Chapter 10
Nucleotide Metabolism
N
N N
N N N
Teaching target
1. Master the major steps in purine nucleotide synthesis, metabolism, and
end products of catabolism and related diseases.
2. Master the metabolites of purine nucleotides and pyrimidine nucleotides.
3. Master the regulation of the de novo synthesis of purine and
pyrimidine nucleotides
4. Understand the catabolism of pyrimidine nucleotides.
Section 1 Introduction
Degradation of nucleic acid
Nucleoprotein
Nucleic acid Protein
Nuclease
Nucleotide
Nucleotidase
Phosphate Nucleoside
Nucleosidase
Base Ribose
OVERVIE
• W
Ribonucleoside and deoxyribonucleoside phosphates (nucleotides) are
essential for all cells. Without them, neither RNA nor DNA can be produced
and, therefore, proteins cannot be synthesized or cells proliferate.
• Nucleotides also serve as carriers of activated intermediates in the synthesis of
some carbohydrates, lipids, and conjugated proteins, for example, UDP-
glucose and CDP-choline, and are structural components of several essential
coenzymes, such as coenzyme A, FAD, NAD+, and NADP+. Nucleotides,
such as cyclic adenosine monophosphate (cAMP) and cyclic guanosine
monophosphate (cGMP), serve as second messengers in signal transduction
pathways.
• In addition, nucleotides play an important role as “energy currency” in the cell.
• Finally, nucleotides are important regulatory compounds for many of the
pathways of intermediary metabolism, inhibiting or activating key enzymes.
• The purine and pyrimidine bases found in nucleotides can be synthesized de
novo, or can be obtained through salvage pathways that allow the reuse of
the preformed bases resulting from normal cell turnover.
NUCLEOTIDE STRUCTURE
• Nucleotides are composed of a nitrogenous
base, a pentose monosaccharide, and one, two,
or three phosphate groups.
• The nitrogencontaining bases belong to two
families of compounds: the purines and the
pyrimidines.
• A. Purine and pyrimidine structures
Both DNA and RNA contain the same
purine bases: adenine (A) and guanine (G).
Both DNA and RNA contain the pyrimidine
cytosine (C), but they differ in their second
pyrimidine base: DNA contains thymine (T),
whereas RNA contains uracil (U). T and U
differ in that only T has a methyl group.
• Unusual (modified) bases are
occasionally found in some
species of DNA and RNA, for
example, in some viral DNA, and
in transfer RNA. Base
modifications include
methylation, glycosylation,
acetylation, or reduction.
• B. Nucleosides
The addition of a pentose sugar to a
base produces a nucleoside. If the
sugar is ribose, a ribonucleoside is
produced; if the sugar is 2-
deoxyribose, a deoxyribonucleoside
is produced. The ribonucleosides
of A, G, C, and U are named aden
osine, guanosine, cytidine, and
uridine, respectively. The
deoxyribonucleo sides of A, G, C,
and T have the added prefix,
“deoxy-,” for example,
deoxyadenosine.
• C. Nucleotides
• The addition of one or more
phosphate groups to a nucleoside
produces a nucleotide. The first
phosphate group is attached by an
ester linkage to the
5'-OH of the pentose. The second and
third phosphates are each connected
to the nucleotide by a “high-energy”
bond.
• [Note: The phosphate groups are
responsible for the negative charges
associated with nucleotides, and cause
DNA and RNA to be referred to as
“nucleic acids.”]
Significances of nucleotides
1.Precursors for DNA and RNA
synthesis
2.Essential carriers of chemical
energy, especially ATP
3.Components of the cofactors NAD+,
FAD, and coenzyme A
Significances of nucleotides
(continue)
4.Formation of activated intermediates
such as UDP-glucose and CDP-
diacylglycerol.
5.cAMP and cGMP, are also cellular
second messengers.
There are two pathways leading to
nucleotides
De novo synthesis: The synthesis of
nucleotides begins with their
metabolic precursors: amino acids,
ribose-5-phosphate, CO2, and one-
carbon units.
