MetaCyc Pathway: superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)
Inferred from experiment

Pathway diagram: superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)

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

Some taxa known to possess this pathway include : Escherichia coli K-12 substr. MG1655, Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv, Salmonella enterica enterica serovar Typhimurium

Expected Taxonomic Range: Archaea, Bacteria

General Background

Pyrimidine and purine nucleoside triphosphates are the activated precursors of DNA and RNA. Their diphosphates form activated derivatives of other molecules, such as UDP-α-D-glucose, for use in biosynthesis. The pathway for de novo biosynthesis of pyrimidine deoxyribonucleotides is derived from the pathway for superpathway of pyrimidine ribonucleotides de novo biosynthesis as shown above in the pathway links. In addition to de novo biosynthesis, salvage pathways re-utilize 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). These essential, evolutionarily conserved biosynthetic and salvage pathways are found in both prokaryotes and eukaryotes.

The pyrimidine nucleoside triphosphate products of these pathways are incorporated into DNA ( dCTP and dTTP) and RNA ( CTP and UTP). The de novo biosynthetic pathways are necessary in order to supply the cell with nucleoside triphosphates for stable RNA and DNA synthesis when precursors are limiting. These biosynthetic pathways consume relatively large amounts of high energy phosphate and reducing power. In Escherichia coli they are regulated both by allosteric enzymes and at the gene expression level in order to conserve resources under different growth conditions.

The pyrimidine nucleotide de novo biosynthetic pathways derive in part from the central metabolic precursors oxaloacetate and D-ribose 5-phosphate. Oxaloacetate from the TCA cycle I (prokaryotic) gives rise to the aspartate family of amino acids and L-aspartate is a precursor of both pyrimidine ribonucleotides and nicotinamide coenzymes (see L-aspartate biosynthesis). The overall pathway begins with the biosynthesis of carbamoyl phosphate from bicarbonate, phosphate from ATP and nitrogen from glutamine. This compound then condenses with L-aspartate to form N-carbamoyl-L-aspartate as shown in pathways superpathway of pyrimidine ribonucleotides de novo biosynthesis and UMP biosynthesis. The overall pathway branches at carbamoyl phosphate, which is an intermediate in L-arginine biosynthesis (see L-arginine biosynthesis I (via L-ornithine)). The activated intermediate 5-phospho-α-D-ribose 1-diphosphate is derived from D-ribose 5-phosphate and is a precursor in the de novo and salvage pathways for pyrimidine and purine nucleotides, as well as in biosynthetic pathways for nucleotide coenzymes, L-histidine and L-tryptophan (see superpathway of histidine, purine, and pyrimidine biosynthesis, PRPP biosynthesis I and PRPP biosynthesis II).

About This Pathway

The pathway shown here illustrates the point at which the pyrimidine ribonucleotides CDP, CTP, UDP and UTP are converted to their corresponding deoxyribonucleotides and the DNA-specific thymine deoxyribonucleoside triphosphate dTTP is formed. Deoxyribonucleotides are synthesized by reduction of ribonucleotides, which is regulated by the rate-limiting enzyme ribonucleotide reductase that carries out reduction at the C2' position. This enzyme has a central role in DNA replication and repair. In Escherichia coli this ribo- to deoxyribo- conversion is catalyzed by aerobic ribonucleoside diphosphate reductase, or anaerobic ribonucleoside triphosphate reductase. Electrons for these reductions are derived from NADPH and are transferred via a reduced thioredoxin, a reduced glutaredoxin, or a reduced flavodoxin.

The ribonucleotide reductase product of genes nrdA and nrdB functions aerobically and under microaerophilic conditions. A normally cryptic enzyme encoded by genes nrdE and nrdF cannot support aerobic, or microaerophilic growth in a nrdAB deletion mutant. However, it supports aerobic growth in such a mutant when genes nrdHIEF are overexpressed on a plasmid [Gon06]. It has been speculated that this additional aerobic enzyme may enhance ribonucleotide reductase activity under conditions of oxidative stress. The anaerobic enzyme is encoded by gene nrdD which functions in a multienzyme complex with the products of genes nrdG and fpr. Pathways for the reduction of these reductase enzymes have also been studied [Gon06].

The major pathway for the aerobic, de novo formation of the intermediate dUMP, the immediate precursor of thymine-containing nucleotides, is via phosphorylation of dCDP to dCTP and deamination of dCTP to dUTP which is hydrolyzed to dUMP. This pathway supplies 70-80% of total dUMP [Johansson07]. Most of the remainder is presumed to be formed from dUDP, as shown. In Escherichia coli dcd, deoA mutants, an alternate de novo deoxycytidine pathway to dUMP is used that relies on salvage enzymes [Weiss07a]. Formation of the DNA-specific end product dTTP requires reductive methylation of dUMP to dTMP by 5,10-methylenetetrahydropteroyl mono-L-glutamate catalyzed by thymidylate synthase. Two phosphorylations follow to form dTTP. The first step is catalyzed by the highly specific dTMP kinase, while the second step is catalyzed by the product of gene ndk which also catalyzes two preceding reactions.

Review: Neuhard J. and R.A. Kelln, Biosynthesis and Conversions of Pyrimidines, Chapter 35 in [Neidhardt96]

Subpathways: pyrimidine deoxyribonucleotides de novo biosynthesis I, pyrimidine deoxyribonucleotides de novo biosynthesis II

Variants: pyrimidine deoxyribonucleotides de novo biosynthesis III, pyrimidine deoxyribonucleotides de novo biosynthesis IV, superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis

Unification Links: EcoCyc:PWY0-166

Martha Arnaud on Tue Jan 21, 2003:
The pathways "de novo biosynthesis of pyrimidine deoxyribonucleotides" and "salvage pathways of pyrimidine deoxyribonucleotides" supersede the pathway formerly called "deoxypyrimidine nucleotide/nucleoside metabolism.

