12.12.08: Nucleotide Metabolism
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Slideshow is from the University of Michigan Medical School's M1 Renal sequence

Slideshow is from the University of Michigan Medical School's M1 Renal sequence

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12.12.08: Nucleotide Metabolism Presentation Transcript

  • 1. Author(s): Dr. Robert Lyons, 2009License: Unless otherwise noted, this material is made available under the terms ofthe Creative Commons Attribution – Share Alike 3.0 License: http://creativecommons.org/licenses/by-sa/3.0/We have reviewed this material in accordance with U.S. Copyright Law and have tried to maximize your ability to use,share, and adapt it. The citation key on the following slide provides information about how you may share and adapt thismaterial.Copyright holders of content included in this material should contact open.michigan@umich.edu with any questions,corrections, or clarification regarding the use of content.For more information about how to cite these materials visit http://open.umich.edu/education/about/terms-of-use.Any medical information in this material is intended to inform and educate and is not a tool for self-diagnosis or areplacement for medical evaluation, advice, diagnosis or treatment by a healthcare professional. Please speak to yourphysician if you have questions about your medical condition.Viewer discretion is advised: Some medical content is graphic and may not be suitable for all viewers.
  • 2. Citation Key for more information see: http://open.umich.edu/wiki/CitationPolicyUse + Share + Adapt { Content the copyright holder, author, or law permits you to use, share and adapt. } Public Domain – Government: Works that are produced by the U.S. Government. (17 USC §105) Public Domain – Expired: Works that are no longer protected due to an expired copyright term. Public Domain – Self Dedicated: Works that a copyright holder has dedicated to the public domain. Creative Commons – Zero Waiver Creative Commons – Attribution License Creative Commons – Attribution Share Alike License Creative Commons – Attribution Noncommercial License Creative Commons – Attribution Noncommercial Share Alike License GNU – Free Documentation LicenseMake Your Own Assessment { Content Open.Michigan believes can be used, shared, and adapted because it is ineligible for copyright. } Public Domain – Ineligible: Works that are ineligible for copyright protection in the U.S. (17 USC § 102(b)) *laws in your jurisdiction may differ{ Content Open.Michigan has used under a Fair Use determination. } Fair Use: Use of works that is determined to be Fair consistent with the U.S. Copyright Act. (17 USC § 107) *laws in your jurisdiction may differ Our determination DOES NOT mean that all uses of this 3rd-party content are Fair Uses and we DO NOT guarantee that your use of the content is Fair. To use this content you should do your own independent analysis to determine whether or not your use will be Fair.
  • 3. M1 Renal: Nucleotide Metabolism Dr. Robert Lyons Assistant Professor, Biological Chemistry Director, DNA Sequencing Core Web: http://seqcore.brcf.med.umich.edu/mcb500 Fall 2008
