Nucleotide Synthesis De Novo

Nucleosides are composed of a heterocyclic ring (defined as the base) that is attached to a ribose. Addition to a nucleoside of a phosphate, at carbon 5 of the ribose, produces a nucleotide. Nucleotides function as ubiquitous building blocks for the synthesis of all nucleic acids, and also function in enzymatic reactions as cofactors and as a source of energy. These central metabolic roles require their continued biosynthesis from readily available precursors, and this process is defined as de novo nucleotide synthesis. The synthesis of purines starts with ribose-phosphate, to which are attached in a stepwise fashion the individual atoms of the heterocyclic base. Pyrimidine synthesis starts with the stepwise formation of the base, to which is then added the ribose-phosphate. Bases and nucleosides may also be recycled in salvage pathways.

Key concepts:

  • Nucleotides are so essential to metabolism that genetic defects generally are lethal, and for humans only a few gene defects are observed, at a low frequency.
  • Many of the enzymatic reactions in the de novo biosynthesis of nucleotides are combined as two or more reactions catalysed by a single multidomain protein. This has made nucleotide biosynthesis more efficient.
  • For a few of the biosynthetic steps alternate enzymatic strategies have emerged between bacteria and vertebrates, and these present possible targets for drugs as selective antibiotics.

Keywords: nucleotide; purine; pyrimidine; multifunctional protein

Figure 1. Biosynthesis of the purine ring. (a) Precursors of the ring and numbering of the ring atoms. (b) Numbering of atoms in an imidazole ring.
Figure 2. Biosynthesis of inosine-5¢-monophosphate (IMP). Reactions with the same Roman numeral are performed by a single enzyme.
Figure 3. Biosynthesis of AMP and GMP from IMP.
Figure 4. Biosynthesis of the pyrimidine ring. Precursors of the ring and numbering of the ring atoms.
Figure 5. Biosynthesis of pyrimidines. (a) De novo synthesis of uridine-5¢-monophosphate (UMP). (b) Synthesis of cytidine triphosphate (CTP).
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 References
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 Further Reading
    Cansev M (2006) Uridine and cytidine in the brain: their transport and utilization. Brain Research Reviews 52: 389–397.
    Carrey EA (1993) Phosphorylation, allosteric effectors and inter-domain contacts in CAD: their role in regulation of early steps of pyrimidine biosynthesis. Biochemical Society Transactions 21: 191–195.
    Carter NS, Yates P, Arendt CS, Boitz JM and Ullman B (2008) Purine and pyrimidine metabolism in Leishmania. Advances in Experimental Medicine and Biology 625: 141–154.
    Christopherson RI and Lyons SD (1990) Potent inhibitors of de novo pyrimidine and purine biosynthesis as chemotherapeutic agents. Medicinal Research Reviews 10: 505–548.
    Dudzinska W, Hlynczak AJ, Skotnicka E and Suska M (2005) The purine metabolism of human erythrocytes. Biochemistry (Moscow) 71: 467–475.
    Eriksson S and Wang L (2008) Molecular mechanisms of mitochondrial DNA depletion diseases caused by deficiencies in enzymes in purine and pyrimidine metabolism. Nucleosides, Nucleotides and Nucleic Acids 27: 800–808.
    Turnbough CL Jr and Switzer RL (2008) Regulation of pyrimidine biosynthetic gene expression in bacteria: repression without repressors. Microbiology and Molecular Biology Reviews 72: 266–300.
    Zalkin H and Dixon JE (1992) De novo purine nucleotide synthesis. Progress in Nucleic Acid Research and Molecular Biology 42: 259–287.
    Zrenner R, Stitt M, Sonnewald U and Boldt R (2006) Pyrimidine and purine biosynthesis and degradation in plants. Annual Reviews of Plant Biology 57: 805–836.
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Traut, Thomas(Dec 2009) Nucleotide Synthesis De Novo. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001396.pub2]