Last-Curated 24-Mar-2008 by Fulcher CA, SRI International


Gon06: Gon S, Faulkner MJ, Beckwith J (2006). "In vivo requirement for glutaredoxins and thioredoxins in the reduction of the ribonucleotide reductases of Escherichia coli." Antioxid Redox Signal 8(5-6);735-42. PMID: 16771665

Johansson07: Johansson E, Thymark M, Bynck JH, Fano M, Larsen S, Willemoes M (2007). "Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme." FEBS J 274(16);4188-98. PMID: 17651436

Neidhardt96: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low Jr KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE "Escherichia coli and Salmonella, Cellular and Molecular Biology, Second Edition." American Society for Microbiology, Washington, D.C., 1996.

Weiss07a: Weiss B (2007). "The deoxycytidine pathway for thymidylate synthesis in Escherichia coli." J Bacteriol 189(21);7922-6. PMID: 17827303

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

Agrawal04: Agrawal N, Hong B, Mihai C, Kohen A (2004). "Vibrationally enhanced hydrogen tunneling in the Escherichia coli thymidylate synthase catalyzed reaction." Biochemistry 43(7);1998-2006. PMID: 14967040

Allard92: Allard P, Kuprin S, Shen B, Ehrenberg A (1992). "Binding of the competitive inhibitor dCDP to ribonucleoside-diphosphate reductase from Escherichia coli studied by 1H NMR. Different properties of the large protein subunit and the holoenzyme." Eur J Biochem 1992;208(3);635-42. PMID: 1396671

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

Andersson99: Andersson ME, Hogbom M, Rinaldo-Matthis A, Andersson KK, Sjoberg BM, Nordlund P (1999). "The Crystal Structure of an Azide Complex of the Diferrous R2 Subunit of Ribonucleotide Reductase Displays a Novel Carboxylate Shift with Important Mechanistic Implications for Diiron-Catalyzed Oxygen Activation." J. Am. Chem. Soc. 121: 2346-2352.

Andrews11: Andrews SC (2011). "Making DNA without iron - induction of a manganese-dependent ribonucleotide reductase in response to iron starvation." Mol Microbiol 80(2);286-9. PMID: 21371140

Artin09: Artin E, Wang J, Lohman GJ, Yokoyama K, Yu G, Griffin RG, Bar G, Stubbe J (2009). "Insight into the mechanism of inactivation of ribonucleotide reductase by gemcitabine 5'-diphosphate in the presence or absence of reductant." Biochemistry 48(49);11622-9. PMID: 19899770

Assarsson01: Assarsson M, Andersson ME, Hogbom M, Persson BO, Sahlin M, Barra AL, Sjoberg BM, Nordlund P, Graslund A (2001). "Restoring proper radical generation by azide binding to the iron site of the E238A mutant R2 protein of ribonucleotide reductase from Escherichia coli." J Biol Chem 276(29);26852-9. PMID: 11328804

Bairoch93: Bairoch A, Boeckmann B (1993). "The SWISS-PROT protein sequence data bank, recent developments." Nucleic Acids Res. 21:3093-3096. PMID: 8332529

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

Beck75: Beck CF, Eisenhardt AR, Neuhard J (1975). "Deoxycytidine triphosphate deaminase of Salmonella typhimurium. Purification and characterization." J Biol Chem 250(2);609-16. PMID: 234434

Belfort83: Belfort M, Maley G, Pedersen-Lane J, Maley F (1983). "Primary structure of the Escherichia coli thyA gene and its thymidylate synthase product." Proc Natl Acad Sci U S A 1983;80(16);4914-8. PMID: 6308660

Bennett04: Bennett SE, Chen CY, Mosbaugh DW (2004). "Escherichia coli nucleoside diphosphate kinase does not act as a uracil-processing DNA repair nuclease." Proc Natl Acad Sci U S A 101(17);6391-6. PMID: 15096615

Berardi99: Berardi MJ, Bushweller JH (1999). "Binding specificity and mechanistic insight into glutaredoxin-catalyzed protein disulfide reduction." J Mol Biol 292(1);151-61. PMID: 10493864

Bernard00: Bernard MA, Ray NB, Olcott MC, Hendricks SP, Mathews CK (2000). "Metabolic functions of microbial nucleoside diphosphate kinases." J Bioenerg Biomembr 32(3);259-67. PMID: 11768309

Boal10: Boal AK, Cotruvo JA, Stubbe J, Rosenzweig AC (2010). "Structural basis for activation of class Ib ribonucleotide reductase." Science 329(5998);1526-30. PMID: 20688982

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

Brignole12: Brignole EJ, Ando N, Zimanyi CM, Drennan CL (2012). "The prototypic class Ia ribonucleotide reductase from Escherichia coli: still surprising after all these years." Biochem Soc Trans 40(3);523-30. PMID: 22616862

Brombacher03: Brombacher E, Dorel C, Zehnder AJ, Landini P (2003). "The curli biosynthesis regulator CsgD co-ordinates the expression of both positive and negative determinants for biofilm formation in Escherichia coli." Microbiology 149(Pt 10);2847-57. PMID: 14523117

Brown69: Brown NC, Canellakis ZN, Lundin B, Reichard P, Thelander L (1969). "Ribonucleoside diphosphate reductase. Purification of the two subunits, proteins B1 and B2." Eur J Biochem 1969;9(4);561-73. PMID: 4896737

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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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