  • 4. Amino Acid metabolism Folate metabolism Amino acids Met Methylene Cycle Glu, Gln, THF Asp, NH 3 Urea oxaloacetate DNA P u rin e s P y rim id in e s RNA Uric Acid (energy) fumarate TCA Cycle Nucleic Acid metabolismR. Lyons
  • 5. Nucleic Acid metabolism Click on any blue rectangle to see details. am i n o a c id s , Carbamoyl fo la t e Phosphate PRPP PurineSalvage Purine Pyrimidine OMP IM P Biosynthesis Biosynthesis Pyrimidine Salvage P u r in e M P P y r im id in e M P Ribonucleotide Ribonucleotide reductase reductase dNTP DNA dNTP NTP RNA NTP Purine Pyrimidine Degradation Degradation NH4 U ric A cid ( e n e rg y ) R. Lyons
  • 6. Formation of PRPP: Phosphoribose pyrophosphate O O PO P O OH O P O P OH OH OH OH ATP AMP ribose - 5 - phosphate phosphoribose - 1 R. Lyons pyrophosphate PRPP Use in Purine Biosynthesis: H2 O O O NH2PO P O O PO P OH OH glutamine glutamate OH OH phosphoribose - 1 pyrophosphate R. Lyons
  • 7. O N HN The First Purine: Inosine Monophosphate N N (folates are involved in this synthesis) O P O OH OH R. LyonsConversion to Adenosine: O NH 2 GTP GDP + Pi N N HN N N N N N aspartate fumarate ribose-5-P ribose-5-P Inosine monophosphate Adenosine monophosphate R. LyonsConversion to Guanosine: H2O + + O O O NAD NADH + H ATP AMP + PPi N N N HN N HN N N O N N NH N N H 2 gln glu ribose-5-P ribose-5-P ribose-5-P Inosine monophosphate Xanthosine monophosphate Guanosine monophosphate R. Lyons
  • 8. Nucleoside Monophosphate Kinases AMP + ATP <--> 2ADP (adenylate kinase) GMP + ATP <---> GDP + ADP (guanylate kinase) • similar enzymes specific for each nucleotide • no specificity for ribonucleotide vs. deoxyribonucleotide
  • 9. Ribonucleotide Reductase X O P OP O Enzyme• NADH OH OH X O P OP O Enzyme NAD+ OH H R. LyonsHydroxyurea inhibits this enzyme: chemotherapeutic use O HONH C NH 2
  • 10. Regulation of Ribonucleotide Reductase ATP CDP + dCDP dCTP (-) ATP UDP + dUDP dTTP (-) GDP + dGDP dGTP ADP + dADP dATP (-)R. Lyons
  • 11. Nucleoside Diphosphate Kinase N1DP + N2TP <--> N1TP + N2DP dN1DP + N2TP <--> dN1TP + N2DP • No specificity for base • No specificity for ribo vs deoxy
  • 12. Feed-forward regulation by PRPP PRPP IMP ATP GTP GMP AMP GTP ATPR. Lyons
  • 13. Feed-forward regulation by PRPP PRPP + IMP ATP GTP GMP AMP GTP ATPR. Lyons
  • 14. Feed-forward regulation by PRPP PRPP IMP ATP GTP + + GMP AMP GTP ATPR. Lyons
  • 15. Feed-forward regulation by PRPP PRPP + - - IMP - - ATP GTP GMP AMP GTP ATPR. Lyons
  • 16. Degradation of the Purine Nucleosides: + NH 2 HO NH O Pi ribose - 1 - P O 2 4 N N N N HN HN Adenosine purine nucleoside N N N N N N deaminase phosphorylase H ribose (ADA) ribose Adenosine Inosine Hypoxanthine xanthine oxidase Pi ribose - 1 - P O + O O H 2O NH 4 N N HN N HN HN N purine nucleoside NH Guanine O N N NH 2 N N N H H phosphorylase 2 H deaminase ribose Xanthine Guanosine Guanine xanthine oxidase O H N HN Uric acid O O N N H HR. Lyons
  • 17. Salvage Pathways for Purine Nucleotides O N O HN Hypoxanthine- N N N guanine HN H Hypoxanthine phosphoribosyl N N transferase + + PPi O P O OP O O P O P OH OH OH OH Inosine monophosphate PRPP R. Lyons APRT - Adenine phosphoribosyl transferase - performs a similar function with adenine.
