Mechanism of the orotidine 5′-monophosphate decarboxylase-catalyzed reaction

Evidence for substrate destabilization

Kui K. Chan, B. McKay Wood, Alexander A. Fedorov, Elena V. Fedorov, Heidi J. Imker, Tina L. Amyes, John P. Richard, Steven C. Almo, John A. Gerlt

Research output: Contribution to journalArticle

44 Citations (Scopus)

Abstract

The reaction catalyzed by orotidine 5′-monophosphate decarboxylase (OMPDC) involves a stabilized anionic intermediate, although the structural basis for the rate acceleration (kcat/knon, 7.1 × 1016) and proficiency [(kcat/KM)/k non, 4.8 × 1022 M-1] is uncertain. That the OMPDCs from Methanothermobacter thermautotrophicus (MtOMPDC) and Saccharomyces cerevisiae (ScOMPDC) catalyze the exchange of H6 of the UMP product with solvent deuterium allows an estimate of a lower limit on the rate acceleration associated with stabilization of the intermediate and its flanking transition states (≥1010). The origin of the "missing" contribution, ≤107 (∼1017 total - ≥10 10), is of interest. Based on structures of liganded complexes, unfavorable electrostatic interactions between the substrate carboxylate group and a proximal Asp (Asp 70 in MtOMPDC and Asp 91 in ScOMPDC) have been proposed to contribute to the catalytic efficiency [Wu, N., Mo, Y., Gao, J., and Pai, E. F. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 2017-2022]. We investigated that hypothesis by structural and functional characterization of the D70N and D70G mutants of MtOMPDC and the D91N mutant of ScOMPDC. The substitutions for Asp 70 in MtOMPDC significantly decrease the value of kcat for decarboxylation of FOMP (a more reactive substrate analogue) but have little effect on the value of kex for exchange of H6 of FUMP with solvent deuterium; the structures of wild-type MtOMPDC and its mutants are superimposable when complexed with 6-azaUMP. In contrast, the D91N mutant of ScOMPDC does not catalyze exchange of H6 of FUMP; the structures of wild-type ScOMPDC and its D91N mutant are not superimposable when complexed with 6-azaUMP, with differences in both the conformation of the active site loop and the orientation of the ligand vis á vis the active site residues. We propose that the differential effects of substitutions for Asp 70 of MtOMPDC on decarboxylation and exchange provide additional evidence for a carbanionic intermediate as well as the involvement of Asp 70 in substrate destabilization.

Original languageEnglish (US)
Pages (from-to)5518-5531
Number of pages14
JournalBiochemistry
Volume48
Issue number24
DOIs
StatePublished - Jun 23 2009

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Decarboxylation
Carboxy-Lyases
Deuterium
Catalytic Domain
Methanobacteriaceae
Uridine Monophosphate
Substitution reactions
Substrates
Viperidae
Static Electricity
Saccharomyces cerevisiae
Ligands
Coulomb interactions
Crystal orientation
Yeast
Conformations
Stabilization
orotidylic acid

ASJC Scopus subject areas

  • Biochemistry

Cite this

Chan, K. K., Wood, B. M., Fedorov, A. A., Fedorov, E. V., Imker, H. J., Amyes, T. L., ... Gerlt, J. A. (2009). Mechanism of the orotidine 5′-monophosphate decarboxylase-catalyzed reaction: Evidence for substrate destabilization. Biochemistry, 48(24), 5518-5531. https://doi.org/10.1021/bi900623r

Mechanism of the orotidine 5′-monophosphate decarboxylase-catalyzed reaction : Evidence for substrate destabilization. / Chan, Kui K.; Wood, B. McKay; Fedorov, Alexander A.; Fedorov, Elena V.; Imker, Heidi J.; Amyes, Tina L.; Richard, John P.; Almo, Steven C.; Gerlt, John A.

In: Biochemistry, Vol. 48, No. 24, 23.06.2009, p. 5518-5531.

Research output: Contribution to journalArticle

Chan, KK, Wood, BM, Fedorov, AA, Fedorov, EV, Imker, HJ, Amyes, TL, Richard, JP, Almo, SC & Gerlt, JA 2009, 'Mechanism of the orotidine 5′-monophosphate decarboxylase-catalyzed reaction: Evidence for substrate destabilization', Biochemistry, vol. 48, no. 24, pp. 5518-5531. https://doi.org/10.1021/bi900623r
Chan, Kui K. ; Wood, B. McKay ; Fedorov, Alexander A. ; Fedorov, Elena V. ; Imker, Heidi J. ; Amyes, Tina L. ; Richard, John P. ; Almo, Steven C. ; Gerlt, John A. / Mechanism of the orotidine 5′-monophosphate decarboxylase-catalyzed reaction : Evidence for substrate destabilization. In: Biochemistry. 2009 ; Vol. 48, No. 24. pp. 5518-5531.
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T2 - Evidence for substrate destabilization

AU - Chan, Kui K.

AU - Wood, B. McKay

AU - Fedorov, Alexander A.

AU - Fedorov, Elena V.

AU - Imker, Heidi J.

AU - Amyes, Tina L.

AU - Richard, John P.

AU - Almo, Steven C.

AU - Gerlt, John A.

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