Nucleotide Metabolism Student Edition 6/3/13 version Pharm. 304 Biochemistry Fall 2014 Dr. Brad Chazotte 213 Maddox Hall Web Site: Original material only © B. Chazotte

Goals Do NOT memorize the De Novo purine and pyrimidine nucleotide biosynthetic pathway details, i.e. enzymes and specific intermediate products. 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.

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 Lehninger 2000 Figure 22.31e imine enamine C=C-NR’ 2 C-C=NR

De Novo Synthesis of Purine Nucleotide 6: Air Carboxylase (N 5 -CAIR Synthetase) Rx Lehninger 2000 Figure 22.31f (5-aminoimidazole ribotide)

De Novo Synthesis of Purine Nucleotide 7: N 5 -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-base- specific nucleoside diphosphate kinases (∆G ≈ 0). e.g. GDP + ATP  GTP + ADP

Purine Biosynthesis: Controls Voet, Voet & Pratt 2013 Fig 23.4 Control points Ribophosphatepyrokinase Amidophosphoribosyl transferase Adenylsuccinate synthetase IMP dehydogenase

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 Voet, Voet & Pratt 2013 Figure 23.8 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

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 Voet, Voet & Pratt 2013 Fig 23.9a “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)

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 Lehninger 2000 Figure Voet, Voet & Pratt 2013 Box 23.1 Azaerine & Acivicin: Glutamine amidotransferase inhibitors Thymidylate Synthesis Inhibitors: Chemotherapeutics

Thymidylate synthesis & Folate Metabolism as Chemotherapy Targets Voet, Voet & Pratt 2013 Figure fluorouracil

Nucleotide Metabolism: Summary Voet, Voet & Pratt 2013 Figure 23.18

End of Lectures