FCH 532 Lecture 31

Chapter 28: Nucleotide metabolismQuiz on Mon (4/16): IMP synthesis-Purine synthesisQuiz on Wed(4/18): Pyrimidine biosynthesis/regulationQuiz on Friday(4/20): Ribonucleotide reductase

mechanismFriday (4/20): extra credit seminar, Dr. Jimmy Hougland,145 Baker, 3-4PM.ACS exam has been moved to Monday (4/30)Quiz on Final is scheduled for May 4, 12:45PM-2:45PM,

in 111 Marshall

Pag

e 10

77

Pag

e 10

80

Proposed mechanism for rNDP reductase

Proposed reaction mechanism for ribonucleotide reductase

1. Free radical abstracts H from C3’

2. Acid-catalyzed cleavage of the C2’-OH bond

3. Radical mediates stabilizationof the C2’ cation (unshared electron pair)

4. Radical-cation intermediate is reduced by redox-active sulhydryl pair-deoxynucleotide radical

5. 3’ radical reabstracts the H atom from the protein to restore the enzyme to the radical state.

Catabolism of purines• All pathways lead to formation of uric acid.• Intermediates could be intercepted into salvage pathways.• 1st reaction is the nucleotidase and second is catalyzed by purine nucleoside

phosphorylase (PNP)

• Ribose-1-phosphate is isomerized by phosphoribomutase to ribose-5-phosphate (precursor to PRPP).

Purine nucleoside + Pi Purine base + ribose-1-P

• Adenosine and deoxyadenosine are not degraded by PNP but are deaminated by adenosine deaminase (ADA) and AMP deaminase in mammals

Purine nucleoside phosphorylase

Figure 28-23Major pathways of purine catabolism in animals.

Pag

e 10

93

ADA

Genetic defects in ADA kill lymphocytes and result in severe combined immunodeficiencey disese (SCID).

No ADA results in high levels of dATP that inhibit ribonucleotide reductase-no other dNTPs

Figure 28-24a Structure and mechanism of adenosine deaminase. (a) A ribbon diagram of murine

adenosine deaminase in complex with its transition state analog HDPR.

Pag

e 10

94

Figure 28-24b (b) The proposed catalytic mechanism of adenosine deaminase.

Pag

e 10

94

1. Zn2+ polarized H2O molecule nucleophilically attacks C6 of the adenosine. His is general base catalyst, Glu is general acid, and Asp orients water.

2. Results in tetrahedral intermediate which decomposes by elimination of ammonia.

3. Product is inosine in enol form (assumes dominant keto form upon release from enzyme).

Purine nucleotide cycle• Deamination of AMP to IMP combined with synthesis of AMP

from IMP results in deaminating Asp to yield fumarate.• Important role in skeletal muscle-increased activity requires

increased activity in the citric acid cycle.• Muscle replenishes citric acid cycle intermediates through the

purine nucleotide cycle.

Figure 28-25The purine nucleotide cycle.

Pag

e 10

95

Xanthine oxidase• Xanthine oxidse (XO) converts hypoxanthine to xanthine, and xanthine

to uric acid.• In mammals, found in the liver and small intestine mucosa• XO is a homodimer with FAD, two [2Fe-2S] clusters and a molybdopterin

complex (Mo-pt) that cycles between Mol (VI) and Mol (IV) oxidation states.

• Final electron acceptor is O2 which is converted to H2O2

• XO is cleaved into 3 segments. The uncleaved enzyme is known as xanthine dehydrogenase (uses NAD+ as an electron acceptor where XO does not).

• XO hydroxylates hypoxanthine at its C2 position and xanthine at the C8 positon to produce uric acid in the enol form.

Figure 28-26a X-Ray structure of xanthine oxidase from cow’s milk in complex with salicylic acid.

Pag

e 10

95

N-terminal domain is cyan

Central domain is gold

C-terminal domain is lavender

Mechanism for XO1. Reaction initiated by attack of enzyme nucleophile on the C8

position of xanthine.

2. The C8-H atom is eliminated as a hydride ion that combines with Mo (VI) complex, reducing it to Mo (IV).

3. Water displaces the enzyme nucleophile producing uric acid.

Figure 28-27Mechanism of xanthine oxidase.

Pag

e 10

96

Figure 28-23Major pathways of purine catabolism in animals.

Pag

e 10

93

ADA

Genetic defects in ADA kill lymphocytes and result in severe combined immunodeficiencey disese (SCID).

No ADA results in high levels of dATP that inhibit ribonucleotide reductase-no other dNTPs

Purine degredation in other animals

Primates, birds, reptiles, insects-final degradation product id uric acid which is excreted in urine.

Goal is the conservation of water.

Figure 28-29The Gout, a cartoon by James Gilroy (1799).

Pag

e 10

97

Gout is a disease characterized by elevated levels of uric acid in body fluids. Caused by deposition of nearly insoluble crystals of sodium urate or uric acid.

Clinical disorders of purine metabolism

Excessive accumulation of uric acid: Gout

The three defects shown each result in elevated de novo purine biosynthesis

Common treatment for gout: allopurinol

Allopurinol is an analogue of hypoxanthine that strongly inhibits xanthine oxidase. Xanthine and hypoxanthine, which are soluble, are accumulated and excreted.

Catabolism of pyrimidines

• Animal cells degrade pyrimidines to their component bases.• Happen through dephosphorylation, deamination, and

glycosidic bond cleavage.• Uracil and thymine broken down by reduction (vs. oxidation

in purine catabolism).

Pag

e 10

98

Pag

e 10

99

Biosynthesis of of NAD and NADP+

Produced from vitamin precursors Nicotinate and Nicotinamide and from quinolinate, a Trp degradation product

Pag

e 11

00

Biosynthesis of FMN and FAD from riboflavin

FAD is synthesized from riboflavin in a two-reaction pathway.

Flavokinase phosphorylates the 5’OH group to give FMN

FAD pyrophosphorylase catalyzes the next step (coupling of FMN to ADP).

Pag

e 11

01

Biosynthesis of CoA from pantothenate