Orotidine 5'-phosphate decarboxylase

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Orotidine-5'-phosphate decarboxylase

E. coli OMP decarboxylase.[1]

Identifiers

EC number 4.1.1.23

CAS number 9024-62-8

Databases

IntEnz IntEnz view

BRENDA BRENDA entry

ExPASy NiceZyme view

KEGG KEGG entry

MetaCyc metabolic pathway

PRIAM profile
 PDB structures RCSB PDB PDBe PDBsum

Gene Ontology AmiGO / QuickGO

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Orotidine 5'-phosphate decarboxylase (OMP decarboxylase) or orotidylate decarboxylase is

an enzyme involved in pyrimidine biosynthesis. It catalyzes the decarboxylation of orotidine
monophosphate (OMP) to form uridine monophosphate (UMP). The function of this enzyme is
essential to the de novo biosynthesis of the pyrimidine nucleotides uridine triphosphate, cytidine
triphosphate, and thymidine triphosphate. OMP decarboxylase has been a frequent target for
scientific investigation because of its demonstrated extreme catalytic efficiency and its usefulness as
a selection marker for yeast strain engineering.

Schematic of reaction catalyzed by OMP decarboxylase

Contents

 1Catalysis
 2Vs UMP synthase
 3Importance in yeast genetics
 4See also
 5References

Catalysis[edit]
OMP decarboxylase is known for being an extraordinarily efficient catalyst capable of accelerating
the uncatalyzed reaction rate by a factor of 1017. To put this in perspective, a reaction that would
take 78 million years in the absence of the orotic acid enzyme takes 18 milliseconds when it is
enzyme catalyzed.[2] This extreme enzymatic efficiency is especially interesting because OMP
decarboxylases uses no cofactor and contains no metal sites[3] or prosthetic groups.[4] The catalysis
relies on a handful of charged amino acid residues positioned within the active site of the enzyme.
Image representing the structure of the active site of OMP decarboxylase when bound to the inhibitor BMP.
Note the Lys and Asp residues surrounding the 6-hydroxyl of the substrate. (Image captured from pymol viewer
snapshot of 1LOR crystal structure)[5]

The exact mechanism by which OMP decarboxylase catalyzes its reaction has been a subject of
rigorous scientific investigation. The driving force for the loss of the carboxyl linked to the C6 of the
pyrimidine ring comes from the close proximity of an aspartate residue carboxyl group in the
enzyme's active site, which destabilizes the ground state relative to the transition state of the
uncatalyzed reaction. There have been multiple hypotheses about what form the transition state
takes before protonation of the C6 carbon occurs to yield the final product. Many studies
investigated the binding of a potent inhibitor of OMP decarboxylase, 6-hydroxy uridine
monophosphate (BMP, a barbituric acid derivative), within the active site, to identify which essential
amino acid residues are directly involved with stabilization of the transition state. (See figure of
enzyme bound to BMP) Several mechanisms for enzymatic decarboxylation of OMP have been
proposed, including protonation at O2 to form a zwitterionic species as an intermediate,[6] anion
stabilization of O4,[7] or nucleophilic attack at C5.[8] Current consensus suggests that the mechanism
proceeds through a stabilized carbanion at the C6 after loss of carbon dioxide. This mechanism was
suggested from studies investigating kinetic isotope effects in conjunction with competitive inhibition
and active site mutagenesis.[9][10][11][12] In this mechanism the short-lived carbanion species is stabilized
by a nearby lysine residue, before it is quenched by a proton. (See schematic of catalytic
mechanism) The intermediacy of a highly basic vinyl carbanion not benefiting from electronic
stabilization is rare in an enzymatic system and in biological systems in general. Remarkably, the
enzyme microenvironment helps stabilize the carbanion considerably. The pKaH of the enzyme-
bound carbanionic intermediate was measured to be less than or equal to 22 based on deuterium
exchange studies. While still highly basic, the corresponding pKaH of the free carbanionic
intermediate is estimated to be much higher, around 30-34 (based on measurements on the
analogous 1,3-dimethyluracil), leading to the conclusion that the enzyme stabilizes the carbanion by
at least 14 kcal/mol.[12]
Reaction schematic showing the mechanism of OMP decarboxylase catalysis through a putative vinyl
carbanion at the C6 position. This carbanion is likely stabilized by the nearby protonated lysine residue. The
Lys93 and Asp91 residue numbering corresponds to the sequence for OMP decarboxylase from S
cerevisiae.[13]

Vs UMP synthase