Salvage pathways: The synthesis of
nucleotide by recycle the free bases
or nucleosides released from nucleic
acid breakdown.
Section 2 Synthesis of
Purine Nucleotides
§ 2.1 De novo synthesis
• Site: in cytosol of liver, small
intestine and thymus
• Characteristics:
a.Purines are synthesized using 5-
phosphoribose as the starting
material step by step.
b. PRPP is active donor of R-5-P.
c.AMP and GMP are synthesized
further at the base of IMP.
1. Element sources of purine bases
CO2 Gly
Asp C
N
6 7
N1 C
5 8C One
4 9 carbon
3 C unit
One 2 N N
C
carbon
unit
Gln
SYNTHESIS OF PURINE NUCLEOTIDES
• The atoms of the purine ring
are contributed by a number of
compounds, including amino
acids (aspartic acid, glycine,
and glutamine), CO2, and N10–
formyltetrahydrofolate.
• The purine ring is constructed
primarily in the liver by a
series of reactions that add the
donated carbons and nitrogens
to a preformed ribose 5-
phosphate.
• A. Synthesis of 5-phosphoribosyl-1-pyrophosphate (PRPP)
• B. Synthesis of 5'-phosphoribosylamine
• C. Synthesis of inosine monophosphate (IMP), the “parent”
purine nucleotide
• D. Synthetic inhibitors of purine synthesis
• E. Conversion of IMP to AMP and GMP
Synthesis of IMP
ATP AMP Gln Glu
R-5-P PRPP 5-phospho-
PRPP amidotransferase ribosylamine
kinase (PRA)
O 9 steps
N
HN
N N
R- 5'-P
inosine 5-monophosphate
( IMP )
P O CH2 P O CH2
ATP AMP O H
O H 2+
Mg
H H
H H PRPP H O P
H OH O
OH kinase OH OH
P
5-phosphoribose
OH 1-
5-phosphoribose pyrophosphate
(R-5-P) （ PRPP ）
PPi Gln
amidotransferase
P O CH2
Glu
O
NH2
HOH H
H OH H
5-phosphoribosyl-
amine (PRA)
PRPP synthetase
NH2 NH2
Gly H2C H2C
O C H
P O CH2 O N10-CHO FH4
OH GAR P O CH2 FH4 N
HN H2C CH
O NH2 synthetase O
H H C C
H H O O
H HH transformylase NH
ATP ADP+Pi H
OH OH R-5'-P
OH OH
Formylglycinamide
PRA ribonucleotide
Glycinamide
ribonucleotide （ FGAR ）
O （ GAR Gln
） H
H2 O FGAM
N carboxylase N
HO C HC ATP N synthetas
C CH H2C CH Glu
CH e
C C AIR ATP
N N synthetase C O
H2N CO2 H2 N HN NH
R-5'-P R-5'-P
R-5'-P
Carboxyamino-
imidazole 5-aminoimidazole Formylglycinamidine
ribonucleotide ribonucleotide
（ AIR ） ribonucleotide
（ CAIR ） （ FGAM ）
O O O
COOH
Asp Fumarate
N H2O N N
HO C ATP HC N C H2N C
C CH C CH C CH
C CH 2 H C lyase C
N synthetase N N
H2N H2N H2N
R-5'-P COOH R-5'-P R-5'-P
Carboxyamino- 5-aminoimidazole- 5-aminoimidazole-
imidazole 4-(N-succinylcarboxamide) 4-carboxamide
ribonucleotide ribonucleotide (SAICAR) ribonucleotide
（ CAIR ） （ AICAR ）
O transformylase
O
C H2 O C N N10-CHO FH4
N H2N C
HN C
CH CH
HC C cyclohydrolase O H C FH4
N C N N
N
R-5'-P H R-5'-P
5-formaminoimidazole-
IMP 4-carboxamide
（ FAICAR ）
N10-CHOFH4
N10-CHOFH4
Synthesis of AMP and
GMP HOOC CH CH COOH
NH Fumarate
2
NH2
N N
HN
H2O HN
AMPS lyase
N N N
N
Asp GTP R-5'-P
R-5'-P
O AMPS Adenylsuccinate
synthetase AMP
N （ AMPS ）
HN
N NAD+ + H2O
N
H R-5'-P NADH + H+ O
O Gln Glu
I N
IMP N ATP HN
M HN
dehydrogenase
P GMP N
O N N synthetas H2 N
R-5'-P e N R-5'-P
H
GMP
X
M
4. Formation of NDP and NTP
Adenylate kinase
AMP + ATP 2 ADP
nucleoside
diphosphate kinase
NDP + ATP
NTP + ADP
Conversion of nucleoside monophosphates to
nucleoside diphosphates and triphosphates
• Nucleoside diphosphates are synthesized from the corresponding
nucleoside monophosphates by base-specific nucleoside monophosphate
kinases.
