A proficient enzyme.
@article{Radzicka1995APE, title={A proficient enzyme.}, author={Anna Radzicka and Richard Wolfenden}, journal={Science}, year={1995}, volume={267 5194}, pages={ 90-3 } }
Orotic acid is decarboxylated with a half-time (t1/2) of 78 million years in neutral aqueous solution at room temperature, as indicated by reactions in quartz tubes at elevated temperatures. Spontaneous hydrolysis of phosphodiester bonds, such as those present in the backbone of DNA, proceeds even more slowly at high temperatures, but the heat of activation is less positive, so that dimethyl phosphate is hydrolyzed with a t1/2 of 130,000 years in neutral solution at room temperature. These…
648 Citations
Catalytic proficiency: the unusual case of OMP decarboxylase.
- Biology, ChemistryAnnual review of biochemistry
- 2002
Several mechanisms of transition state stabilization are considered in terms of ODCase crystal structures observed in the presence and absence of bound analogs of the substrate, transition state, and product.
Uroporphyrinogen decarboxylation as a benchmark for the catalytic proficiency of enzymes
- Chemistry, BiologyProceedings of the National Academy of Sciences
- 2008
It is proposed that a protonated basic residue furnishes a counterion that helps the scissile carboxylate group of the substrate leave water and enter a relatively nonpolar environment, stabilizes the incipient carbanion generated by the departure of CO2, and supplies the proton that takes its place.
Benchmark reaction rates, the stability of biological molecules in water, and the evolution of catalytic power in enzymes.
- Chemistry, BiologyAnnual review of biochemistry
- 2011
By reducing the time required for early chemical evolution in a warm environment, these findings counter the view that not enough time has passed for terrestrial life to have evolved to its present level of complexity.
Insight into the catalytic mechanism of orotidine 5'-phosphate decarboxylase from crystallography and mutagenesis
- Biology, Chemistry
- 2004
Current proposals for the mechanism of enzymatic decarboxylation are discussed in light of recent computational, structural, and mutagenesis studies.
Catalysis by enzyme conformational change as illustrated by orotidine 5'-monophosphate decarboxylase.
- Chemistry, BiologyCurrent opinion in structural biology
- 2003
Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog.
- Chemistry, BiologyProceedings of the National Academy of Sciences of the United States of America
- 2000
Interactions between the enzyme and the phosphoribosyl group anchor the pyrimidine within the active site, helping to explain the phosphorus group's remarkably large contribution to catalysis despite its distance from the site of decarboxylation.
The Depth of Chemical Time and the Power of Enzymes as
- Biology, Chemistry
- 2001
Thermodynamic comparisons between spontaneous and enzyme-catalyzed reactions, coupled with structural information, suggest that in addition to electrostatic and H-bonding interactions, the liberation of water molecules from an enzyme’s active site into bulk solvent sometimes plays a prominent role in determining the relative binding affinities of the altered substrate in the ground state and transition state.
Thermodynamic and extrathermodynamic requirements of enzyme catalysis.
- Chemistry, BiologyBiophysical chemistry
- 2003
A persistent pesticide residue and the unusual catalytic proficiency of a dehalogenating enzyme.
- Biology, ChemistryProceedings of the National Academy of Sciences of the United States of America
- 2005
CaaD achieves an approximately 10(12)-fold rate enhancement, matching or surpassing the rate enhancements produced by many enzymes that act on more conventional biological substrates, including 4-oxalocrotonate tautomerase, with which CaaD seems to share a common evolutionary origin.
Catalysis in Enzymatic Decarboxylations: Comparison of Selected Cofactor-dependent and Cofactor-independent Examples.
- BiologyACS catalysis
- 2013
The enzyme OMPDC has posed a challenge to the enzymologist attempting to explain a 1017-fold rate acceleration in the absence of cofactors or even metal ions, so a comparison of the available evidence on the three types of decarboxylases underlines some common features and more differences.
References
SHOWING 1-10 OF 27 REFERENCES
Transition state stabilization by deaminases: Rates of nonenzymatic hydrolysis of adenosine and cytidine
- Chemistry, Biology
- 1987
Investigation of the enzymatic mechanism of yeast orotidine-5'-monophosphate decarboxylase using 13C kinetic isotope effects.
- Biology, ChemistryBiochemistry
- 1991
Data from ODCase and the pH profile of Vmax/km fit a kinetic model in which an enzyme proton necessary for catalysis is titrated at high pH, thus providing evidence for the catalytic mechanism of Beak and Siegel (1976).
A unique catalytic and inhibitor-binding role for Lys93 of yeast orotidylate decarboxylase.
- Biology, ChemistryBiochemistry
- 1992
The presence of a proton-donating catalytic amino acid side chain in orotidylate decarboxylase (ODCase) was sought by site-directed mutagenesis and Lys93 is apparently critical for catalysis of the substrate to product and for the binding of anionic inhibitors.
Purification and properties of the phosphotriesterase from Pseudomonas diminuta.
- Biology, ChemistryThe Journal of biological chemistry
- 1989
The catalytic mechanism of carbonic anhydrase.
- ChemistryProceedings of the National Academy of Sciences of the United States of America
- 1973
Proposed mechanisms for carbonic anhydrase involving HCO(3) (-) as the substrate in the dehydration reaction and a proton transfer reaction, EH(+) right harpoon over left harpoon E + H(+), as an obligatory step during catalysis obey the rule of microscopic reversibility.
Orotidine-5'-monophosphate decarboxylase catalysis: kinetic isotope effects and the state of hybridization of a bound transition-state analogue.
- Biology, ChemistryBiochemistry
- 1990
No significant change in kcat or kcat/KM was found to result, suggesting that C-5 does not undergo significant changes in geometry before or during the step that determines the rate of the catalytic process, consistent with a nitrogen ylide mechanism.
Purification and characterization of yeast orotidine 5'-monophosphate decarboxylase overexpressed from plasmid PGU2.
- BiologyThe Journal of biological chemistry
- 1991
Transition state analog inhibitors and enzyme catalysis.
- Chemistry, BiologyAnnual review of biophysics and bioengineering
- 1976
It can be shown, on the basis of any rate theory that assumes the existence of an equilibrium of activation, that the substrate in its passage to product acquires a fleeting, but greatly elevated, affinity for the enzyme.
The uncatalyzed rates of enolization of dihydroxyacetone phoshate and of glyceraldehyde 3-phosphate in neutral aqueous solution. The quantitative assessment of the effectiveness of an enzyme catalyst.
- Chemistry, BiologyBiochemistry
- 1975
It is apparent that the enzyme increases the enolization rate of dihydroxyacetone phosphate by a factor of more than 10(9) over that of the uncatalyzed reaction.
Specificity and kinetics of triose phosphate isomerase from chicken muscle.
- Chemistry, BiologyThe Biochemical journal
- 1972
The enzyme-catalysed exchange of the methyl hydrogen atoms of the ;virtual substrate' monohydroxyacetone phosphate with solvent (2)H(2)O or (3)H(-1)O) was shown, and this exchange is about 10(4)-fold slower than the corresponding Exchange of the C-3 hydrogen of dihydroxy acetone phosphate.