chapter 8. nucleotide metabolism
DESCRIPTION
1. Biosynthesis of purine nucleotites: 1) The origins of the atoms in the purine ring: One C unit One C unitTRANSCRIPT
Chapter 8. Nucleotide Metabolism
Functions of nucleotites:They are precursors of DNA and RNAATP is a universal currency of energyPhysiological 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:
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Glutamine
N10-Formyl-tetrahydrofolate
CO2
Aspartate
N10-Formyl-tetrahydrofolate
Glycine
N
CN
C
CC
N
C
N
One C unit
One C unit
2) Formation of phosphoribosylamine
Ribose 5-phosphate PRPPPRPP synthase ADPATP
PRPP: 5-Phosphoribose-1-pyrophosphate
OCH2
HH
OH
OP
O-O
O-H
OH
OH
H OCH2
HH
OH
OP
O-O
O-H
OH
O
H
P O P O-O
O-O-
OATP AMP
PRPP synthase
PRPP 5-phosphoribosyl-1-amineGln PRPP
Amidotransferase
Glutamine glutamate + PPi
OCH2
HH
OH
OP
O-O
O-H
OH
O
H
P O P O-O
O-O-
O OCH2
HH
OH
OP
O-O
O-H
OH
H
NH2
Aminophosphoribosyltransferase
Gln Glu + PPi
3) Formation of inosinate (IMP)
OCH2
HH
OH
OP
O-O
O-H
OH
H
NH2
Ribose-P
N
CHN
C
CN
CO
HN
CH
Ribose -P
NH
C
CH2
NH
HN
CO H
Ribose-PN
CHN
HCCH2N
Ribo se -P
NH
C
CH2
NH
O
CHO
Ribose-P
N
CHN
CCH2N
-OOC
Ribose-P
N
CHN
CCH2N
C
O
NHCH-OOC
CH2
COO-
Ribose-P
N
CHN
C
CH2N
C
O
H2N
Ribose-P
N
CHN
CCN
CO
H2N
COH
Ribose-P
NH
C
CH2
NH 3+
OGly,ATP
N10-formylFH4
Gln,ATP -H2O
CO2
Asp,ATPFumarate
N10-formylFH4
-H2O
(IMP)
4) Formation of AMP and GMP
(IMP)Ribose-P
N
CHN
C
CN
CO
HN
CH
Ribose-P
N
CHN
C
CN
CNH
N
CH
CH COO-CH2-OOC
Ribose-P
N
CHN
C
CN
C
NH2
N
CH
Ribose-P
N
CHN
C
CN
CO
HN
CO
H Ribose-P
N
CHN
C
CN
CO
HN
CH2N
Asp,GTP
Fumarate
H2O,NAD+
Gln,ATP
(AMP)
(GMP)
5) Formation of ATP and GTP
AMP ADP ATP
GMP GDP GTP
Kinase
Kinase Kinase
Phosphorylation
ATP ADP
ATP ADPATP ADP
Pi
6) Regulation of purine nucleotite synthesisFeedback inhibitors: AMP, ADP, GMP, GDP, IMP
AMP ADP ATPR-5-P PRPP PRA IMP GMP GDP GTP
PRA: 5-phosphoribosyl-1-amine . activation inhibition
7) Salvage pathways for purine nucleotite synthesis
PRPP Purine ribonucleotide
Adenine + PRPP AMP + PPiHypoxanthine + PRPP IMP + PPiGuanine + PRPP GMP + PPiAdenosine + ATP AMP +ADP
OCH2
HH
OH
OP
O-O
O-H
OH
O
H
P O P O-O
O-O-
OOCH2
HH
OH
OP
O-O
O-H
OH
H
PurinePurine PPi
8) Biosynthesis of deoxyribonucleotides(At the NDP level)
Ribonucleoside deoxyribonucleoside diphosphate diphosphate
Base=purine or pyrimidine
OCH2
HH
OH
OP
O
O
O-H
OH
H
BaseP
O
O-
-O OCH2
HH
OH
OP
O
O
O-H
H
H
BaseP
O
O-
-ONADPH+H+ NADP+ + H2O
Ribonucleotide reductase
The mechanism for ribonucleotide reduction:NDP dNDP
Ribonucleotide SHreductase SH
FADH2
Ribonucleotide Sreductase S
Thioredoxin SH SH
Thioredoxin S S
FAD
NADP+ NADPH + H+
Thioredoxinreductase
8) Inhibition of purine nucleotide biosynthesis by some anticancer drugs
Reaction InhibitorPRPP PRA 6-mercaptopurine(6MP)Glycinamide ribonucleotide Methotrexate(MTX)Formylglycinamide ribonucleotide Formylglycinamide ribonucleotide AzaserineFormylglycinamidine ribonucleotideIMP AMP 6MPIMP GMP 6MP, AzaserineAdenine AMP 6MPGuanine GMP 6MP
