6. PMID: 14114858

Pyne92: Pyne C, Bognar AL (1992). "Replacement of the folC gene, encoding folylpolyglutamate synthetase-dihydrofolate synthetase in Escherichia coli, with genes mutagenized in vitro." J Bacteriol 174(6);1750-9. PMID: 1548226

Richey69: Richey DP, Brown GM (1969). "The biosynthesis of folic acid. IX. Purification and properties of the enzymes required for the formation of dihydropteroic acid." J Biol Chem 1969;244(6);1582-92. PMID: 4304228

Swedberg93: Swedberg G, Fermer C, Skold O (1993). "Point mutations in the dihydropteroate synthase gene causing sulfonamide resistance." Adv Exp Med Biol 338;555-8. PMID: 8304179

Vasudevan92: Vasudevan SG, Paal B, Armarego WL (1992). "Dihydropteridine reductase from Escherichia coli exhibits dihydrofolate reductase activity." Biol Chem Hoppe Seyler 373(10);1067-73. PMID: 1418677

Vedantam98: Vedantam G, Guay GG, Austria NE, Doktor SZ, Nichols BP (1998). "Characterization of mutations contributing to sulfathiazole resistance in Escherichia coli." Antimicrob Agents Chemother 42(1);88-93. PMID: 9449266

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

Achari97: Achari A, Somers DO, Champness JN, Bryant PK, Rosemond J, Stammers DK (1997). "Crystal structure of the anti-bacterial sulfonamide drug target dihydropteroate synthase." Nat Struct Biol 4(6);490-7. PMID: 9187658

Appleman90: Appleman JR, Howell EE, Kraut J, Blakley RL (1990). "Role of aspartate 27 of dihydrofolate reductase from Escherichia coli in interconversion of active and inactive enzyme conformers and binding of NADPH." J Biol Chem 1990;265(10);5579-84. PMID: 2108144

Arai05: Arai M, Iwakura M (2005). "Probing the interactions between the folding elements early in the folding of Escherichia coli dihydrofolate reductase by systematic sequence perturbation analysis." J Mol Biol 347(2);337-53. PMID: 15740745

Arai07: Arai M, Kondrashkina E, Kayatekin C, Matthews CR, Iwakura M, Bilsel O (2007). "Microsecond Hydrophobic Collapse in the Folding of Escherichia coli Dihydrofolate Reductase, an alpha/beta-Type Protein." J Mol Biol 368(1);219-29. PMID: 17331539

Arai11: Arai M, Iwakura M, Matthews CR, Bilsel O (2011). "Microsecond subdomain folding in dihydrofolate reductase." J Mol Biol 410(2);329-42. PMID: 21554889

Baccanari75: Baccanari D, Phillips A, Smith S, Sinski D, Burchall J (1975). "Purification and properties of Escherichia coli dihydrofolate reductase." Biochemistry 1975;14(24);5267-73. PMID: 46

Baccanari77: Baccanari DP, Averett D, Briggs C, Burchall J (1977). "Escherichia coli dihydrofolate reductase: isolation and characterization of two isozymes." Biochemistry 16(16);3566-72. PMID: 19054

Baccanari82: Baccanari DP, Daluge S, King RW (1982). "Inhibition of dihydrofolate reductase: effect of reduced nicotinamide adenine dinucleotide phosphate on the selectivity and affinity of diaminobenzylpyrimidines." Biochemistry 1982;21(20);5068-75. PMID: 6814484

Batruch10: Batruch I, Javasky E, Brown ED, Organ MG, Johnson PE (2010). "Thermodynamic and NMR analysis of inhibitor binding to dihydrofolate reductase." Bioorg Med Chem 18(24);8485-92. PMID: 21084197

Benkovic08: Benkovic SJ, Hammes GG, Hammes-Schiffer S (2008). "Free-energy landscape of enzyme catalysis." Biochemistry 47(11);3317-21. PMID: 18298083

Bermingham02: Bermingham A, Derrick JP (2002). "The folic acid biosynthesis pathway in bacteria: evaluation of potential for antibacterial drug discovery." Bioessays 24(7);637-48. PMID: 12111724

Bershtein12: Bershtein S, Wu W, Shakhnovich EI (2012). "Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations." Proc Natl Acad Sci U S A 109(13);4857-62. PMID: 22411825

Bhabha11: Bhabha G, Lee J, Ekiert DC, Gam J, Wilson IA, Dyson HJ, Benkovic SJ, Wright PE (2011). "A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis." Science 332(6026);234-8. PMID: 21474759

Bhabha11a: Bhabha G, Tuttle L, Martinez-Yamout MA, Wright PE (2011). "Identification of endogenous ligands bound to bacterially expressed human and E. coli dihydrofolate reductase by 2D NMR." FEBS Lett 585(22);3528-32. PMID: 22024482

Boehr06: Boehr DD, McElheny D, Dyson HJ, Wright PE (2006). "The dynamic energy landscape of dihydrofolate reductase catalysis." Science 313(5793);1638-42. PMID: 16973882

Boehr08: Boehr DD, Dyson HJ, Wright PE (2008). "Conformational relaxation following hydride transfer plays a limiting role in dihydrofolate reductase catalysis." Biochemistry 47(35);9227-33. PMID: 18690714

Boehr10: Boehr DD, McElheny D, Dyson HJ, Wright PE (2010). "Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands." Proc Natl Acad Sci U S A 107(4);1373-8. PMID: 20080605

Bognar87: Bognar AL, Osborne C, Shane B (1987). "Primary structure of the Escherichia coli folC gene and its folylpolyglutamate synthetase-dihydrofolate synthetase product and regulation of expression by an upstream gene." J Biol Chem 262(25);12337-43. PMID: 3040739

Bolin82: Bolin JT, Filman DJ, Matthews DA, Hamlin RC, Kraut J (1982). "Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate." J Biol Chem 257(22);13650-62. PMID: 6815178

Bowden89: Bowden K, Hall AD, Birdsall B, Feeney J, Roberts GC (1989). "Interactions between inhibitors of dihydrofolate reductase." Biochem J 1989;258(2);335-42. PMID: 2495789

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 19, 2014, biocyc14.