Nucleotide Metabolism
Student Edition
6/3/13 version
Dr. Brad Chazotte
213 Maddox Hall
chazotte@campbell.edu
Web Site:
http://www.campbell.edu/faculty/chazotte
Original material only ©2004-14 B. Chazotte
Pharm. 304
Biochemistry
Fall 2014
Goals
•Have a generalized overview of the de novo biosynthesis of ribonucleotides and
deoxyribonucleotides including basic principles.
•Learn the basic structure of the nucleotides & that the ring structures are formed
from multiple molecules.
•Understand the control of nucleotide biosynthesis.
•Know how di- and tri-phosphates are synthesizes from monophosphates.
•Have an understanding of the role of ribonucleotide reductase.
•Understand in general the catabolism of nucleotides and end products.
•Understand the role of the salvage pathways.
•Understand the importance of the biosynthetic pathways in developing
chemotherapeutic agents.
Do NOT memorize the De Novo purine and pyrimidine
nucleotide biosynthetic pathway details, i.e. enzymes and specific
intermediate products.
Nucleotide Metabolism
Biosynthesis Overview
Matthews et al., 1999 Fig 22.1
De novo Pathways
•Do not use free bases: guanine, adenine, thymine, cytidine & uracil!
•The purine ring is built up one or a few atoms at a time and attached to
ribose throughout the process.
•In purine de novo synthesis enzymes are present as large multienzyme
complexes.
•The pyrimidine ring is synthesized as orotate attached to ribose phosphate
and then converted to common pyrimidine nucleotides.
•Cellular nucleotide pools are quite small, ~1%, except for ATP. Thus
nucleotide synthesis must occur during nucleic acid synthesis as well and
can limit DNA replication and transcription. Significance: These
processes are important in dividing cells and agents that inhibit nucleotide
synthesis are important in modern medicine, e.g. cancer!
De novo Purine Synthesis: Origins
of Ring Atoms
Voet, Voet & Pratt 2008 Chap 23 p. 974
Inosine Monophosphate
IMP is the precursor of both AMP & GMP.
It is the nucleotide containing the base hypoxanthine.
IMP is synthesized in an eleven reaction pathway
De novo
Synthesis
of IMP
Voet, Voet & Pratt 2002 Fig 22.1 ; 2013 Figure 23.1
De Novo Synthesis of Purine Nucleotide 1:
Glutamine-PRPP Amindotransferase Rx
Lehninger 2000 Figure 22.31b
De Novo Synthesis of Purine Nucleotide 2:
Amidophosphoribosyl Transferase Rx
Lehninger 2000 Figure 22.31b
De Novo Synthesis of Purine Nucleotide
3: GAR Transformylase Rx
Lehninger 2000 Figure 22.31c
De Novo Synthesis of Purine Nucleotide 4:
FGAM Synthetase
(FGAR Amidotransferase) Rx
Lehninger 2000 Figure 22.31d
De Novo Synthesis of Purine Nucleotide
5: FGAM Synthetase (Cyclase) Rx
C-C=NR
imine
enamine
C=C-NR’2
Lehninger 2000 Figure 22.31e
De Novo Synthesis of Purine Nucleotide 6:
Air Carboxylase (N5-CAIR Synthetase) Rx
(5-aminoimidazole ribotide)
Lehninger 2000 Figure 22.31f
De Novo Synthesis of Purine
Nucleotide 7: N5-CAIR Mutase Rx
Lehninger 2000 Figure 22.31g
De Novo Synthesis of Purine
Nucleotide 8: SAICAIR Synthetase Rx
Lehninger 2000 Figure 22.31h
De Novo Synthesis of Purine Nucleotide
9: SAICAIR (adenylosuccinate) Lyase Rx
Lehninger 2000 Figure 22.31i
De Novo Synthesis of Purine Nucleotide
10: AICAIR Transformylase Rx
Lehninger 2000 Figure 22.31ja
De Novo Synthesis of Purine Nucleotide
11: IMP Synthase (Cyclohydrase) Rx
Lehninger 2000 Figure 22.31ka
Conversion of IMP to AMP or GMP
Voet, Voet & Pratt 2008 Figure 23.3
Synthesis of Di- and Tri-Phosphates
Nucleosides diphosphates are synthesized from their
corresponding nucleoside monophosphates by BASE-specific
nucleoside monophosphate kinases
For adenosine: AMP + ATP  2 ADP
adenylate kinase
Nucleosides triphosphates are converted from their
corresponding nucleoside diphosphates by a NON-basespecific nucleoside diphosphate kinases (∆G ≈ 0).
e.g.
GDP + ATP
 GTP + ADP
Purine Biosynthesis: Controls
Control
points
Ribophosphatepyrokinase
Amidophosphoribosyl
transferase
Adenylsuccinate
IMP dehydogenase
synthetase
Voet, Voet & Pratt 2013 Fig 23.4
Pyrimidine Ring Structure
Text Information
Voet, Voet & Pratt 2008 Chap 23 page 800
De Novo Synthesis of UMP
Voet, Voet & Pratt 2008 Fig 23.5
Synthesis of CTP from UTP
Voet, Voet & Pratt 2013 Figure 23.7
Pyrimidine Biosynthesis: Controls
In animals pyrimidine biosynthesis
is controlled by the activity of
carbamoyl phosphate synthetase II.
Inhibited by UDP and UTP
•Activated by ATP and PRPP.
In mammals:
• additional control at OMP
decarboxylase
•UMP & CMP are competitive
inhibitors
Voet, Voet & Pratt 2013 Figure 23.8
Salvage Pathways
•Most organisms can synthesize nucleotides from
nucleosides or bases that are made available in the diet or
from nucleic acid breakdown.
•Represent important targets for the treatment of microbial
or parasitic diseases and as sites for manipulation of
biological systems such as mutagenesis studies, etc.
Purine & Pyrimidine Bases: Recycling
Matthews et al., 1999 Fig 22.1
Ribonuclease Reductase
“Deoxyribonucleotides are synthesized from
their correpsonding ribonucleotides by the
reduction of the C2’ OH to H”
There are four classes of ribonucleotide
reductases – all use a free radical mechanism.
Fe-containing enzyme in most eukaryotes
(E. Coli)
Voet, Voet & Pratt 2013 Fig 23.9a
Ribonucleotide Reductase:
Enzymatic Mechanism
Voet, Voet & Pratt 2013 Fig 23.10
Purine Catabolism:
Major Pathways in Animals
Voet, Voet & Pratt 2013 Figure 23.19
Pyrimidine Catabolism:
Major Pathways in Animals
Voet, Voet & Pratt 2008 Figure 23.24
Chemotherapeutics & the Enzymes of
Nucleotide Biosynthetic Pathways
An increasing number of chemotherapeutic agents act by
inhibiting one or more enzymes in the nucleotide biosynthetic
pathways.
Inhibitors of Nucleotide
Biosynthesis
Thymidylate Synthesis Inhibitors:
Chemotherapeutics
Voet, Voet & Pratt 2013 Box 23.1
Lehninger 2000 Figure 22.46
Azaerine &
Acivicin:
Glutamine
amidotransferase
inhibitors
Thymidylate synthesis & Folate
Metabolism as Chemotherapy Targets
fluorouracil
Voet, Voet & Pratt 2013 Figure 23.16
Nucleotide Metabolism: Summary
Voet, Voet & Pratt 2013 Figure 23.18
End of Lectures