MetaCyc Pathway: pyrimidine deoxyribonucleotides de novo biosynthesis III
Traceable author statement to experimental support

Enzyme View:

Pathway diagram: pyrimidine deoxyribonucleotides de novo biosynthesis III

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: BiosynthesisNucleosides and Nucleotides Biosynthesis2'-Deoxyribonucleotides BiosynthesisPyrimidine Deoxyribonucleotides De Novo Biosynthesis
BiosynthesisNucleosides and Nucleotides BiosynthesisPyrimidine Nucleotide BiosynthesisPyrimidine Nucleotides De Novo BiosynthesisPyrimidine Deoxyribonucleotides De Novo Biosynthesis
Metabolic Clusters

Some taxa known to possess this pathway include : Aeropyrum pernix, Aquifex aeolicus, Aquifex aeolicus VF5, Borrelia burgdorferi, Campylobacter jejuni, Campylobacter jejuni jejuni NCTC 11168 = ATCC 700819, Chlamydia pneumoniae, Chlamydia psittaci , Chlamydia trachomatis, Chlamydia trachomatis D/UW-3/CX, Corynebacterium glutamicum, Corynebacterium glutamicum ATCC 13032, Dictyostelium discoideum, Halobacterium salinarum, Helicobacter pylori, Mycobacterium bovis, Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv, Pyrobaculum aerophilum, Pyrococcus abyssi, Pyrococcus furiosus, Pyrococcus horikoshii, Rhodobacter capsulatus, Rickettsia prowazekii, Rickettsia prowazekii Madrid E, Sulfolobus solfataricus, Sulfolobus tokodaii, Thermoplasma acidophilum, Thermoplasma volcanium, Thermotoga maritima, Treponema pallidum

Expected Taxonomic Range: Archaea, Bacteria , Dictyostelium, Viruses

General Background

Pyrimidine and purine nucleoside triphosphates are the activated precursors of DNA and RNA. The pyrimidine deoxyribonucleoside triphosphates dCTP and dTTP are incorporated into DNA while the ribonucleoside triphosphates CTP and UTP are incorporated into RNA. In addition, their diphosphates form activated derivatives of other molecules, such as UDP-α-D-glucose, CMP-3-deoxy-β-D-manno-octulosonate and dTDP-α-D-fucopyranose, for use in biosynthesis of polysaccharides, glycoproteins and phospholipids [Zhou98a, Giermann02, Schroder05, Zrenner06].

In addition to de novo biosynthesis, salvage pathways reutilize exogenous free bases and nucleosides and some of the resulting pyrimidine nucleotides can enter the de novo biosynthesis pathways (see pyrimidine ribonucleosides salvage I, pyrimidine nucleobases salvage I and pyrimidine deoxyribonucleosides salvage). The de novo biosynthetic pathways consume relatively large amounts of high energy phosphate and reducing power, and thus organisms prefer to use salvage pathways when possible. However, the de novo biosynthetic pathways are necessary when exogenous precursors are limiting. In order to conserve resources, the de novo pathways are regulated both by allosteric enzymes and at the gene expression level. These essential, evolutionarily conserved biosynthetic and salvage pathways are found in both prokaryotes and eukaryotes.

The pyrimidine nucleotide de novo biosynthetic pathway derives in part from the central metabolic precursors oxaloacetate and D-ribose 5-phosphate. L-aspartate, a precursor of pyrimidine ribonucleotides, is derived from oxaloacetate, which is generated in the TCA cycle.

About This Pathway

The pathway shown here is similar to pathway pyrimidine deoxyribonucleotides de novo biosynthesis I with the exception of the flavin-dependent thymidylate synthase reaction EC (catalyzed by ThiX), which substitutes for the more common thymidylate synthase reaction EC (catalyzed by ThiA).

In 2002 it was discovered that some organisms do not posses the thyA gene (named TYMS in animals), and instead have an alternate, novel flavin-dependent thymidylate synthase encoded by gene thyX.

