Download 5-Metabolism of Pyrimidine Nucleotides

SYNTHESIS OF PYRIMIDINE
NUCLEOTIDES
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Dr. Shumaila Asim
Lecture # 5
DE-NOVO SYNTHESIS OF PYRIMIDINES (URACIL,
THYMINE & CYTOSINE)

Biosynthesis of pyrimidines is simple than that of
purines.

Unlike purine synthesis, pyrimidines are synthesized as
bases and latter it is added to ribose sugar, i.e., the ring is
completed before being it is linked to ribose-5phosphate.
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Synthesis of Pyrimidine Nucleotides

Precursors

Amino acids (Aspartate, Glutamine)

CO2 (from HCO3-)

Ribose-5-phosphate (HMP shunt & nucleosides)

Enzymes

Coenzymes and Cofactors


NAD+, NADPH, Mg++
ATPs

Energy

PRPP formation
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SOURCES OF ATOMS OF PYRIMIDINE NUCLEUS
N1, C6, C5 and C4 are
derived from aspartate
 N3 is derived from
glutamine
 C2 is derived from
HCO3- (bicarbonate)

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5
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
Step-1: Synthesis of carbamoyl phosphate: With the
hydrolysis of two ATP molecules, bicarbonate and amide
nitrogen of glutamine combine to form carbamoyl
phosphate in the presence of enzyme
carbamoylphosphate synthetase II.

Step-2: Synthesis of carbamoyl aspartate: Carbamoyl
phosphate reacts with aspartate to yield carbamoyl
aspartate catalyzed by the enzyme aspartate
transcarbamoylase (ATCase).

Step-3: Ring closure & dihydroorotate formation: By
the elimination (condensation reaction) of one molecule
of water, the carbamoyl aspartate is converted to a ring
compound – dihydroorotate catalyzed by dihydroorotase
enzyme.
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
Step-4: Oxidation of dihydroorotate: Dihydroorotate
is dehydrogenated to form orotate with the enzyme
dihydroorotate dehydrogenase.

Step-5: Acquisition of the ribose phosphate moiety:
Orotate reacts with PRPP to produce orotidine-5′monophosphate (OMP) with the enzyme orotate
phosphoribosyl transferase. The anomeric form of
pyrimidine nucleotides is fixed in in the βconfiguration.

Step-6: Decarboxylation to form UMP:OMP
undergoes decarboxylation with assistance of enzyme
OMP decarboxylase (ODCase) to form uridine
monophosphate (UMP).
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Synthesis of Pyrimidine Nucleotides
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SYNTHESIS OF UTP FROM UMP

UMP is converted to UTP in two step kinase reaction
with 2 molecules of ATP
UMP + ATP ⇌ UDP + ADP
UDP + ATP ⇌ UTP + ADP
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SYNTHESIS OF CTP

CTP is synthesized by the amination of UTP by the
enzyme CTP synthase.

In animals amino group is donated by glutamine whereas
in bacteria, the amino group is donated directly by
ammonia
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SYNTHESIS OF THYMINE (5-METHYLURACIL) AS
DEOXYTTP:

Thymine, which is present in DNA and not in RNA, is a
methylated uracil residue.

Thymine in the cell is synthesized as dTTP from dUMP
by methylation in four steps.
Step-1: dUTP is hydrolyzed to dUMP and PPi by the
enzyme dUTP diphosphohydrolase (dUTPase)
 Step-2: dUMP is then methylated to form dTMP
 Step-3 & 4: dTMP is then phosphorylated with ATP in
two rounds to form dTTP

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FORMATION OF DTMP
UDP
dUDP
dCMP
dCDP
dUMP
N5,N10-methylenetetrahydrofolic Acid
dTMP synthetase
dTMP
ATP
ATP
dTDP
ADP
dTTP
ADP
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REGULATORY CONTROL OF PYRIMIDINE
SYNTHESIS

Regulation at carbamoyl phosphate synthetase II


UDP and UTP inhibit enzyme; ATP and PRPP activate it
UMP and CMP competitively inhibit OMP Decarboxylase
*Purine synthesis inhibited by ADP and GDP at ribose phosphate
pyrophosphokinase step, controlling level of PRPP  also
regulates pyrimidines
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SYNTHESIS OF PYRIMIDINE
NUCLEOTIDES BY SALVAGE PATHWAY
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SALVAGE OF URACIL

The salvage of pyrimidine bases has less clinical
significance than that of the purines, owing to the
solubility of the by-products of pyrimidine catabolism.

Uracil can be salvaged to form UMP through the action
of uridine phosphorylase and uridine kinase, as
indicated:
uracil + ribose-1-phosphate <——> uridine + Pi
uridine + ATP ——> UMP + ADP
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SALVAGE OF DEOXYURIDINE

Deoxyuridine is also a substrate for uridine phosphorylase.

Formation of dTMP, by salvage of dTMP requires thymine
phosphorylase and the previously encountered thymidine
kinase:
thymine + deoxyribose-1-phosphate <——> thymidine + Pi
thymidine + ATP ——> dTMP + ADP
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SALVAGE OF DEOXYCYTIDINE

The salvage of deoxycytidine is catalyzed by
deoxycytidine kinase:
deoxycytidine + ATP <——> dCMP + ADP

Deoxyadenosine and deoxyguanosine are also substrates
for deoxycytidine kinase, although the Km for these
substrates is much higher than for deoxycytidine.
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SALVAGE OF THYMIDINE

The salvage pathway to dTTP synthesis involves the
enzyme thymidine kinase which can use either thymidine
or deoxyuridine as substrate:
thymidine + ATP <——> TMP + ADP
deoxyuridine + ATP <——> dUMP + ADP
 The activity of thymidine kinase (one of the various
deoxyribonucleotide kinases) is unique in that it
fluctuates with the cell cycle, rising to peak activity
during the phase of DNA synthesis; it is inhibited by
dTTP.
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Synthesis of deoxyribonucleotides
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SUMMARY OF PYRIMIDINE BIOSYNTHESIS
dTTP
dTMP
dTDP
dUMP
dUDP
UMP
UDP
UTP
CDP
CTP
dCMP
dCDP
dCTP
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