NUCLEOTIDE METABOLISM

Purine Nucleotide de novo synthesis

Substrate Product Enzyme / Coenzyme Atoms added Regulation Notes
+ = Pi, ADP, AMP, GMP, IMP, 2,3- Ribose5P from HMP or Ribose1P from
5’-phosphoribosyl-1-
Ribose-5-P + ATP PRPP synthetase bipshophoglycerate nucleoside degradation
pyrophosphate (PRPP) + AMP
- = purine nucleoside di- & triPO4 PRPP α anomer
- = allosteric for IMP/GMP& AMP β5PRA β anomer
Β 5-phosphoribosyl amine
PRPP + Glu Amidophosphoribosyl transferase (APPT) By Glu, PRPP rate limiting / committed / most
(β5PRA)
regulated. irreversible
IMP Synthesis
β5PRA + Gly Glycinamide ribotide (GAR) GAR synthetase C4, C5, N7 Reversible
GAR FGAR GAR transformylase
FGAR FGAM FGAM synthase
FGAM + ATP AIR + ADP + Pi AIR synthetase
AIR + ATP + HCO3- CAIR AIR carboxylase (AIRCX) C6 No biotin required
GAIR + Asp SAICAR SAICAR synthetase
SAICAR AICAR + Fum Adenylosuccinate lyase (ASL)
AICAR + N10 formyl THF FAICAR AICAR transformylase
FAICAR IMP IMP cyclohydrolase / synthase (IMPCH / IMPS) C2, C8 multistep IMP synthesis, uses 6 ATP
AMP Synthesis
IMP + GTP + Asp Adenylosuccinate + GDP + Pi Adenylosuccinate synthetase (ASS) - = AMP, 6-mercaptopurine
Adenylosuccinate AMP + Fum Adenylosuccino lyase
GMP Synthesis
Xanthosine monophosphate - = GMP, 6-mercaptopurine,
IMP + NAD IMP DH
(XMP) + NADH+H tiazopurine
XMP + Glu + ATP GMP + Gln + AMP + PPi GMP synthetase
Salvage Pathways
Hypoxanthine + PRPP IMP + PPi Hypoxanthine-guanine
Guanine + PRPP GMP + PPi phosphoribosyltransferase (HGPRT)
Adenosyl transferase / Adenine
Adenine + PRPP AMP + PPi
phosphoribosyltransferase (APRT)
adenosine AMP
Adenosine kinase
d-adenosine dAMP
Deoxycytidine dCMP
D-adenosine dAMP Deoxycytidine kinase
2’d-guanosine dGMP

AMP IMP
IMP / GMP Inosine / guanosine 5’-nucleotidase
Inosine / guanosine Hypoxanthine / guanine Purine nucleoside phosphorylase
Guanine Xanthine
Hypoxanthine Xanthine Xanthine oxidase - = allopurinol Has molybdenum, Fe, sulfur,
Xanthine Uric acid Xanthine oxidase Final degradation product
• Enzyme protein complexes: (1) GAR synthetase + GAR transformylase + AIR synthetase, (2) AIR CX + SAICAR synthetase, (3) AICAR transformylase, IMP CH
Pyrimidine Nucleotide de novo synthesis
Substrate Product Enzyme / Coenzyme Atoms added Regulation Notes
Carbamoyl phosphate synthase II (CPS II) N3, C2 + = ATP Most regulated step
Glu + HCO3- + 2 ATP Carbamoyl phosphate + Gln + 2 ADP + 2 Pi
- = UTP, CTP
Aspartate transcabamylase (ATCase) N1, C4, C5, Rate limiting step
Carbamoyl PO4 + Asp Carbamoyl aspartate
C6
Carbamoyl aspartate Dihydroorotate (DHO) Dihydroorotase (DHOase) 1st ring ?
DHO + Ubiquinone Orotate (Oro) + QH2 DHO DH mitochondrial
Oro phosphoribosyltransferase (OPRT) + = ATP
Oro + PRPP OMP + PPi
- = UMP, CMP
OMP UMP + CO2 OMP DX - = UMP, CMP
UMP + ATP UDP + ADP Nucleoside monoPO4 kinase / UMP kinase
UDP + ATP UTP + ADP Nucleoside diPO4 kinase
UTP + Glu + ATP CTP + Gln + ADP + Pi CTP synthetase - = CTP
Salvage Pathways
Pyrimidine + PRPP Pyrimidine nucleoside monoPO4 + PPi Pyrimidine phosphoribosyltransferase
Uracil + Ribose1P Uridine + Pi Uridine phosphorylase
Uridine + ATP UMP + ADP Uridine kinase
Deoxycytidine + ATP dCMP + ADP Deoxycytidine kinase
Thymidine + ATP TMP + ADP Thymidine kinase
U UMP
U-C kinase
C CMP
T dTMP T kinase
dC dCMP dC kinase
Degradation
Uracil β-alanine Acetyl CoA precursor
Thymine β-aminoisobutyrate Succinyl CoA precursor
• Enzyme protein complexes: (1) CPS II + ATCase + DHOase, (2) OPRT + OMP DX