Both thymidylate synthases catalyze a reductive methylation involving the transfer of the methylene group of 5,10-methylenetetrahydropteroyl mono-L-glutamate to the C5-position of dUMP and a two electron reduction of the methylene group to a methyl group. However, the reductive mechanisms of ThyA and ThyX are distinctly different. The ThyA reductive mechanism uses folate as both a 1-carbon donor and a source of reducing equivalents, producing dUMP and 7,8-dihydrofolate monoglutamate as products, and does not involve a flavin coenzyme or a third substrate. In contrast, the ThyX mechanism uses a flavin coenzyme as a source of reducing equivalents, which are derived from NADPH. This NAD(P)H oxidase uses FAD to mediate hydride transfer in a methylation reaction that results in tetrahydropteroyl mono-L-glutamate as a product, rather than the 7,8-dihydrofolate monoglutamate that is produced by ThyA. The chemical and kinetic mechanisms of ThyX and progress in the design of specific inhibitors are reviewed in [Koehn10]. Inhibitor design has been specifically addressed in [Chernyshev07, Esra08].

Homologs of the thyX gene have been identified in some eubacterial, archaeal, slime mold and viral genomes [Myllykallio02]. The genomes of some of these organisms contain only thyX, while others, such as those of Mycobacterium and Corynebacterium species, including Mycobacterium tuberculosis, Mycobacterium bovis and Corynebacterium glutamicum ATCC 13032 contain both thyA and thyX. The two proteins may function under different phases of the growth cycle (in [Park10a, Myllykallio02, Lesley02, Graziani06, Leduc07] and reviewed in [Murzin02, Leduc04, Koehn10]).

Because ThyX is found in some important human and animal pathogens, it is of interest as a drug target [Chernyshev07]. Some of the bacterial pathogens that appear to posses only ThyX include Helicobacter pylori, Campylobacter jejuni, Rickettsia prowazekii, Borrelia burgdorferi, Treponema pallidum, Chlamydia pneumoniae, Chlamydia psittaci and Chlamydia trachomatis (in [Myllykallio02, Mathews03]). Other bacteria that posses only ThyX include Rhodobacter capsulatus [Leduc07] and the hyperthermophiles Thermotoga maritima and Aquifex aeolicus [Leduc04].

Some archaea apparently posses only ThyX and others only ThyA. Those with only ThyX include Aeropyrum pernix, Pyrobaculum aerophilum, Pyrococcus abyssi, Pyrococcus furiosus, Pyrococcus horikoshii, Thermoplasma acidophilum, Thermoplasma volcanium, Sulfolobus solfataricus and Sulfolobus tokodaii [Myllykallio02, Leduc04], and Halobacterium salinarum [Giladi02]. Conversely, archaea that possess only ThyA include Archaeoglobus fulgidus, Methanocaldococcus jannaschii, Methanopyrus kandleri, and Methanothermobacter thermautotrophicus [Leduc04]. It should be noted that many archaea do not contain the substrate tetrahydrofolate as shown in these pathways, and utilize chemically modified tetrahydromethanopterins instead [Leduc04].

ThyX shows no sequence homology with ThyA and substantially differs from ThyA in crystal structure and reaction mechanism. Evidence has been presented that ThyX is less catalytically efficient than ThyA and it may limit chromosomal replication in bacteria and archaea that posses it [Escartin08].

Variants: pyrimidine deoxyribonucleotides de novo biosynthesis I, pyrimidine deoxyribonucleotides de novo biosynthesis II, pyrimidine deoxyribonucleotides de novo biosynthesis IV, superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis, superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)

Relationship Links: KEGG:PART-OF:map00240

Created 15-Jul-2010 by Fulcher CA, SRI International
Revised 21-Jan-2013 by Caspi R, SRI International


Chernyshev07: Chernyshev A, Fleischmann T, Kohen A (2007). "Thymidyl biosynthesis enzymes as antibiotic targets." Appl Microbiol Biotechnol 74(2);282-9. PMID: 17216455

Escartin08: Escartin F, Skouloubris S, Liebl U, Myllykallio H (2008). "Flavin-dependent thymidylate synthase X limits chromosomal DNA replication." Proc Natl Acad Sci U S A 105(29);9948-52. PMID: 18621705

Esra08: Esra Onen F, Boum Y, Jacquement C, Spanedda MV, Jaber N, Scherman D, Myllykallio H, Herscovici J (2008). "Design, synthesis and evaluation of potent thymidylate synthase X inhibitors." Bioorg Med Chem Lett 18(12);3628-31. PMID: 18513963

