denovo synthesis

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De novo synthesis of nucleotides
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De novo synthesis

• De novo is a Latin phrase, meaning "from the
  new,
• De novo pathways do not use free bases adenine
  (A), guanine (G), cytosine (C), thymine (T), or
  uracil (U).
• The purine ring is built up one or a few at a
  time and attached to ribose throughout the
  process.
• De novo synthesis enzymes are present as large
  multienzyme complexes in purines.
• Pyrimidine ring is synthesized as orotate and
  attached to ribose phosphate and later converted
  to common pyrimidine nucleotides.
• De novo originates from aspartate, glycine,
  folate, glutamine and carbon dioxide.

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De Novo Synthesis of Pyrimidine Nucleotides

• Since pyrimidine molecules are simpler than
  purines, so is their synthesis simpler but is
  still from readily available components.
• Glutamine's amide nitrogen and carbon dioxide
  provide atoms 2 and 3 or the pyrimidine ring.
  They do so, however, after first being converted
  to carbamoyl phosphate.
• The other four atoms of the ring are supplied by
  aspartate..

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Synthesis of Purine Nucleotides

• We use for purine nucleotides
• the entire glycine molecule (atoms 4, 5,7),
• the amino nitrogen of aspartate (atom 1),
• amide nitrogen of glutamine (atoms 3, 9),
• components of the folate-one-carbon pool(atoms 2,
  8),
• carbon dioxide,
• ribose 5-P from glucose and
• a great deal of energy in the form of ATP. In de
  novo synthesis, IMP is the first nucleotide
  formed. It is then converted to either AMP or
  GMP.

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PRPP

• Ribose 5-phosphate reacts with ATP to form
  5-Phosphoribosyl-1-pyrophosphate (PRPP).
• This reaction occurs in many tissues because PRPP
  has a number of roles - purine and pyrimidine
  nucleotide synthesis, salvage pathways, NAD and
  NADP formation.

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Commitment Step

• De novo purine nucleotide synthesis occurs
  actively in the cytosol of the liver where all of
  the necessary enzymes are present as a
  macro-molecular aggregate.
• The first step is a replacement of the
  pyrophosphate of PRPP by the amide group of
  glutamine.
• The product of this reaction is
  5-Phosphoribosylamine.
• The amine group that has been placed on carbon 1
  of the sugar becomes nitrogen 9 of the ultimate
  purine ring.
• This is the commitment and rate-limiting step of
  the pathway.

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Formation of IMP

• Once the commitment step has produced the
  5-phosphoribosyl amine, the rest of the molecule
  is formed by a series of additions to make first
  the 5- and then the 6-membered ring.
• The whole glycine molecule, at the expense of ATP
  adds to the amino group to provide what will
  eventually be atoms 4, 5, and 7 of the purine
  ring
• The amino group of 5-phosphoribosyl amine becomes
  nitrogen N of the purine ring.
• One more atom is needed to complete the
  five-membered ring portion and that is supplied
  as 5, 10-Methenyl tetrahydrofolate.

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Cont..

• Before ring closure occurs, however, the amide of
  glutamine adds to carbon 4 to start the
  six-membered ring portion (becomes nitrogen 3).
  This addition requires ATP.
• The next step is the addition of carbon dioxide
  (as a carboxyl group) to form carbon 6 of the
  ring.
• The final atom of the purine ring, carbon 2, is
  supplied by 10-Formyl tetrahydrofolate. Ring
  closure produces the purine nucleotide, IMP.

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Formation of AMP and GMP

• IMP can then become either AMP or GMP.
• GMP formation requires that IMP be first oxidized
  to XMP using NAD. The oxygen at position 2 is
  substituted by the amide N of glutamine at the
  expense of ATP.
• Similarly, GTP provides the energy to convert IMP
  to AMP. The amino group is provided by aspartate
  in a mechanism similar to that used in forming
  nitrogen 1 of the ring.

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De Novo Synthesis of Pyrimidine Nucleotides

• Glutamine's amide nitrogen and carbon dioxide
  provide atoms 2 and 3 or the pyrimidine ring.
• They do so, however, after first being converted
  to carbamoyl phosphate.
• The other four atoms of the ring are supplied by
  aspartate.
• As is true with purine nucleotides, the sugar
  phosphate portion of the molecule is supplied by
  PRPP.

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Carbamoyl Phosphate

• Pyrimidine synthesis begins with carbamoyl
  phosphate synthesized in the cytosol of those
  tissues capable of making pyrimidines
• This uses a different enzyme than the one
  involved in urea synthesis. Carbamoyl phosphate
  synthetase II (CPS II) prefers glutamine to free
  ammonia and has no requirement for
  N-Acetylglutamate.

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Formation of Orotic Acid

• Carbamoyl phosphate condenses with aspartate in
  the presence of aspartate transcarbamylase to
  yield N-carbamylaspartate which is then converted
  to dihydroorotate.
• Oxidation of the ring by a complex, poorly
  understood enzyme produces the free pyrimidine,
  orotic acid.
• This enzyme is located on the outer face of the
  inner mitochondrial membrane, in contrast to the
  other enzymes which are cytosolic.

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Formation of the Nucleotides

• Orotic acid is converted to its nucleotide with
  PRPP.
• OMP is then converted sequentially - not in a
  branched pathway - to the other pyrimidine
  nucleotides.
• Decarboxylation of OMP gives UMP. O-PRT and OMP
  decarboxylase.
• After conversion of UMP to the triphosphate, the
  amide of glutamine is added, at the expense of
  ATP, to yield CTP.

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K.Shanmugha Rajan