1. FCH 532 Lecture 28 Chapter 28: Nucleotide metabolism
Quiz on Monday essential amino acids
Wed. April 11-Exam 3
ACS exam is on Monday 5/30
Final is scheduled for May 4, 12:45-2:45 PM, in 111 Marshall

2. Figure The biosynthesis of the “aspartate family” of amino acids: lysine, methionine, and threonine.
Page 1039

3. Figure The biosynthesis of the “pyruvate family” of amino acids: isoleucine, leucine, and valine.
Page 1040

4. Figure 26-62 The biosynthesis of chorismate, the aromatic amino acid precursor.
Page 1042

5. Figure 26-63 The biosynthesis of phenylalanine, tryptophan, and tyrosine from chorismate.
Page 1043

6. Figure 26-64 A ribbon diagram of the bifunctional enzyme tryptophan synthase from S. typhimurium
Page 1044

7. Figure 26-65 The biosynthesis of histidine.
Page 1045

8. Hypoxanthine

11. Purine synthesis Purine components are derived from various sources.
First step to making purines is the synthesis of inosine monophosphate.

12. De novo biosynthesis of purines: low molecular weight precursors of the purine ring atoms

13. Initial derivative is Inosine monophosphate (IMP)
AMP and GMP are synthesized from IMP H O
Hypoxanthine
base -O P O-
Inosine monophosphate

14. Inosine monophosphate (IMP) synthesis
Pathway has 11 reactions.
Enzyme 1: ribose phosphate pyrophosphokinase
Activates ribose-5-phosphate (R5P; product of pentose phosphate pathway) to 5-phosphoriobysl--pyrophosphate (PRPP)
PRPP is a precursor for Trp, His, and pyrimidines
Ribose phosphate pyrophosphokinase regualtion: activated by PPi and 2,3-bisphosphoglycerate, inhibited by ADP and GDP.

15. Page 1071

16. Activation of ribose-5-phosphate to PRPP N9 of purine added
Page 1071

17. Anthranilate synthase Anthranilate phosphoribosyltransferase
N-(5’-phosphoribosyl) anthranilate isomerase
Indole-3-glycerol phosphate synthase
Tryptophan synthase
Tryptohan synthase,  subunit
Chorsmate mutase
Prephenate dehydrogenase
Aminotransferase
Prephenate dehydratase
aminotransferase
Page 1043

18. ATP phosphoribosyltransferase Pyrophosphohydrolase
Phosphoribosyl-AMP cyclohydrolase
Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide isomerase
Imidazole glycerol phosphate synthase
Imidazole glycerol phosphate dehydratase
L-histidinol phosphate aminotransferase
Histidinol phosphate phosphatase
Histidinol dehydrogenase
Page 1045

19. Page 1074

20. Nucleoside diphosphates are synthesized by phosphorylation of nucleoside monophosphates
Reactions catalyzed by nucleoside monophosphate kinases
Adenylate kinase
AMP + ATP
2ADP
Guanine specific kinase
GMP + ATP
GDP + ADP
Nucleoside monophosphate kinases do not discriminate between ribose and deoxyribose in the substrate (dATP or ATP, for example)

21. Can use any NTP or dNTP or NDP or dNDP
Nucleoside triphosphates are synthesized by phosphorylation of nucleoside monophosphates
Nucleoside diphosphates
Reactions catalyzed by nucleoside diphosphate kinases
Adenylate kinase
ATP + GDP
ADP + GTP
Can use any NTP or dNTP or NDP or dNDP

22. Regulation of purine biosynthesis
Pathways synthesizing IMP, ATP and GTP are individually regulated in most cells.
Control total purines and also relative amounts of ATP and GTP.
IMP pathway regulated at 1st 2 reactions (PRPP and 5-phosphoribosylamine)
Ribose phosphate pyrophosphokinse- is inhibited by ADP and GDP
Amidophosphoribosyltransferase (1st committed step in the formation of IMP; reaction 2) is subject to feedback inhibition (ATP, ADP, AMP at one site and GTP, GDP, GMP at the other).
Amidophosphoribosyltransferase is allosterically activated by PRPP.

