Nucleotide Metabolism

Nucleotide Metabolism - Chapter 28 Nucleotide Metabolism...

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Unformatted text preview: Chapter 28 Nucleotide Metabolism Nucleotide metabolism • Nucleotides are the building blocks of nucleic acids • Nucleotides also perform wide range of other biochemical functions – ATP and nucleotide coenzymes • Nearly all cells can synthesize nucleotides both de novo (anew) and from the degradation products of nucleic acids (salvage pathway) • Unlike carbohydrates, amino acids, and fatty acids, nucleotides do not provide a significant source of metabolic energy Nucleotides Bases Bases ATP Nucleotide coenzymes NAD+ FAD NAD+ Coenzyme A De novo synthesis of purine ribonucleotide • The initially synthesized purine derivative is inosine monophosphate (IMP), the nucleotide of the base hypoxanthine • IMP is the precursor of both AMP and GMP • Purines are initially formed as ribonucleotides rather than as free bases • Virtually identical pathway throughout all organisms including E. coli, yeast, pigeons, and humans. Origin of the ring atoms of purines De novo biosynthesis of IMP Conversion of IMP to AMP or GMP Synthesis of NDPs and NTPs • Nucleoside diphosphates are synthesized from the corresponding nucleoside monophosphates by basespecific nucleoside monophosphate kinases, which do not discriminate between ribose and deoxyribose in the substrate Adenylate kinase: AMP + ATP ↔ 2 ADP Guadylate kinase: GMP + ATP ↔ GDP + ADP • Nucleoside triphosphates are synthesized from the corresponding nucleoside diphosphates by nucleoside diphosphate kinase, which exibits no preference for the bases of its substrates or for ribose over deoxyribose GDP + ATP ↔ GTP + ADP ΔG ≈ 0 Regulation of purine nucleotide biosynthesis • The IMP pathway is regulated at its first two reactions by feedback inhibition or feedforward activation – Ribose phosphate pyrophosphokinase, the enzyme catalyzing the conversion of ribose-5-phosphate to PRPP is inhibited by both ADP and GDP – Amidoribosyl transferase, the enzyme catalyzing the conversion of PRPP to 5-phosphoribosylamine is inhibited by AMP (ADP or ATP) at one site, and by GMP (GDP or GDP) at anther site – Amidoribosyl transferase is allosterically stimulated by PRPP (feedforward activation) • • GMP inhibits formation of xanthylate from inosinate by IMP dehydrogenase (without affecting formation of AMP), whereas AMP inhibits formation of adenylosuccinate by adenylosuccinate synthetase (without affecting formation of GMP) Since GTP powers the synthesis of AMP from IMP, whereas ATP powers the synthesis of GMP from IMP, the rate of synthesis of GMP increases with [ATP], whereas that of AMP increases with [GTP] Control of the purine biosynthesis pathway 9 steps Salvage of purines • • • • Adenine, guanine, and hypoxanthine released from the turnover of nucleic acids, particularly some types of RNA are reconverted to their corresponding nucleotides through salvage pathways In contrast to the de novo purine biosynthetic pathway, which is virtually identical in all cells, salvage pathways are diverse in character and distribution In mammals, purines are mostly salvaged by two different enzymes, adenine phosphoribosyltransferase (APRT) and hypoxanthineguanine phosphoribosyltransferase (HGPRT) APRT: Adenine + PRPP ↔ AMP + PPi HGPRT: Hypoxanthine + PRPP ↔ IMP + PPi Guanine + PRPP ↔ GMP + PPi Lesch-Nyhan syndrome results from HGPRT deficiency – Excessive production of uric acid, a purine degradation product and neurological abnormalities such as spasticity, mental retardation, and highly aggrasive and destructive behavior, including a bizarre compulsion toward self-mutilation De novo synthesis of pyrimidine ribonucleotide • In contrast to purine nucleotide synthesis, the pyrimidine ring is first synthesized and subsequently coupled to the ribose-5-phosphate moiety • UMP, which is also the precursor of CMP, is synthesized in a six-reaction pathway • CTP is synthesized from UTP in a single reaction De novo synthesis of UMP OMP decarboxylase • The most catalytically proficient enzyme known • The rate enhancement is 2 X 1023 over the uncatalyzed reaction and results from the preferential transition state binding Synthesis of UTP and CTP • UTP is synthesized from UMP by sequential actions of a nucleoside monophosphate kinase and nucleoside diphosphaphate kinase UMP + ATP ↔ UDP + ADP UDP + ATP ↔ UTP + ADP • CTP is formed by amination of UTP by CTP synthetase NH3 or Regulation of pyrimidine nucleotide biosynthesis • In bacteria, ATCase, the enzyme catalyzing the conversion of carbamoyl phosphate to carbamoyl aspartate is stimulated by ATP and