Orotidine 5'-phosphate decarboxylase

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

Orotidine-5'-phosphate decarboxylase
E. coli OMP decarboxylase.[1]
Identifiers
EC no.	4.1.1.23
CAS no.	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
Search PMC articles PubMed articles NCBI proteins

Catalysis

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, the uncatalysed reaction which would take 78 million years to convert half the reactants into products is accelerated to 18 milliseconds when catalyzed by OMP decarboxylase.^[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 pK_aH 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 pK_aH 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]

Relation to UMP synthase

In yeast and bacteria, OMP decarboxylase is a single-function enzyme. However, in mammals, OMP decarboxylase is part of a single protein with two catalytic activities. This bifunctional enzyme is named UMP synthase and it also catalyzes the preceding reaction in pyrimidine nucleotide biosynthesis, the transfer of ribose 5-phosphate from 5-phosphoribosyl-1-pyrophosphate to orotate to form OMP. In organisms utilizing OMP decarboxylase, this reaction is catalyzed by orotate phosphoribosyltransferase.^[14]

Importance in yeast genetics

Mutations in the gene encoding OMP decarboxylase in yeast (URA3) leads to auxotrophy in uracil. In addition, a function OMP decarboxylase renders yeast strains sensitive to the molecule 5-fluoroorotic acid (5-FOA).^[15] The establishment of the URA3 gene as a selection marker with both positive and negative selection strategies has made the controlled expression of OMP decarboxylase a significant laboratory tool for the investigation of yeast genetics.

See also

• Circe effect

References

1. PDB: 1EIX​; Harris P, Navarro Poulsen JC, Jensen KF, Larsen S (April 2000). "Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase". Biochemistry. 39 (15): 4217–24. doi:10.1021/bi992952r. PMID 10757968.
2. Radzicka A, Wolfenden R (January 1995). "A proficient enzyme". Science. 267 (5194): 90–3. doi:10.1126/science.7809611. PMID 7809611.
3. Miller BG, Smiley JA, Short SA, Wolfenden R (August 1999). "Activity of yeast orotidine-5'-phosphate decarboxylase in the absence of metals". J. Biol. Chem. 274 (34): 23841–3. doi:10.1074/jbc.274.34.23841. PMID 10446147.
4. Miller BG, Wolfenden R (2002). "Catalytic proficiency: the unusual case of OMP decarboxylase". Annu. Rev. Biochem. 71: 847–85. doi:10.1146/annurev.biochem.71.110601.135446. PMID 12045113.
5. Wu N, Pai EF (August 2002). "Crystal structures of inhibitor complexes reveal an alternate binding mode in orotidine-5'-monophosphate decarboxylase". J. Biol. Chem. 277 (31): 28080–7. doi:10.1074/jbc.M202362200. PMID 12011084.
6. Beak P, Siegel B (1976). "Mechanism of decarboxylation of 1,3-dimethylorotic acid. A model for orotidine 5'-phosphate decarboxylase". J Am Chem Soc. 98 (12): 3601–6. doi:10.1021/ja00428a035. PMID 1270703.
7. Lee JK, Houk KN (May 1997). "A proficient enzyme revisited: the predicted mechanism for orotidine monophosphate decarboxylase". Science. 276 (5314): 942–5. doi:10.1126/science.276.5314.942. PMID 9139656.
8. Silverman, R.B.; Groziak, M.P. (1982). "Model Chemistry for a Covalent Mechanism of Action of Orotidine 5'-Phosphate Decarboxylase". J. Am. Chem. Soc. 104 (23): 6434–6439. doi:10.1021/ja00387a047.
9. Lee, Jeehiun K; Tantillo, Dean J (2004-06-25). Orotidine Monophosphate Decarboxylase: A Mechanistic Dialogue. ISBN 9783540205661.
10. Richavy MA, Cleland WW (2000). "Determination of the Mechanism of Orotidine 5'-Monophosphate Decarboxylase by Isotope Effects". Biochemistry. 39 (16): 4569–4574. doi:10.1021/bi000376p. PMID 10769111.
11. Toth K, Amyes TL, Wood BM, Chan K, Gerlt JA, Richard JP (October 2007). "Product Deuterium Isotope Effect for Orotidine 5'-Monophosphate Decarboxylase: Evidence for the Existence of a Short-Lived Carbanion Intermediate". J. Am. Chem. Soc. 129 (43): 12946–7. doi:10.1021/ja076222f. PMC 2483675. PMID 17918849.
12. Amyes TL, Wood BM, Chan K, Gerlt JA, Richard JP (February 2008). "Formation and Stability of a Vinyl Carbanion at the Active Site of Orotidine 5′-Monophosphate Decarboxylase: pKa of the C-6 Proton of Enzyme-Bound UMP". J. Am. Chem. Soc. 130 (5): 1574–5. doi:10.1021/ja710384t. PMC 2652670. PMID 18186641.
13. Van Vleet JL, Reinhardt LA, Miller BG, Sievers A, Cleland WW (January 2008). "Carbon isotope effect study on orotidine 5'-monophosphate decarboxylase: support for an anionic intermediate". Biochemistry. 47 (2): 798–803. doi:10.1021/bi701664n. PMID 18081312.
14. Yablonski MJ, Pasek DA, Han BD, Jones ME, Traut TW (1996). "Intrinsic activity and stability of bifunctional human UMP synthase and its two separate catalytic domains, orotate phosphoribosyltransferase and orotidine-5'-phosphate decarboxylase". J Biol Chem. 271 (18): 10704–10708. doi:10.1074/jbc.271.18.10704. PMID 8631878.
15. Boeke JD, LaCroute F, Fink GR (1984). "A positive selection for mutants lacking orotidine-5'-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance". Mol Gen Genet. 197 (2): 345–346. doi:10.1007/BF00330984. PMID 6394957.