23. Activation of ribose-5-phosphate to PRPP N9 of purine added
Page 1071

24. Figure 28-5 Control network for the purine biosynthesis pathway.
Feedback inhibition is indicated by red arrows
Feedforward activation by green arrows.
Page 1075

25. Salvage of purines
Free purines (adenine, guanine, and hypoxanthine) can be reconverted to their corresponding nucleotides through salvage pathways.
In mammals purines are salvaged by 2 enzymes
Adeninephosphoribosyltransferase (APRT)
Adenine + PRPP  AMP + PPi
Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)
Hypoxanthine + PRPP  IMP + PPi
Guanine + PRPP  GMP + PPi

27. Synthesis of pyrimidines
Pyrimidines are simpler to synthesize than purines.
N1, C4, C5, C6 are from Asp.
C2 from bicarbonate
N3 from Gln
Synthesis of uracil monoposphate (UMP) is the first step for producing pyrimidines.

28. Figure 28-6 The biosynthetic origins of pyrimidine ring atoms.
Page 1077

29. Page 1077

30. Reaction 4: Oxidation of dihydroorate Reactions catalyzed by eukaryotic dihydroorotate dehydrogenase.
Page 1078

31. Oxidation of dihydroorotate
Irreversible oxidation of dihydroorotate to orotate by dihydroroorotate dehydrogenase (DHODH) in eukaryotes.
In eukaryotes-FMN co-factor, located on inner mitochondrial membrane. Other enzymes for pyrimidine synthesis in cytosol.
Bacterial dihydroorotate dehydrogenases use NAD linked flavoproteins (FMN, FAD, [2Fe-2S] clusters) and perform the reverse reaction (orotate to dihydroorotate)

32. Enhances kcat/KM of decarboxylation by 2 X 1023 No cofactors
Figure 28-9 Reaction 6: Proposed catalytic mechanism for OMP decarboxylase.
Decarboxylation to form UMP involves OMP decarboxylase (ODCase) to form UMP.
Enhances kcat/KM of decarboxylation by 2 X 1023
No cofactors
Page 1079

33. Synthesis of UTP and CTP
Synthesis of pyrimidine nucleotide triphosphates is similar to purine nucleotide triphosphates.
2 sequential enzymatic reactions catalyzed by nucleoside monophosphate kinase and nucleoside diphosphate kinase respectively:
UMP + ATP  UDP + ADP
UDP + ATP  UTP + ADP

34. Figure 28-10 Synthesis of CTP from UTP.
Page 1080
CTP is formed by amination of UTP by CTP synthetase
In animals, amino group from Gln
In bacteria, amino group from ammonia

35. Regulation of pyrimidine nucleotide synthesis
Bacteria regulated at Reaction 2 (ATCase)
Allosteric activation by ATP
Inhibition by CTP (in E. coli) or UTP (in other bacteria).
In animals pyrimidine biosynthesis is controled by carbamoyl phosphate synthetase II
Inhibited by UDP and UTP
Activated by ATP and PRPP
Mammals have a second control at OMP decarboxylase (competitively inhibited by UMP and CMP)
PRPP also affects rate of OMP production, so, ADP and GDP will inhibit PRPP production.

36. Page 1080

37. Production of deoxyribose derivatives
Derived from corresponding ribonucleotides by reduction of the C2’ position.
Catalyzed by ribonucleotide reductases (RNRs)
dADP
ADP

38. Overview of dNTP biosynthesis
One enzyme, ribonucleotide reductase,
reduces all four ribonucleotides to their
deoxyribose derivatives.
A free radical mechanism is involved
in the ribonucleotide reductase
reaction.
There are three classes of ribonucleotide
reductase enzymes in nature:
Class I: tyrosine radical, uses NDP
Class II: adenosylcobalamin. uses NTPs
(cyanobacteria, some bacteria,
Euglena).
Class III: SAM and Fe-S to generate
radical, uses NTPs.
(anaerobes and fac. anaerobes).

39. Figure 28-12a. Class I ribonucleotide reductase from E. coli
Figure 28-12a Class I ribonucleotide reductase from E. coli. (a) A schematic diagram of its quaternary structure.
Page 1082

40. Proposed mechanism for rNDP reductase

41. Proposed reaction mechanism for ribonucleotide reductase
Free radical abstracts H from C3’
Acid-catalyzed cleavage of the C2’-OH bond
Radical mediates stabilizationof the C2’ cation (unshared electron pair)
Radical-cation intermediate is reduced by redox-active sulhydryl pair-deoxynucleotide radical
3’ radical reabstracts the H atom from the protein to restore the enzyme to the radical state.