6MP
N
CHN
C
CN
CSH
N
CH
H
+N N CH2 C
O
O CH2 CH
NH2
COO-
Azaserine
N
CN
C
CC
NCH
CN
NH2
H2N
CH2 N
CH3
C
O
NH CH
COO-
CH2 CH2 COO-
Methotrexate (MTX)
2. Degradation of purine nucleotides:
AMP IMP Hypoxanthine Xanthine Uric acidGMP Guanine Xanthine Uric acid
N
CN
C
CN
CO
HN
CO
H H
H
O
N
CN
C
CN
COH
N
CHO
H
O-
Uric acid Urate
N
CHN
C
CN
CO
HN
CO
H HN
CHN
C
CN
CO
HN
CH
H
N
CN
C
CN
CO
HN
CO
H H
H
O
Ribose-P
N
CHN
C
CN
CO
HN
CH
IMP Hypoxanthine Xanthine Uric acid
Ribose-P
N
CHN
C
CN
CO
HN
CH2NN
CHN
C
CN
CO
HN
CH2N
H
N
CHN
C
CN
CO
HN
CO
H H
GMP XanthineGuanine
Ribose-P
N
CHN
C
CN
CO
HN
CH
Ribose-P
N
CHN
C
CN
CNH2
N
CH
AMP IMP
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.
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.
N
NC
C
CN
COH
N
CH
H
H
N
NC
C
CN
COH
N
CHO
H
H
Allopurinol Alloxanthine
Xanthine oxidase
3. Synthesis of pyrimidine nucleotides:
1) Origins of the atoms in the pyrimidine ring
C N C
C C N
Carbamoylphosphate
Aspartate
2) Pathway of pyrimidine nucleotide synthesisA) Formation of carbamoyl phosphate
2ATP + HCO3- + 2ADP+ PiH2N C
O
O P O-O
O-
Gln Glu
Differences between carbamoyl phosphate biosynthesis in the pyrimidine pathway and that in the urea cycle
In pyrimidine pathway In urea cycleLocation Cytosol Mitochondria-NH2 from: Gln NH4
+
Enzyme Carbamoyl phosphate Carbamoyl phosphate synthase-II synthase-IN-acetyl-Glu No effect Activator
B) Formation of orotate
H2N C
O
O P O-O
O-+ H2N C
COO-
H
CH2
COO-
Asp transcarbamoylase
PiH2N C
O
HN C
COO-
H
CH2
COO-
Carbamoyl phosphate Asp N-Carbamoylaspartate
Dihydroorotase
CHN
CN
CH
CH2
O
O
H
COO-
H+
H2O
Dihydroorotate
Dihydroorotatedehydrogenase
NADH + H+ NAD+C
HN
CN
C
CH
O
O
H
COO-
Orotate
C) Formation of UMP
CHN
CN
C
CH
O
O
H
COO-
PRPP PPi
OCH2
HH H
OHOHH
OP-O
O
O-
CHN
CN
CCH
O
OCOO- H+ CO2
OCH2
HH H
OHOHH
OP-OO
O-
CHN
CN
CHCH
O
OOrotatephosphoribosyl
transferase
Orotidylatedecarboxylase
Orotate Orotidylate UMP
C) Formation of other pyrimidine nucleotides
UMP UDP UTPATP ADPATP ADP
Kinase Kinase
UTP
OPOPHOO O
O- O-OCH2
HH H
OHOHH
OPO
O-
CHN
CN
CHCH
O
OOPOPHO
O O
O- O-OCH2
HH H
OHOHH
OPO
O-
CNC
NCHCH
NH2
O
CTP
Gln, ATP Glu, ADP H2O Pi, 2H+
CTP synthase
UDP dUDP dUTP
dUTP dUMP
dUMP
OCH2
HH H
HOHH
OP-OO
O-
CHN
CN
CHCH
O
O
OCH2
HH H
HOHH
OP-OO
O-
CHN
CN
CHC
O
O
CH3
dTMP
Thymidylate synthase
N5N10-MethyleneFH4
FH2
NADPH NADP+, H2O
Ribonucleotidereductase
ATP ADP
Kinase
H2O PPi
dUTPase
D) Regulation of pyrimidine nucleotide synthesis
CO2 + Gln + ATP
Carbamoyl phosphate
N-Carbamoylaspartate
UMP
Inhibited by UMP
Inhibited by CTP
-
-
3) Salvage pathway for pyrimidine nucleotide biosynthesis
Pyrimidine Pyrimidine ribonucleoside monophosphate
Orotate Orotidylate UMP
PRPP PPi
PyrimidinePhosphoribosyltransferase
PRPP PPi
OrotatePhosphoribosyltransferase
H+ CO2
Orotidylatedecarboxylase
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.