5. Regulation of de novo synthesis
The significance of regulation:
(1)Fulfill the need of the body,
without wasting.
(2) [GTP]=[ATP]
Regulation of E
Activity
• Zymogen activation
• Allosteric regulation
• Covalent modification
Regulation of E Quantity
• Constitutive enzymes (house-keeping):
enzymes whose concentration
essentially remains constant over time
• Adaptive enzymes: enzymes whose
quantity fluctuate as body needs and well-
regulated.
• Regulation of enzyme quantity is
accomplished through the control of the
genes expression.
Regulation of de novo synthesis
of purine nucleotides
AMPS AMP ADP ATP
－
R-5-P ＋－－ ＋－
PRPP PRA IMP ＋
－
ATP — － ＋
－
XMP GMP GDP GTP
§ 2.2 Salvage pathway
The significance of salvage pathway :
a. Save the fuel.
b.Some tissues and organs such as
brain and bone marrow are only
capable of synthesizing nucleotides
by a salvage pathway.
The course of salvage pathway :
Hypoxanthine Guanine Adenine
PRPP PRPP
HGPRT APR
- T -
PPi PPi
IMP GMP AMP
adenylate kinase
adenosin AMP
e
ATP ADP
• HGPRT: Hypoxanthine-guanine
phosphoribosyl transferase
• APRT: Adenine
phosphoribosyl transferase
• Absence of activity of HGPRT
leads to Lesch-Nyhan
syndrome.
G. Salvage pathway for purines
• Purines that result from the normal turnover of
cellular nucleic acids, or the small amount that is
obtained from the diet and not degraded, can be
converted to nucleoside triphosphates and used
by the body. This is referred to as the “salvage
pathway” for purines.
• 1. Conversion of purine bases to nucleotides: Two
enzymes are involved: adenine
phosphoribosyltransferase (APRT) and
hypoxanthine-guanine phosphoribosyltransferase
(HGPRT). Both enzymes use PRPP as the source of
the ribose 5-phosphate group.
• 2. Lesch-Nyhan syndrome: This syndrome is a
rare, X-linked, recessive disorder associated with a
virtually complete deficiency of HGPRT. This
deficiency results in an inability to salvage
hypoxanthine or guanine, from which excessive
amounts of uric acid, the end product of purine
degradation, are produced. In addition, the lack of
this salvage pathway causes increased PRPP levels
and decreased IMP and GMP levels.
§ 2.3 Exchange between
purines
AMP GMP
H2O NADPH + H+
ad
de eno + ine
am si NH3 NADP os se
ina ne an ta
s
e NH3 gu duc
re
AMPS IMP XMP
§ 2. 4 Formation of
•
deoxyribonucleotide
Formation of
deoxyribonucleotide involves the
reduction of the sugar moiety of
ribonucleoside diphosphates
(ADP, GDP, CDP or UDP).
• Deoxyribonucleotide synthesis at the
nucleoside diphosphate level.
SYNTHESIS OF
DEOXYRIBONUCLEOTIDES
• The nucleotides described thus far all contain ribose
(ribonucleotides). The nucleotides required for DNA
synthesis, however, are 2'-deoxyribonucleotides, which are
produced from ribonucleoside diphosphates by the
enzyme ribonucleotide reductase during the S-phase of
the cell cycle.
