Transcript Chapter 8. Nucleotide Metabolism (sP739, cP191)

Chapter 8. Nucleotide Metabolism
Functions of nucleotites:
They are precursors of DNA and RNA
ATP is a universal currency of energy
Physiological mediators (cAMP, cGMP)
They are activated intermediates in many
biosynthesis (UDP-glucose, CDP-choline)
Adenine nucleotides are components of
some coenzymes (NAD+, NADP+ and FAD )
1. Biosynthesis of purine nucleotites:
1) The origins of the atoms in the purine ring:
CO2
Aspartate
C
N1 6
10
N -FormylOne
C unit
Glycine
5
C
C2 3 4C
N
tetrahydrofolate
Glutamine
10
N
7
8
9
N
C
N One
-FormylC unit
tetrahydrofolate
2) Formation of phosphoribosylamine
ATP
ADP
PRPP synthase
Ribose 5-phosphate
PRPP
O
O
-
O
P O CH2
O
-
H
H
H
O
ATP
AMP
-
O
P O CH2
O-
H
OH
OH OH
PRPP synthase
H
H
H
O
H
O
OH OH
PRPP: 5-Phosphoribose-1-pyrophosphate
O
O
P O
P O
O-
O-
-
Glutamine
PRPP
glutamate + PPi
5-phosphoribosyl-1-amine
Gln PRPP
Amidotransferase
O
-
O
O
P O CH2
O
-
H
H
H
O
H
O
OH OH
-
Gln
O
O
P O
P O
O
-
O
-
Glu + PPi
O
P O CH2
O
Aminophosphoribosyl
transferase
-
H
H
NH2
O
H
H
OH OH
3) Formation of inosinate (IMP)
O
+
O
-
O
NH 3
P
O
O
CH2
-
NH 2
O
H
Gly,ATP
O
H
H
H
OH
CH2
OH
C
N10-formyl
FH4
H
C
O
H
C
NH
NH
CH2
CH2
O
Gln,ATP
C
HN
C
N
HC
-H2O
CH
H2N C N
NH
NH
NH
Ribos e-P
Ribo se -P
Ribose -P
Ribose-P
CO2
O
O
H2 N
C
-
N
C
H2 N C
Fumarate
CH
OOC
CH NH C
CH2
N
C
H2N C
COO-
Ribose -P
N
Ribose-P
10
H2N
H
O C N
N
C
C
CH
N
OOC
CH
N -formy l
FH 4
O
C
-
N
HN
-H2O
H
C
O
C
C
N
C
Ribose-P
N
CH
N
Ribose-P
(IMP)
Asp,ATP
N
C
H2N C
CH
N
Ribose-P
4) Formation of AMP and GMP
-
OOC
CH2
H
COO -
CH
N
NH
C
C
C
C
N
HN
H
C
C
N
C
Fumarate
N
CH
H
N
C
N
N
C
C
CH
C
N
N
Ribose-P
Ribose-P
Asp,GTP
O
C
NH2
(AMP)
N
CH
N
Ribose-P
(IMP)
H2O,NAD+
HN
O
C
O
C
C
N
H
C
N
CH
N
HN
Gln,ATP
H2N
C
O
C
C
N
C
Ribose-P
N
CH
N
Ribose-P
(GMP)
5) Formation of ATP and GTP
Kinase
AMP
ADP
ATP
Kinase
Kinase
GDP
ATP
ADP
ATP
Pi
ADP
GMP
Phosphorylation
GTP
ATP
ADP
6) Regulation of purine nucleotite synthesis
Feedback inhibitors: AMP, ADP, GMP, GDP, IMP
R-5-P
PRPP
PRA
AMP
ADP
ATP
GMP
GDP
GTP
IMP
PRA: 5-phosphoribosyl-1-amine .