F-dUMP
OCH2
HH H
HOHH
OP-OO
O-
CHN
CN
CHC
O
O
F
OCH2
HH H
HOHH
OP-OO
O-
CHN
CN
CHC
O-
O
F
S Enzyme OCH2
HH H
HOHH
OP-OO
O-
CHN
CN
CHC
O
OF
S Enzyme
CH2 FH4
HS-E Methylene FH4
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.
N
N
N
NH2N
NH2
CH2
H
NH C
O
NH CHCOO-
CH2 CH2 COO-
Aminopterin
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.
OCH2
HH HO
HOHH
HO
CNC
NCHCH
NH2
O
Cytosine arabinoside
UMP UTP CTP CDP dCDP
UDP dUDP dUMP dTMP
Azaserine Cytosine arabinoside
5-FU
Aminopterin
-
-
-
-
4. Degradation of pyrimidine nucleotide The pyrimidine ring can be completely de
graded in humans. The products include: NH3, CO2, -alanine, and -aminoisobutyrate. Both -alanine, and -aminoisobutyrate can be further converted into acetyl-CoA and succinyl-CoA, respectively, or are excreted in the urine.
CMPHO OCH2
HH H
OHOHH
CHN
CN
CHCH
O
OHO OCH2
HH H
OHOHH
CNC
NCHCH
NH2
OH2O Pi H2O NH3
UMP
OCH2
HH H
OHOHH
OP-OO
O-
CHN
CN
CHCH
O
O
Cytidine Uridine
Pi H2O
CHN
CN
CHCH
O
OH
Pi Ribose 1-phosphate
UracilDihydrouracil
CHN
CN
CH2
CH2
O
OH
NADP+ NADPHC
CN
CH2
CH2
O
OH
H3N+
-O
-Ureidopropionate
H2OC
H3N+ CH2
CH2
O-O
-Alanine
CO2 +NH3 H2O
C
CHOCH2
O-O
Malonatesemialdehyde
COCH3
SCoA
Acetyl-CoA
NAD+ NADHHSCoA CO2
Pyruvate
Alanine
dCMPO OCH2
HH H
HOHH
CHN
CN
CHC
O
O
CH3
PO
-O
O-
H2O NH3 FH4=CH2 FH2
dUMP
OCH2
HH H
HOHH
OP-OO
O-
CHN
CN
CHCH
O
O
dTMP
CHN
CN
CHC
O
OH
CH3
Pi Ribose 1-phosphate
ThymineDihydrothymine
CHN
CN
CH2
CH
O
OH
CH3NADP+ NADPHC
CN
CH2
CH
O
OH
H3N+
-OCH3
-Ureido- -methylpropionate
H2OC
H3N+ CH2
CH
O-O
CH3
-Amino-isobutyrate
CO2 +NH3 H2O
C
CHOCH
O-O
CH3
Methylmalonatesemialdehyde
COCH2
SCoA
CH3
Propionyl-CoA
NAD+ NADHHSCoA CO2
Pyruvate
Alanine
OCH2
HH H
HOHH
CHN
CN
CHC
O
O
CH3
HO
Deoxythymidine
H2O Pi
COCH2
SCoA
CH2 COO-
Succinyl-CoA
5. Dysmetabolism of nucleotides Disease Deficiency SymptomsGout PRPP synthetase hyper uricemiaLesch-Nyhan HGPRT purine and uricsyndrom acid, cerebral
paralysisImmunodeficiency adenosine deaminase deoxyadenosineDiseases uria, dysostosisKidney stone APRT kidney stone,
urodynia, hematuriaXanthinuria xanthine oxidase kidney stone,
no symptoms