Giermann02: Giermann N, Schroder M, Ritter T, Zrenner R (2002). "Molecular analysis of de novo pyrimidine synthesis in solanaceous species." Plant Mol Biol 50(3);393-403. PMID: 12369616

Giladi02: Giladi M, Bitan-Banin G, Mevarech M, Ortenberg R (2002). "Genetic evidence for a novel thymidylate synthase in the halophilic archaeon Halobacterium salinarum and in Campylobacter jejuni." FEMS Microbiol Lett 216(1);105-9. PMID: 12423760

Graziani06: Graziani S, Bernauer J, Skouloubris S, Graille M, Zhou CZ, Marchand C, Decottignies P, van Tilbeurgh H, Myllykallio H, Liebl U (2006). "Catalytic mechanism and structure of viral flavin-dependent thymidylate synthase ThyX." J Biol Chem 281(33);24048-57. PMID: 16707489

Koehn10: Koehn EM, Kohen A (2010). "Flavin-dependent thymidylate synthase: a novel pathway towards thymine." Arch Biochem Biophys 493(1);96-102. PMID: 19643076

Leduc04: Leduc D, Graziani S, Meslet-Cladiere L, Sodolescu A, Liebl U, Myllykallio H (2004). "Two distinct pathways for thymidylate (dTMP) synthesis in (hyper)thermophilic Bacteria and Archaea." Biochem Soc Trans 32(Pt 2);231-5. PMID: 15046578

Leduc07: Leduc D, Escartin F, Nijhout HF, Reed MC, Liebl U, Skouloubris S, Myllykallio H (2007). "Flavin-dependent thymidylate synthase ThyX activity: implications for the folate cycle in bacteria." J Bacteriol 189(23);8537-45. PMID: 17890305

Lesley02: Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC (2002). "Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline." Proc Natl Acad Sci U S A 99(18);11664-9. PMID: 12193646

Mathews03: Mathews II, Deacon AM, Canaves JM, McMullan D, Lesley SA, Agarwalla S, Kuhn P (2003). "Functional analysis of substrate and cofactor complex structures of a thymidylate synthase-complementing protein." Structure 11(6);677-90. PMID: 12791256

Murzin02: Murzin AG (2002). "Biochemistry. DNA building block reinvented." Science 297(5578);61-2. PMID: 12029066

Myllykallio02: Myllykallio H, Lipowski G, Leduc D, Filee J, Forterre P, Liebl U (2002). "An alternative flavin-dependent mechanism for thymidylate synthesis." Science 297(5578);105-7. PMID: 12029065

Park10a: Park M, Cho S, Lee H, Sibley CH, Rhie H (2010). "Alternative thymidylate synthase, ThyX, involved in Corynebacterium glutamicum ATCC 13032 survival during stationary growth phase." FEMS Microbiol Lett 307(2);128-34. PMID: 20636973

Schroder05: Schroder M, Giermann N, Zrenner R (2005). "Functional analysis of the pyrimidine de novo synthesis pathway in solanaceous species." Plant Physiol 138(4);1926-38. PMID: 16024685

Zhou98a: Zhou L, Lacroute F, Thornburg R (1998). "Cloning, expression in Escherichia coli, and characterization of Arabidopsis thaliana UMP/CMP kinase." Plant Physiol 117(1);245-54. PMID: 9576794

Zrenner06: Zrenner R, Stitt M, Sonnewald U, Boldt R (2006). "Pyrimidine and purine biosynthesis and degradation in plants." Annu Rev Plant Biol 57;805-36. PMID: 16669783

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

Agrawal04a: Agrawal N, Lesley SA, Kuhn P, Kohen A (2004). "Mechanistic studies of a flavin-dependent thymidylate synthase." Biochemistry 43(32);10295-301. PMID: 15301527

Almaula95: Almaula N, Lu Q, Delgado J, Belkin S, Inouye M (1995). "Nucleoside diphosphate kinase from Escherichia coli." J Bacteriol 177(9);2524-9. PMID: 7730286

Arakawa04: Arakawa T, Tokunaga M (2004). "Electrostatic and hydrophobic interactions play a major role in the stability and refolding of halophilic proteins." Protein Pept Lett 11(2);125-32. PMID: 15078200

Bajaj07: Bajaj M, Moriyama H (2007). "Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana." Acta Crystallogr Sect F Struct Biol Cryst Commun 63(Pt 5);409-11. PMID: 17565183