  • 18. Adenosine Deaminase Deficiency: NH 2 N O O N N N HN HN N N N N N N HO O Adenosine H deaminase 2-deoxyribose (ADA) Hypoxanthine Deoxyinosine OH H Deoxyadenosine Guanine Xanthine dAMP dADP Uric acid dATPR. Lyons
  • 19. OHN N Gout: deposition of urate crystals in joints, N N tophi in cooler periphery H Hypoxanthine xanthine Hyperuricemia can be caused by: oxidase O Accelerated degradation of purines: HN N O N H N H •Accelerated synthesis of purines Xanthine •Increased dietary intake of purines xanthine oxidase Impaired renal clearance of uric acid O H N OHHN H O N NO N H N H Allopurinol inhibits xanthine oxidase N N Uric acid and reduces blood uric acid levels: Allopurinol R. Lyons R. Lyons
  • 20. An 80-year-old man with a 30-year history of gout, this patient had been treated intermittently to reduce his serum urate levels. The New England Journal of Medicine
  • 21. Lesch-Nyhan Syndrome: Defective HGPRT • hyperuricemia • spasticity • mental retardation • self-mutilation behavior O N O HN Hypoxanthine- N N N guanine HN H Hypoxanthine phosphoribosyl N N transferase + + PPi O P O O P O O P O P OH OH OH OH Inosine monophosphate PRPP R. LyonsA defect in APRT does NOT have similar consequences
  • 22. Myoadenylate Deaminase Fills the TCA Cycle in Muscle H 2O NH 3 myoadenylate deaminase NH 2 O N N N HN N N N N ribose-5-P ribose-5-P Adenosine monophosphate Inosine monophosphate Asp, GTP Fumarate GDP + Pi To TCA Cycle R. Lyons
  • 23. Carbamoyl phosphate synthetase II - a cytoplasmic enzyme… O - 2- 2ATP + HCO3 + + glutamate + 2ADP + Pi NH2 C OP glutamine + H 2O carbamoyl phosphate R. Lyons …used for pyrimidine synthesis O O - O O NH2 - O C C CH2 NH2 CH2 HN C 2- + O OP CH C CH O - - N CO2 NH3 CO2 O N CO2 H + carbamoyl H phosphate aspartate orotate R. Lyons
  • 24. Orotate is linked to PRPP to form Uridine monophosphate: O HN O O O N CO2 H HN HN orotate O N CO2 O N + O P O O P O OP O CO2 O P OP OH OH OH OH OH OH orotidine uridine phosphoribose - 1 monophosphate monophosphate pyrophosphateR. Lyons
  • 25. Newly-synthesized uridine monophosphate will be phosphorylated to UDP and UTP, as described for the purine nucleotides. UTP can be converted to CTP by CTP Synthetase: O NH 2 HN N O N gln glu O N O O P OP O P O P OP O P O OH OH ATP ADP OH OH + + uridine H 2O Pi cytidine triphosphate triphosphateR. Lyons
  • 26. Some UDP is converted to dUDP via ribonucleotide reductase. UDP dUDP dUTP dUMP ribo- nucleotide reductase ATP ADP H 2O Pi R. LyonsThe Thymidylate Synthase Reaction: O O HN HN CH3 O N O N O O P O P O thymidylate synthase OH H OH H deoxyuridine 5 10 deoxythymidine monophosphate N ,N methylene monophosphate dihydrofolate tetrahydrofolate DHFR NADH **** methylene THF NAD+ donor R. Lyons
  • 27. Methotrexate Inhibits Dihydrofolate Reductase: O O HN HN CH3 O N O N O OP O P O thymidylate synthase OH H OH H deoxyuridine deoxythymidine monophosphate N 5, N10 methylene monophosphate dihydrofolate tetrahydrofolate DHFR NADH **** X Methotrexate methylene THF donor NAD+ R. LyonsDihydrofolate builds up, levels of THF become limiting,thymidylate synthase is unable to proceed. Follow it with a dose of Leucovorin, a.k.a. formyl-THF.
  • 28. FdUMP Inhibits The Thymidylate Synthase Reaction: O O HN F HN CH3 O N O N O OP O P O thymidylate synthase OH H X OH H 5-fluorodeoxyuridine deoxythymidine monophosphate N 5, N10 monophosphate (F-dUMP) methylene dihydrofolate tetrahydrofolate DHFR NADH **** methylene THF NAD+ donorR. Lyons
  • 29. Complicated Pathways for Pyrimidine Production: dCTP CTP UTP dUTP dTTP *** dCDP CDP UDP dUDP dTDP *** *** UMP dUMP dTMP ***de-novo synthesis OMP R. LyonsThis figure is primarily a study aid; you do not need to memorize it or reproduce it. The information here merely summarizes material from previous sections.