• A. Ribonucleotide reductase
Ribonucleotide reductase
(ribonucleoside diphosphate reductase)
is specific for the reduction of purine
nucleoside diphosphates (ADP and
GDP), and pyrimidine nucleoside
diphosphates, cytidine diphosphate
(CDP) and uridine diphosphate (UDP) to
their deoxyforms (dADP, dGDP, dCDP,
and dUDP).
P P O CH2 O Base P P O CH2 O
Base
ribonucleotide
reductase
Mg2+
OH OH H2O OH H
thioredoxin SH S
NDP thioredoxin dNDP
（ N=A, G, C, AT P
S
U） FAD
SH kinase
+
NADP + NADPH + H
thioredoxin ADP
reductase
dNTP
Regulation of ribonucleotide reductase
CDP dCDP dCTP
ATP
UDP dUDP dTTP
GDP dGDP dGTP
ADP dADP dATP
Summary of purine biosynthesis
dAD dATP
P
AM AD ATP
IMP P P
GMP GDP GTP
dGDP dGTP
§ 2. 5 Antimetabolites of
purine nucleotides
• Antimetabolites of purine
nucleotides are structural analogs of
purine, amino acids and folic acid.
They can interfere, inhibit or block
synthesis pathway of purine
nucleotides and further block
synthesis of RNA, DNA, and proteins.
1. Purine analogs
• 6-Mercaptopurine (6-MP) is a analog of
hypoxanthine.
OH SH
N N
N N
N N N N
H H
hypoxanthine 6-
MP
• 6-MP nucleotide is a analog of IMP
de novo synthesis
-
amidotransferase
-
IMP
6-MP 6-MP nucleotide
-
- AMP and GMP
HGPR
T
salvage
- pathway
2. Amino acid analogs
• Azaserine (AS) is a analog of Gln.
O NH2
H2N C CH2 CH2 CH COOH Gln
O NH2
N N CH2 C O CH2 CH COOH AS
3. Folic acid analogs
• Aminopterin (AP) and Methotrexate
(MTX)
NH2 R O COOH
N
N CH2 C NH C CH2 2 CH
COOH H
H2 N N N N
R＝H： R ＝ CH3 ：
AP TXT
OH H O COOH
N
N CH2 C NH C CH2 2 CH
COOH H
H2 N N N
N folic acid
NADPH + H+ NADPH + H+
NADP+ NADP+
folate FH2 FH4
FH2 reductase FH2 reductase
- -
AP or MTX
Section 3 Catabolism
of Purine Nucleotides
nucleotide pentose
phosphate
R-5-P pathway
H2 O
nucleotidase PRPP salvage
pathwa
y
Pi R-1-P
Pi
nucleoside purine uric acid
nucleoside oxidatio
phosphorylas n
e
NH2 O
C N
C N
N C HN C
CH CH
HC C HC C O
N N N
N
C N
Ribose-P Ribose-P
HN C
IMP CH
AMP
HC C
N N
Xanthine Oxidase
H
Hypoxanthine
O O
C N C N
HN C HN C
C O CH
C C C C
O N N O N N
H H H H GMP
Uric Acid Xanthine
• Uric acid is the excreted end product
of purine catabolism in primates,
birds, and some other animals.
• The rate of uric acid excretion by the
normal adult human is about 0.6
g/24 h, arising in part from ingested
purines and in part from the turnover
of the purine nucleotides of nucleic
acids.
• The disease gout, is a disease of the
joints, usually in males, caused by an
elevated concentration of uric acid in
the blood and tissues. The joints
become inflamed, painful, and arthritic,
owing to the abnormal deposition of
crystals of sodium urate. The kidneys
are also affected, because excess uric
acid is deposited in the kidney tubules.
DEGRADATION OF PURINE
NUCLEOTIDES
• Degradation of dietary nucleic acids occurs in the small
intestine, where a family of pancreatic enzymes
hydrolyzes the nucleic acids to nucleotides.
• Inside the intestinal mucosal cells, purine nucleotides are
sequentially degraded by specific enzymes to nucleosides
and free bases, with uric acid as the end product of
this pathway.