activation
inhibition
7) Salvage pathways for purine nucleotite
synthesis
O
-
O
O
P O CH2
O
-
H
-
H
O
H
H
O
OH OH
O
Purine
O
O
P O
P O
O
-
PRPP
Adenine + PRPP
Hypoxanthine + PRPP
Guanine + PRPP
Adenosine + ATP
O
-
PPi
P
O
O
CH2
-
H
-
H
Purine
O
H
H
OH OH
Purine ribonucleotide
AMP + PPi
IMP + PPi
GMP + PPi
AMP +ADP
8) Biosynthesis of deoxyribonucleotides
(At the NDP level)
O
-
O
O
O
+
+
NADP + H2O
Base NADPH+H
P O P O CH2 O
OOH
H
H
H
Ribonucleotide reductase
OH OH
Ribonucleoside
diphosphate
Base=purine or pyrimidine
O
O
Base
P O P O CH2 O
OO
H
H
H
H
OH H
deoxyribonucleoside
diphosphate
The mechanism for ribonucleotide reduction:
NDP
Ribonucleotide
reductase
Thioredoxin
FADH2
NADP+
dNDP
SH
SH
S
S
Ribonucleotide
reductase
Thioredoxin
Thioredoxin
reductase
S
S
SH
SH
FAD
NADPH + H+
8) Inhibition of purine nucleotide biosynthesis
by some anticancer drugs
Reaction
PRPP
PRA
Glycinamide ribonucleotide
Formylglycinamide ribonucleotide
Formylglycinamide ribonucleotide
Formylglycinamidine ribonucleotide
IMP
AMP
IMP
GMP
Adenine
AMP
Guanine
GMP
Inhibitor
6-mercaptopurine(6MP)
Methotrexate(MTX)
Azaserine
6MP
6MP, Azaserine
6MP
6MP
N
H
C
SH
C
C
+
CH
C
N
O
N
NH2
N N CH2 C O CH2 CH COO -
N
H
Azaserine
6MP
NH2
C
H2N
CH3
N
N
C
C
C
C
CH
N
CH2 N
O
COO
-
C NH CH CH2 CH2 COO
N
Methotrexate (MTX)
-
2. Degradation of purine nucleotides:
AMP
GMP
IMP
Hypoxanthine
Guanine
Xanthine
HN
O
C
H
O
C
C
N
Xanthine
Uric acid
Uric acid
C
H
Uric acid
OH
C
N
N
C
N
C O
N
HO
C
N
C
H
N
H
Urate
C O
NH2
C
C
N
C
H
N
CH
C
N
HN
C
H
N
O
C
C
N
C
H2N
C
C
N
C
N
HN
CH
N
C
H2N
O
C
C
N
C
Ribose-P
HN
H
C
C
N
C
IMP
HN
CH
Ribose-P
HN
CH
O
N
H
C
O
C
C
N
C
N
N
H
Hypoxanthine
O
N
C
N
CH
C
N
H
Xanthine
HN
CH
C
O
C
H
Guanine
N
N
N
H
GMP
O
C
N
IMP
AMP
HN
CH
Ribose-P
Ribose-P
O
C
N
C
O
C
C
N
C
H
Xanthine
N
HN
CH
N
H
O
C
H
O
C
C
N
H
C
N
C O
N
H
Uric acid
Gout is induced by high serum levels of urate, a disease that
affects the joints and kidneys.
Allopurinol is an analog of hypoxanthine. It is extensively
used to treat gout.
N
H
C
OH
C
C
N
C
H
C
N
N
H
Allopurinol
Xanthine oxidase
HO
N
C
OH
C
C
N
C
H
C
N
N
H
Alloxanthine
In the body, allopurinol is converted into alloxanthine, which
then remains tightly bound to the active site of xanthine
oxidase and thus inhibits the production of urate.