  • 30. Pathologies of pyrimidine nucleotide biosynthesis: Orotic acidurea due to OTC deficiency - please review your Urea Cycle notes. Hereditary orotic acidurea - deficiency of the enzyme that convert orotate to OMP to UMP. Not common.
  • 31. Pyrimidine degradation: Cytidine deaminase converts cytidine to uridine NH2 O HN O N N O N cytidine HO O deaminase HO O OH OH OH OH Cytidine Uridine R. Lyons A phosphorylase removes the sugar O O HN CH3 O HN N CH3 Pi pyrimidine phosphorylase O N H thymine + HO O HO + O OP OH H (deoxy)thymidine OH H deoxyribose-1-phosphate R. Lyons Degradation of the base proceeds (products are unimportant here)
  • 32. Pyrimidines can be salvaged as well: Enzyme: Pyrimidine nucleoside phosphorylases Thymine + deoxyribose-1-phosphate --> thymidine (NOT thymidine monophosphate!) O O HN CH3 HN CH3 O N pyrimidine H O N Pi phosphorylase thymine + O + HO O OP HO OH H (deoxy)thymidine OH H deoxyribose-1-phosphate R. Lyons Enzyme: Thymidine kinase - adds the monophosphate back Thymidine + ATP --> thymidine monophosphate Herpes Simplex Virus carries its own tk gene
  • 33. Certain drugs act via the pyrimidine salvage pathway: G HSV G HO O thymidine P O O kinase H H H H Acyclovir AcycloGMP R. Lyons O HN F O O HN F O N HN F H pyrimidine O N uridine 5-fluorouracil phosphorylase kinase O N O + HO O O P O HO OP OH H OH H OH H deoxyribose-1-phosphate fluorodeoxyuridine fluorodeoxyuridine monophosphate (FdUMP) R. Lyons
  • 34. 5-FU efficacy depends on rate of degradation vs activation O HN F O O HN F O N HN F H pyrimidine O N uridine 5-fluorouracil phosphorylase kinase O N O + HO O O P O HO OP OH H OH H OH H deoxyribose-1-phosphate fluorodeoxyuridine fluorodeoxyuridine monophosphate (FdUMP) R. Lyons 5-FU --> --> FdUMP + methylene-THF + Thymidylate Synthase --> inactivation of TS Degradation (via dihydropyrimidine dehydrogenase, DPD DPD inhibitors can potentiate 5FU activity
  • 35. Capecitabine mode of action: O CH3 O HN N F O O N cytidine pyrimidine dealkylation deaminase phoshorylase HN F O HO O N H OH OH fluorouracil capecitabine R. Lyons Cytosine arabinoside (araC) activation and inactivation: O NH2 NH2 HN N N O N cytidine O N cytidine O N O deaminase O kinase HO O OH HO P O OH OH OH OH OH Uridine arabinoside Cytosine arabinoside (araC) Cytosine arabinoside monophosphate (INACTIVE) (ACTIVE) R. Lyons
  • 36. Additional Source Information for more information see: http://open.umich.edu/wiki/CitationPolicySlide 4: Robert LyonsSlide 5: Robert LyonsSlide 6: Robert LyonsSlide 7: Robert LyonsSlide 9: Robert LyonsSlide 10: Robert LyonsSlide 12: Robert LyonsSlide 13: Robert LyonsSlide 14: Robert LyonsSlide 15: Robert LyonsSlide 16: Robert LyonsSlide 17: Robert LyonsSlide 18: Robert LyonsSlide 19: Robert LyonsSlide 20: The New England Journal of Medicine, http://content.nejm.org/cgi/content/full/353/23/e20Slide 21: Robert LyonsSlide 22: Robert LyonsSlide 24: Robert LyonsSlide 25: Robert LyonsSlide 26: Robert LyonsSlide 27: Robert LyonsSlide 28: Robert LyonsSlide 30: Robert LyonsSlide 32: Robert LyonsSlide 33: Robert LyonsSlide 34: Robert LyonsSlide 35: Robert LyonsSlide 36: Robert Lyons