• A. Degradation of dietary nucleic
acids in the small intestine
Dietary purine bases are not used
to any appreciable extent for the
synthesis of tissue nucleic acids.
Instead, they are generally
converted to uric acid in intestinal
mucosal cells. Most of the uric acid
enters the blood, and is eventually
excreted in
the urine.
• B. Formation of uric acid
C. Diseases associated with purine degradation
Gout is a disorder characterized by high levels of uric acid—
the end product of purine catabolism—in blood
(hyperuricemia), as a result of either the overproduction or
underexcretion of uric acid. The hyperuricemia can lead to the
deposition of monosodium urate crystals in the joints, and an
inflammatory response to the crystals, causing first acute and
then progressing to chronic gouty arthritis.
Allopurinol – a suicide inhibitor used to treat Gout
O O
C C H
N
HN C HN C C
CH N
HC C HC C
N N N
N
H H
Hypoxanthine Allopurinol
Adenosine deaminase (ADA) deficiency
• ADA is expressed in a variety of tissues, but, in humans, lymphocytes have
the highest activity of this cytoplasmic enzyme. A deficiency of ADA
results in an accumulation of adenosine, which is converted to its
ribonucleotide or deoxyribonucleotide forms by cellular kinases. As dATP
levels rise, ribonucleotide reductase is inhibited, thus preventing the
production of all deoxyribose-containing nucleotides. Consequently, cells
cannot make DNA and divide.
• It is estimated that in the United States, ADA deficiency accounts for
approximately 14% of all cases of severe combined immunodeficiency
disease (SCID).
• Treatment requires either bone marrow transplantation (BMT) or enzyme
replacement therapy (ERT). Without appropriate treatment, children with
this disorder usually die by the age of two.
Section 4 Synthesis of
Pyrimidine Nucleotides
§ 4.1 De novo synthesis
Characteristics:
• The enzymes mostly lie in cytosol, but
some enzymes exist in mitochondria.
• The pyrimidine ring is first synthesized,
then combines with PRPP.
• UMP is first synthesized, then UMP is
used for synthesizing other pyrimidine
nucleotides.
1. Element source of
pyrimidine base
C
Gln 4
N3 5C
Asp
CO2 C2 1 6C
N
2. Synthesis of UMP
2ATP
2ADP+Pi H2 N
Gln + HCO -3
C OPO3H 2
+ Glu
O
Carbamoyl phosphate Carbamoy
synthetase Ⅱ l
(CPS-II) phosphate
Difference ofcarbamoyl phosphate
synthetaseⅠand Ⅱ
CPSⅠ CPSⅡ
location Cytosol (all the
Mit （ liver)
cell)
source of NH3 Gln
nitrogen
allosteric agent AGA none
function urea pyrimidine
synthesis biosynthesis
O O
NH2 Aspartate HO C dihydroorotase
HN CH2
C transcarbamoylase NH2 CH2 C
O O CH C CH
O C O N COOH
P O N COOH
carbamoyl HO C Pi H H
phosphate CH2 H 2O dihydroorotate
carbamoyl
CH aspartate NAD+
H2 N COOH dihydroorotate
dehydrogenase
Asp NADH+H+
O orotate O
O OMP phosphoribosyl
HN decarboxylase HN transferase HN
O N CO2 O N PRPP
PPi O N COOH
R-5'-P COOH H
R-5'-P
UMP orotidine orotic acid
monophosphate
（ OMP
UTP ）
3. Synthesis of CTP
Amidation at the nucleoside triphosphate
level.
O Glu + ADP + Pi NH2
Gln + ATP
HN N
CTP synthetase O N
O N
5' PPP 5' PPP
UTP CTP
R
R
4. Formation of dTMP
The immediate precursor of
thymidylate (dTMP) is dUMP.
