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Lecture 30
Pyrimidine Metabolism/Disease
Raymond B. Birge, PhD
Pyrimidine metabolism (Overview)
1. Nomenclature/nucleotide structure
2. Synthesis pathways
3. Synthesis of deoxy-ribonucleotides
4. Salvage & degradation pathways
5. Metabolic disease of pyrimidine
metabolism (orotic aciduria)
Suggested reading: Lippencott’s Chapter 22
Structure of Pyrimidines
O
NH2
O
O
Uracil
Cytosine
O
O
CH3
O
O
Thymine
C= 2 oxy, 4 amino
T= 2,4 dioxy 5-methyl
Orotic
OroticAcid
acid
U= 2,4 dioxy
O= 2,4 dioxy 6 carboxy
Nomenclature of Pyrimidines
Cytosine
Base
Cytidine
Nucleoside*
Base + ribose
Cytidine Monophosphate
Nucleotide
Base + ribose + P04 ester
* when the base is purine, then the nucleoside ends in OSINE (AdenOSINE, GuanOSINE, InOSINE)
when the base is pyrimidine, then the nucleoside ends in IDINE (UrIDINE, CytIDINE, ThymIDINE)
PO4 is an acid: cytidylic acid/cytidylate; note thymidine only deoxyribose
1st Step is Regulated
(occurs in cytosol)
Inhibited by UTP; Activated by ATP & PRPP
5-phosphoribosylpyrophosphate
From Figure 22.21 in Lippincott
Multifunctional enzyme synthesis: CAD
Carbamoyl phosphate
synthase II
Aspartate
transcarbamylase
Dihyroorotase
C arbamoyl phosphate synthetase II:
A spartate transcarbamylase
D ihydroorotase
1 polypeptide, 3 domains, 3 activities
by UTP; by ATP & PRPP;
Contrast to purines:
Pyrimidines synthesized as free ring
Making a pyrimidine
Carbamoyl phosphate
synthase II
Desaturating the ring
gives the pyrimidine,
OROTATE.
From Figure 22.21 in Lippincott
Aspartate
transcarbamylase
Dihyroorotase
Dihyroorotate
dehydrogenase
Precursors
Which of the following contributes nitrogen atoms
DIRECTLY to both purine and pyrimidine rings?
1.
2.
3.
4.
5.
Aspartate
Carbamoyl phosphate
Bicarbonate
Glutamate
Tetrahydrofolate
Making UMP: another multifunctional enzyme
UMP synthase: Orotate phosphoribosyl transferase
OMP decarboxylase
1 polypeptide, 2 domains, 2 activities
OMP decarboxylase
Orotate phosphoribosyl
transferase
Low UMP activity
Orotic aciduria (abnormal growth; megaloblastic anemia;
treat with uridine-rich diet)
From Figure 22.21 in Lippincott
Synthesis of CTP
(Uracil)
(Cytosine)
ATP, Gln
ADP, Pi, Glu
CTP Synthetase
Ribose-Tri-P04
UTP
Ribose-Tri-P04
CTP
Clinical Significance-pyrimidine metabolism
ID: A 2 year old female referred to a pediatric clinic
Chief Complaint: My baby doesn’t play, sleeps all the time and is weak.
History Present Illness: Baby was treated for anemia by family doctor but did
not respond to vitamin B12, folic acid, iron or vitamin C. She is the third-born
child of a healthy white couple; her mother had an uneventful pregnancy and a
eutopic delivery. Both brothers are healthy.
Physical Exam: Low weight and height for age, marked pallor; flacidity &
lethargy; sleepiness
Pathology: CBC: megaloblastic anemia; UA: increased orotic acid excretion
with formation of orotic acid crystals.
Pyrimidine Biosynthesis-IV
AMP
Purine biosynthesis
PRPP
PRPP
_
+
CPS II
_
ATC
DHO
DHOD
OA
OPRT
ODC
UMP
_
UTP
Eukaryote
Prokaryote
Committed Steps
ATCase is feedback inhibited by the end-products of
pyrimidine biosynthesis
C02 + Glutamine + ATP
ATP
Carbamoyl Phosphate
Carbamoyl Asparate
Rate
Inhibited by CTP
CTP
UMP
UTP
CTP
[Aspartate]
Ribonucleotides to Deoxyribonucleotides
1. Ribonucleotide Reductase
2. Thymidylate Synthase:
(prevent incorporation into RNA)
Ribonucleotides to Deoxyribonucleotides
Ribonucleotide reductase
Thioredoxin reductase
Inhibited by dATP; Activated by ATP
ADP
GDP
UDP
CDP
Ribonucleotide Reductase
dADP
dGDP
dUDP
dCDP
ATP
ADP
dUTP
H20
ATP
ATP
ATP
PPi
ATP
ADP
ADP
dUMP
ADP
ADP
DHF
dTDP
ATP
dATP
dGTP
ADP
dCTP
5,10 THF
dTTP
Thymidine biosynthesis
dUMP Thymidylate synthase TDP
reduced
N5,N10-methylenetetrahydrofolate
oxidized
Dihydrofolate
NADPH
Dihydrofolate
reductase
Serine
transhydroxymethylase
Tetrahydrofolate
NADP+
Salvage & degradation of pyrimidines
Salvage: uridine-cytidine kinase: nucleoside to nucleotide
(deoxycytidine kinase)
(thymidine kinase)
Degradation:
pyrimidine rings cleaved and degraded to soluble structures
(contrast to purines)
5FU is a simple derivative of Uracil
F
Uracil
5-Fluoro-Uracil (5FU)
Targets of drug therapy
Fluorodeoxyuradylate (5-FU)
dUMP Thymidylate synthase dTMP
reduced
N5,N10-methylenetetrahydrofolate
oxidized
Dihydrofolate
NADPH
Dihydrofolate
reductase
Tetrahydrofolate
NADP+
Methotrexate
Aminopterin
Conversion of Serine to Glycine
H
Dihydrofolate
reductase
Folate
H2 N
N
N
CO 2 -
N
N
OH
CH 2 NHR
H C NH3 +
H
Tetrahydrofolate
(FH4)
Serine
CH2 OH
Serine hydroxymethyl
transferase (PLP-dep.)
H
N
Key intermediate
in biosynthesis of
purines and
formation of
thymine
CO 2 N
Glycine
CH 2
H C NH3
N
H2 C
N5, N10-Methylene FH4
+
H
Important in
biosynthesis of heme,
porphyrins, and purines
Using nucleotides for selecting hybrid
cells
AZT inhibits HIV reverse transcriptase
(RNA-dependent DNA polymerase)
3’ AZido-2’3’ dideoxyThymine (AZT)
This class of compounds (chemotherapeutics, viral inhibitors, etc.)
are called nucleoside analogs.
Bottom Line
Recognize names and structures of pyrimidines; NMPs/dNTPs
Orotate, Uracil, Cytosine, Thymine; CTP/dCTP, TTP
Name the sources of atoms in the pyrimidine ring:
carbamoyl phosphate (C,N: from Gln, CO2 ); Aspartate (C,N)
Recognize the regulated reaction:
Carbamoyl phosphate synthase II: UTP; ATP, PRPP
Contrast the synthesis of purines & pyrimidines
Explain the cause of Orotic aciduria; Contrast with hyperuricemia
Explain mechanisms of the following treatments:
sulfonamides, methotrexate, 5-Fluorouracil