3. Synthesis of pyrimidine nucleotides:
1) Origins of the atoms in the pyrimidine ring
C
Carbamoyl
phosphate
N
C
C
C
N
Aspartate
2) Pathway of pyrimidine nucleotide synthesis
A) Formation of carbamoyl phosphate
Gln
2ATP + HCO3-
Glu
O
O
H2N C O P O
-
O
+ 2ADP+ Pi
Differences between carbamoyl phosphate
biosynthesis in the pyrimidine pathway and that
in the urea cycle
Location
-NH2 from:
Enzyme
N-acetyl-Glu
In pyrimidine pathway
Cytosol
Gln
Carbamoyl phosphate
synthase-II
No effect
In urea cycle
Mitochondria
NH4+
Carbamoyl phosphate
synthase-I
Activator
B) Formation of orotate
O
COO-
O
-
H2N C O P O
+
H2N C H
-
O
-
COO
O
Pi
H2N C HN C H
Asp transcarbamoylase
CH2
CH2
-
COO-
COO
N-Carbamoylaspartate
Asp
Carbamoyl phosphate
H+
Dihydroorotase
O
O
HN
O
C
C
+
NADH + H
C COO
H
Orotate
NAD
+
HN
CH
-
N
H2O
Dihydroorotate
dehydrogenase
O
C
C
CH2
-
N
CH COO
H
Dihydroorotate
C) Formation of UMP
O
O
HN
O
C
C
PRPP
CH
PPi
N
H
Orotate
C
Orotate
phosphoribosyl
transferase
CH
-
C
C COO
O
N
O P O CH2 O
O
-
C COO
HN
O
-
O
H
H
H
H
OH OH
Orotidylate
+
H
CO2
HN
C
C
CH
O
N
O P O CH2 O
O
Orotidylate
decarboxylase
CH
O-
H
H
H
H
OH OH
UMP
C) Formation of other pyrimidine nucleotides
ATP
UMP
ATP
ADP
UDP
Kinase
ADP
Kinase
UTP
O
HN
C
NH2
CH
C
CH
O
N
HO P O P O P O CH2 O
O
O
-
-
O
O
O
O-
H
H
H
H
OH OH
UTP
Gln, ATP
H2O
Glu, ADP
Pi, 2H+
CTP synthase
N
O
O
O C
O
HO P O P O P O CH2 O
O
O
O-
H
H
C
N
H
H
OH OH
CTP
CH
CH
UDP
NADP+, H2O
NADPH
dUDP
ATP
Ribonucleotide
reductase
H2O
dUTP
ADP
dUTP
Kinase
PPi
dUTPase
dUMP
O
HN
C
O
CH
C
CH
O
N
O P O CH2 O
O
O-
H
H
OH H
dUMP
5 10
N N -Methylene
FH4
FH2
Thymidylate synthase
H
H
HN
O
O C
-
C
N
O P O CH2 O
OH H
H
H
OH H
dTMP
C
CH
CH3
D) Regulation of pyrimidine nucleotide
synthesis
CO2 + Gln + ATP
-
Inhibited by UMP
Carbamoyl phosphate
N-Carbamoylaspartate
UMP
Inhibited by CTP
3) Salvage pathway for pyrimidine nucleotide
biosynthesis
PRPP
Pyrimidine
PPi
Pyrimidine ribonucleoside
Pyrimidine
Phosphoribosyl monophosphate
transferase
PRPP
H+
PPi
Orotate
CO2
Orotidylate
Orotate
Phosphoribosyl
transferase
UMP
Orotidylate
decarboxylase
4) Anticancer drugs that block the pyrimidine
nucleotide biosynthesis
A) 5-Fluorouracil (5-FU): is converted in vivo
into fluorodeoxyuridylate (F-dUMP), which
is an analog of dUMP and irreversibly
inhibits thymidylate synthase.
O
HN
O
O C
C
N
F
C
HN
CH
O
-
O P O CH2 O
OH H
H
H
OH H
F-dUMP
-
HS-E
O C
O-
O
C
C
N
O P O CH2 O
OH H
H
H
OH H
HN
F
C
CH
S
O
Enzyme
Methylene
-
O C
N
O P O CH2 O
OH H
FH4
H
H
OH H
CH2 FH4
C
F
CH
S
Enzyme
B) Aminopterin and methotrexate (MTX):
both are analogs of dihydrofolate. They are
potent competitive inhibitors of
dihydrofolate reductase and thus block the
reactions using one-carbon units.