The formation of dUMP either by
deamination of dCMP or by
hydrolyzation of dUDP. The former is
the main route.
dTMP synthesis at the nucleoside
monophosphate level.
dUDP
H2 O
O O
Pi CH3
HN thymidylate synthase HN
O
NH 3 O N N
N 5
, N 10
-CH -FH FH 2
d R 5' P 2 4 d R 5' P
H2 O
dUMP FH 2 NADPH dTMP
dCMP reductase + H+
FH 4
NADP+
5. Regulation of de novo synthesis
ATP + CO2 + Gln
carbamoyl phosphate
carbamoyl aspartate purine nucleotide
PRPP
pyrimidine
ATP + R-5-P nucleotide
UTP
UMP CTP
§ 4. Salvage pathway
2
uridine uridine-cytidine kinase
cytidine + ATP UMP
CMP+ ADP
thymidine kinase
deoxythymidine + ATP dTMP + ADP
deoxycytidine
deoxycytidine kinase dCMP + ADP
+ ATP
uracil ribosyltransferase
pyrimidine phosphate UMP
thymine + PRPP dTMP + PPi
orotic acid OMP
§ 4. 3 Antimetabolites of
pyrimidine nucleotides
• Antimetabolites of pyrimidine
nucleotides are similar with them of
purine nucleotides.
1. Pyrimidine analogs
• 5-fluorouracil (5-FU) is a analog of
thymine.
O O
F CH3
HN HN
O N O N
H H
5-FU thymine
dUMP dTMP
5-FdUMP
5-FU
5-FUTP Synthesis of RNA
Destroy structure of RNA
2. Amino acid analogs
• AS inhibits the synthesis of CTP.
3. Folic acid analogs
• MTX inhibits the synthesis of dTMP.
4. Nucleoside analogs
• Arabinosyl cytosine (ara-c) inhibits
the synthesis of dCDP.
NH2
NH2
O O
N
ON ON
CH2OH CH2OH
N
OH H
H H
H H H H
OH H OH OH
ara-c cytosine
Section 5 Catabolism of
Pyrimidine Nucleotides
+
CO2, NH3
NH2 O O
H2O NH3 CH3
N HN HN
O N O N O
H H N thymin
uraci H
cytosine e
l
HOOC HOOC
β-ureidopropionate NH2 NH2 CH
CH2 CH2 CH3 CH2
O N O N β-ureido-
H H isobutyrat
e
H2O H2O
H2N CH2 CH2 COOH H2N CH2 CH COOH
CO2 + 3
NH CH3
β-alanine β-aminoisobutyrate
Summary of pyrimidine biosynthesis
• The sources of the atoms in the pyrimidine ring are glutamine, CO2, and aspartic
acid.
• A. Synthesis of carbamoyl phosphate
• B. Synthesis of orotic acid
• C. Formation of a pyrimidine nucleotide
• D. Synthesis of UTP and cytidine triphosphate (CTP)
• E. Synthesis of thymidine monophosphate (TMP) from dUMP
• F. Salvage of pyrimidines
Summary of pyrimidine biosynthesis
dTMP dTDP dTTP
dUMP dUDP
UMP UDP UTP
CDP CTP
dCMP dCDP dC P
T
SUMMARY OF DEGRADATION OF
PYRIMIDINE NUCLEOTIDES
Unlike the purine ring, which is not cleaved human
cells, the pyrimidine ring is opened and degraded
to highly soluble products, β-alanine and β-
aminoisobutyrate, with the production of NH3
and CO2.
NH2 O O
H2O NH3 CH3
N HN HN
O N O N O
H H N thymin
uraci H
cytosine e
l
HOOC HOOC
β-ureidopropionate NH2 NH2 CH
CH2 CH2 CH3 CH2
O N O N β-ureido-
H H isobutyrat
e
H2O H2O
H2N CH2 CH2 COOH H2N CH2 CH COOH
CO2 + 3
NH CH3
β-alanine β-aminoisobutyrate
PROGRESS
Shiguo,Zheng Zhou,et al.
Associations between
interleukin and interleukin
receptor gene polymorphisms
and risk of gout.
Questions
1. Briefly describe the sources and pathways of
formyl phosphate in liver cells.
2. Briefly describe the physiological significance of
purine nucleotide salvage pathway
3. Briefly describe the anticancer mechanism of 5-
fluorouracil (5-Fu).
4. Describe the anticancer mechanism of
methotrexate.