inhibited by UTP or CTP • Two levels of regulation in animals – Carbomoyl synthetase II is inhibited by UDP and UTP and activated by ATP and PRPP – OMP decarboxylase is competitively inhibited by UMP and CMP (a lesser extent) • In all organisms, the rate of OMP production depends on the amount of its precursor PRPP, the product of ribose phosphate pyrophosphokinase, which is inhibited by ADP and GDP Regulation of pyrimidine biosynthesis Formation of deoxyribonucleotides • Ribonucleotide reductases (RNRs) synthesize deoxyribonucleotides from their corresponding ribonucleotides by reduction (deoxygenation) at their C2' position • Thymidylate synthase synthesizes thymidylate (dTMP) from dUMP by methylation Reduction of ribonucleotides to deoxyribonucleotides by ribonucleotide reductase Class I ribonucleotide reductase from E. coli R1 R2 Proposed mechanism for ribonucleotide reductase Thioredoxin reduces ribonucleotide reductase X-ray structure of human thioredoxin in its reduced state An electron-transfer pathway for NDP reduction Regulation of ribonucleotide reductase • Maintaining the proper intracellular ratios of dNTPs is essential for normal growth – A deficiency of any dNTP is lethal – An excess of any dNTP is mutagenic • The activitie of ribonucleotide reducatases is remarkably responsive to the levels of nucleotides in the cell – ATP induces the reduction of CDP and UDP – dTTP induces the reduction of GDP and inhibits the reduction of CDP and UDP – dATP inhibits the reduction of all NDPs Feedback network of ribonucleotide reductase • • • The binding of ATP, dATP, dGTP, or dTTP to the specificity site induces the catalytically inactive R1 monomers to form a catalytically active dimer, R12 The binding of dATP or ATP to the activity site causes the dimers to form tetramers, R14a that slowly but reversibly change conformation to a catalytically inactive state, R14b The binding of ATP to the hexamerization site induces the tetramers to further aggregate to form catalytically active hexamers, R16, the enzymes’s major active form Synthesis of dNTPs dNTPs are produced by phophorylation of NTPs, which is catalyzed by nucleoside diphosphate kinase, the same enzyme that phosphorylates NDPs dNDP + NTP (or dNTP) ↔ dNTP + NDP (or dNDP) Biosynthesis of thymidylate (dTMP) Thymidylate synthase Catalytic mechanism of thymidylate synthase Regeneration of THF • DHF is reduced to THF by NADPH as catalyzed by dihydrofolate reductase (DHFR) • The hydromethylgroup of serine is transferred to THF to yield N5,N10-methylene-THF and glycine Inhibition of thymidylate synthesis in cancer therapy Inhibition of thymidylate synthase or DHFR blocks dTMP synthesis and is therefore the basis of cancer chemotherapies Mechanism-based inhibitor (suicide inhibitor) of thymidylate synthase Competitive inhibitors of DHFR Suicide inhibition by FdUMP Nucleotide degradation • Dietary nucleic acids are degraded to nucleotides by pancreatic nucleases and intestinal phosphodiesterases • Nucleotides are hydrolyzed to nucleosides, which may be directly absorbed or further degraded to free bases and ribose or ribose-1-phosphate by nucleosidases and nucleoside phosphorylases • Only small fraction of the bases of ingested nucleic acids are incorporated into tissue nucleic acids – the de novo pathways of nucleotide biosynthesis virtually satisfy the nucleotide need • Ingested bases are mostly degraded and excreted Cellular nucleic acids are also degraded for the turnover Purine nucleotides are degraded to uric acid Adenosine deaminase (ADA) Genetic defects in ADA result in severe combined immunodeficiency disease (SCID) – The mutations in ADA leads to high levels of dATP, which inhibit ribonucleotide reductase, thereby preventing the synthesis of the other dNTPs The purine nucleotide cycle Replenish the citric acid cycle in muscle Xanthine oxidase is a mini-electron-transport protein Mechanism of xanthine oxidase Fate of uric acid Gout • A disease caused by an excess of uric acid • Deposition of sodium urate (or uric acid) crystals – Painful arthritic joint inflammation – Kidney stones • Impaired uric acid excretion or other metabolic insuffiencies (e.g. HGPRT deficiency in Lesch-Nyhan syndrome) • Allopurinol, a xanthine oxidase inhibitor alleviates the symptoms of gout by decreasing the rate of uric acid production Catabolism of pyrimidines Biosynthesis of NAD+ and NADP+ Biosynthesis of FMN and FAD Biosynthesis of coenzyme A ...
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This note was uploaded on 10/16/2010 for the course CHEM 60280 taught by Professor Ryu during the Spring '09 term at TCU.

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