Chris Meta

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Proposed mechanisms for the enzyme orotidine
5-monophosphate decarboxylase
Chris Meta
Chem 2810 Prof. Rob Coalson
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Orotidine 5-monophosphate decarboxylase
Catalyzes conversion of orotidine
5-monophosphate (OMP) to uridine
5-monophosphate (UMP)
Final step in de novo pyrimidine nucleotide
biosynthesis
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Introduction to UDCase
Without UDCase, OMP is coverted to UMP over a
period of 78 million years The enzyme enhaces
the rate of decarboxylation by a factor of
1.4x1017
ODCase with OMP in active site
Enzymes lower the activation barrier for a
reaction and exhibit a high degree of
discrimination between substrates in the ground
state and in the altered for present in the
transition state, binding the latter species very
tightly
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Interesting Facets of UDCase
Most decarboxylases stabilize the carbanion
intermediate by delocalizing the negative charge
into an electrophilic pi system of the substrate
or a covalently attached cofactor
ODCase contains no cofactors and the reaction
intermediate is a nonconjugated carbanion ODCase
also lacks any transition metals that could play
a role in the decarboxylation
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Proposed mechanisms of the decarboxylation
Although the enzyme has been studied for multiple
years, a mechanism can not be determined that is
supported by enough experimental data
Mechanisms have been proposed, each with
supporting and opposing evidence - Beak Siegal
proposed a mechanism involving formation of a
zwitterion (1976, J. Am. Chem. Soc. 98,
3601-3606) - Silverman Groziak proposed a
mechanism involving nucleophilic addition by
the enzyme (1982, J. Am. Chem. Soc. 104,
6434-6439) - Lee Houk used quantum mechanical
calculations for their mechanism (1997,
Science, 276, 942-945)
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Beak Siegal Mechanism
Mechanism occurs via a non-covalent zwitterion
Reverse reaction has never been observed
Supported by Levine et al. (1980) from study that
showed BMP inhibits the enzyme activity at
remarkably low concentrations and by comparison
of the structure of BMP to the transition state
of the ODCase reaction
Levine, H.L. Brody, R.S. Westheimer, F.H.
(1980) Biochemistry, 19, 4993-4999.
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Silverman Groziak Mechanism
Mechanism was proposed after using model studies
Acheson et al. provided evidence against this
mechanism from experiments showing no significant
secondary hydrogen isotope effects
Acheson, S.A., Bell, J.B., Jones, M.E.
Wolfenden, R. (1990) Biochemistry, 29, 3198-3202.
Studies of kinetic isotope effects and substrate
analogues provide strong arguments against the
mechanism involving nucleophilic attack
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Lee Houk
Mechanism based on quantum mechanical calculations
Proton transfer to the more basic oxygen
concerted with a loss of carbon dioxide would
give product
Lee, J.K. and Houk, K.N. (1997) Science, 276,
942-945
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Conclusion
All of the mechanisms have strengths and
weaknesses, although none stands out above the
rest Understanding the mechanism is important
for understanding how enzymes work, which would
help scientists in understanding how to treat
problems involving the enzyme Further studies
and experiments are necessary to clarify which
mechanism is being carried out in the
decarboxylation process
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References
Wu, Weiming, et al. Biochemistry, 2000, 39,
1778-1783 Wolfenden, Richard and Anna Radzicka,
Science, 267, 6 January 1995, 90-94 Jones, Mary
Ellen, et al. Biochemistry, 1991, 30, 6216-6223
All graphics have reference site in subscript