H
H2N
N
N
O
N
N
CH2 NH
NH2
Aminopterin
COO-
C NH CH CH2 CH2 COO
C) Cytosine arabinoside and azaserine:
Cytosine arabinoside is an analog of
cytosine riboside and thus inhibits the
reduction of CDP to dCDP, while azaserine
inhibits the conversion of UTP to CTP.
NH2
N
O
HO
C
C
N
CH
CH
CH2 O
H HO
H
H
OH H
Cytosine arabinoside
Cytosine
arabinoside
Azaserine
UMP
UTP
CTP
-
CDP
dCDP
5-FU
UDP
dUDP
dUMP
dTMP
Aminopterin
4. Degradation of pyrimidine nucleotide
The pyrimidine ring can be completely
degraded in humans. The products
include: NH3, CO2, b-alanine, and baminoisobutyrate. Both b-alanine, and baminoisobutyrate can be further
converted into acetyl-CoA and succinylCoA, respectively, or are excreted in the
urine.
NH2
N
H2O
Pi
C
CH
HN
C
CH
O
N
H2O
HO CH2 O
CMP
H
H
NH3
H
H
H
OH OH
Cytidine
-
O C
+
H3N
CH2
CO2 +NH3
O
O C
C
-
H2O
H3N
O
C
N
CH2
CH2
H
b -Alanine
b -Ureidopropionate
Pyruvate
Alanine
NAD+
HSCoA
O
-
O C
NADH
CO2
CH3
CH2
CO
CHO
SCoA
Malonate
semialdehyde
Acetyl-CoA
H2O
Pi
H2O
O-
HN
O
C
N
H
H
Pi
H
H
OH OH
UMP
Ribose
1-phosphate
O
CH2
CH2
H
Dihydrouracil
NADP+
CH
C
CH
O
N
O P O CH2 O
O
H
OH OH
O
C
HN
CH
H
Uridine
+
CH2
C
C
CH
O
N
HO CH2 O
H
O
O
O
NADPH
HN
O
C
C
N
CH
CH
H
Uracil
HN
C
O
H2O
NH3
O
O P O CH2 O
O-
O C
H3N+
CH3
CH
C
C
N
H
CH
HN
CH
C
N
H
dUMP
dTMP
O C
H2O
C
N
O
CH3
CH
CH2
H
b -Ureido- -methyl
propionate
CH
H2O
HN
O
C
H
C
N
Deoxythymidine
Pi
Ribose
1-phosphate
O
O
NADP
H
Dihydrothymine
CH2 COO
-
O C
CH2
CH2
CH
CO
CO
CHO
SCoA
SCoA
CH3
Methylmalonate
semialdehyde
NAD
HSCoA
NADH
CO2
Propionyl-CoA
+
NADPH
HN
CH2
CH3
+
H
OH H
CH3
CH
H
H
Pyruvate
Alanine
Pi
C CH3
C
CH
O
N
HO CH2 O
H
OH H
-
C CH3
H2O
C
HN
H
OH H
O
b -Aminoisobutyrate
H
H
H3N+
CH2
FH2
O
O P O CH2 O
O
-
O-
H
O
CO2 +NH3
O
FH4=CH2
H
-
O
-
dCMP
O
O
Succinyl-CoA
O
C
C
N
C CH3
CH
H
Thymine
5. Dysmetabolism of nucleotides
Disease
Deficiency
Gout
Lesch-Nyhan
syndrom
PRPP synthetase
HGPRT
Immunodeficiency
Diseases
Kidney stone
Xanthinuria
Symptoms
hyper uricemia
purine and uric
acid, cerebral
paralysis
adenosine deaminase deoxyadenosine
uria, dysostosis
APRT
kidney stone,
urodynia, hematuria
xanthine oxidase
kidney stone,
no symptoms