Barabas04: Barabas O, Pongracz V, Kovari J, Wilmanns M, Vertessy BG (2004). "Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase." J Biol Chem 279(41);42907-15. PMID: 15208312

Besir05: Besir H, Zeth K, Bracher A, Heider U, Ishibashi M, Tokunaga M, Oesterhelt D (2005). "Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum." FEBS Lett 579(29);6595-600. PMID: 16293253

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Brundiers99: Brundiers R, Lavie A, Veit T, Reinstein J, Schlichting I, Ostermann N, Goody RS, Konrad M (1999). "Modifying human thymidylate kinase to potentiate azidothymidine activation." J Biol Chem 274(50);35289-92. PMID: 10585390

Chabes00: Chabes A, Domkin V, Larsson G, Liu A, Graslund A, Wijmenga S, Thelander L (2000). "Yeast ribonucleotide reductase has a heterodimeric iron-radical-containing subunit." Proc Natl Acad Sci U S A 97(6);2474-9. PMID: 10716984

Daws84: Daws TD, Fuchs JA (1984). "Isolation and characterization of an Escherichia coli mutant deficient in dTMP kinase activity." J Bacteriol 1984;157(2);440-4. PMID: 6319360

Dyson90: Dyson HJ, Gippert GP, Case DA, Holmgren A, Wright PE (1990). "Three-dimensional solution structure of the reduced form of Escherichia coli thioredoxin determined by nuclear magnetic resonance spectroscopy." Biochemistry 1990;29(17);4129-36. PMID: 2193685

Eklund84: Eklund H, Cambillau C, Sjoberg BM, Holmgren A, Jornvall H, Hoog JO, Branden CI (1984). "Conformational and functional similarities between glutaredoxin and thioredoxins." EMBO J 1984;3(7);1443-9. PMID: 6378624

Familiar08: Familiar O, Munier-Lehmann H, Negri A, Gago F, Douguet D, Rigouts L, Hernandez AI, Camarasa MJ, Perez-Perez MJ (2008). "Exploring acyclic nucleoside analogues as inhibitors of Mycobacterium tuberculosis thymidylate kinase." ChemMedChem 3(7);1083-93. PMID: 18418833

Filpula77: Filpula D, Fuchs JA (1977). "Regulation of ribonucleoside diphosphate reductase synthesis in Escherichia coli: increased enzyme synthesis as a result of inhibition of deoxyribonucleic acid synthesis." J Bacteriol 130(1);107-13. PMID: 67110

Fioravanti03: Fioravanti E, Haouz A, Ursby T, Munier-Lehmann H, Delarue M, Bourgeois D (2003). "Mycobacterium tuberculosis thymidylate kinase: structural studies of intermediates along the reaction pathway." J Mol Biol 327(5);1077-92. PMID: 12662932

Fioravanti05: Fioravanti E, Adam V, Munier-Lehmann H, Bourgeois D (2005). "The crystal structure of Mycobacterium tuberculosis thymidylate kinase in complex with 3'-azidodeoxythymidine monophosphate suggests a mechanism for competitive inhibition." Biochemistry 44(1);130-7. PMID: 15628853

Garton07: Garton S, Knight H, Warren GJ, Knight MR, Thorlby GJ (2007). "crinkled leaves 8--a mutation in the large subunit of ribonucleotide reductase--leads to defects in leaf development and chloroplast division in Arabidopsis thaliana." Plant J 50(1);118-27. PMID: 17346262

Gasse08: Gasse C, Douguet D, Huteau V, Marchal G, Munier-Lehmann H, Pochet S (2008). "Substituted benzyl-pyrimidines targeting thymidine monophosphate kinase of Mycobacterium tuberculosis: synthesis and in vitro anti-mycobacterial activity." Bioorg Med Chem 16(11);6075-85. PMID: 18467107

Ginther74: Ginther CL, Ingraham JL (1974). "Nucleoside diphosphokinase of Salmonella typhimurium." J Biol Chem 249(11);3406-11. PMID: 4364654

Gleason88: Gleason FK, Holmgren A (1988). "Thioredoxin and related proteins in procaryotes." FEMS Microbiol Rev 1988;4(4);271-97. PMID: 3152490

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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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