Comparison
Purine Pyrimidine
Sequence Sugar Ring Ring  Sugar
Sources N1 – Asp; C2, 8 – Formate; N3, 9 – Glu; C4, 5, N7 – Gly; C6 – CO2 N1, C4-6 – Asp; C2 – CO2; N3 – Glu
Committed Step PRPP amidotransferase / APPT ATCase (CPS II = most regulated)
Location cytosol Mitochondria, cytosol
Enzyme Organization Individual and 3 multifunctional Individual and 2 multifunctional
Regulation IMP/AMP/GMP (Product feedback inhibition) UTP - to CPS

Deoxyribonucleotide Synthesis
Substrate Product Enzyme / Coenzyme Regulation Notes
Ribonucleoside DP + thioredoxinH2 deoxyibonucleoside DP + thioredoxin Ribonucleoside reductase - = hydroxyurea Multisubunit enzyme, converts diphosphates into deoxy-forms
Thioredoxin + NADP thioredoxinH2 + NADPH+H Regenerates reduced thioredoxin
TMP Synthesis
dUMP + N5, N10-methylene Thymidelate synthetase / N5, N10-
dTMP + dihydrofolate - = 5-fluorouracil Contribution of carbon and 2 hydrogen atoms
tetrahydrofolate methylene tetrahydrofolate
dihydrofolate tetrahydrofolate DHF reductase - = methotrexate Regenerates reduced thioredoxin
Salvage Pathways
Thymine + deoxyribose-1P Thymidine + Pi Thymine phosphorylase
Thymidine + ATP dTMP + ADP Thymine kinase
Degradation
Step Substrate Product Enzyme Notes
Nucleotidases Remove 5’PO4 = -tides to –sides
Hydrolysis AMP / dAMP Adenosine / deoxyadenosine Generally, removes PO4
Deamination Adenosine / deoxyadenosine Inosine / deoxyinosine Adenosine deaminase (ADA) adenosine  inosine, cytidine  uridine
Inosine + Pi Hypoxanthine + Ribose1P
Guanosine + Pi Guanine + Ribose1P
Phosphorylation Nucleoside phosphorylases Nucleoside + Pi  free bases + ribose1P, reversible
Uridine + Pi Uracil + Ribose1P
Thymidine + Pi Thymine + Ribose1P

Inhibitors
Category Drug
Antimetabolites 6-mercaptopurine, 5-fluorouracil, cytosine arabinoside, 6-thioguanine, azathioprine, allopurinol
Antuifolates Methotraxate, aminpterin, trimethoprim
Glutamine Antagonists 6-diazo-5-oxo-L-norleucine (DON), diacetyl-L-serine (azaserine)
Cell Growth Hydroxyurea, tiazopurine
Pur/Pyr analogs Acycloguanosine (HSV DNA polymerase), azidothymidine (HIV DNA polymerase)

Diseases
• Gout
o Precipitation of sodium urate in joints and kidneys due to exceeding serum urate solubility, inflammation and erosion of joints when WBC engulf crystals and rupture
o Abdormal / unresponsive PRPP synthetase to feedback inhibition = ↑ purines
o Partial deficiency of HGPRT = ↑ PRPP = ↑ purines
o Treatment: allopurinol (block urate production) or colchicines – anti-inflammatory, inhibits leukocyte movement
• Lesch-Nyhan syndrome
o Hereditary X-linked recessive, deficiency of HGPRT (inactive or unstable) = ↑ purine synthesis
o Hyperuricemia, gout, urinary tract stones, neurologic symptoms
o Treament: allopurinol (↓ urate production)
• Von Gierke’s disease
o G6PD deficiency --. ↑ Ribose phosphates = ↑ PRPP = ↑ purine synthesis
• Immunodeficiency disorders
o ADA deficiency
 ↑ deoxyadenosine and adenosine = ↑ dATP = ↓ ribonucleotide reductase = ↓ DNA synthesis = ↓ lymphocytes
 Lymphocyte defect, severe combined immunodeficiency = recurrent, chronic infections, fatal by 18 mo.
 Treatment: bone marrow transplant, enzyme replacement, gene therapy
o Purine nucleoside phosphorylase deficiency
 ↑ dGTP = ↓ ribonucleotide reductase to a lesser degree
 T-cell impairment = recurrent / chronic infections
 Treament: prevent exposure to diseases