An examination of the relationship between active site loop size and thermodynamic activation parameters for orotidine 5′-monophosphate decarboxylase from mesophilic and thermophilic organisms

Krisztina Toth, Tina L. Amyes, B. McKay Wood, Kui K. Chan, John Alan Gerlt, John P. Richard

Research output: Contribution to journalArticle

Abstract

Closure of the active site phosphate gripper loop of orotidine 5′-monophosphate decarboxylase from Saccharomyces cerevisiae (ScOMPDC) over the bound substrate orotidine 5′-monophosphate (OMP) activates the bound substrate for decarboxylation by at least 104-fold [Amyes, T. L., Richard, J. P., and Tait, J. J. (2005) J. Am. Chem. Soc. 127, 15708-15709]. The 19-residue phosphate gripper loop of the mesophilic ScOMPDC is much larger than the nine-residue loop at the ortholog from the thermophile Methanothermobacter thermautotrophicus (MtOMPDC). This difference in loop size results in a small decrease in the total intrinsic phosphate binding energy of the phosphodianion group of OMP from 11.9 to 11.6 kcal/mol, along with a modest decrease in the extent of activation by phosphite dianion of decarboxylation of the truncated substrate 1-(β-D-erythrofuranosyl)orotic acid. The activation parameters ΔH‡ and ΔS‡ for kcat for decarboxylation of OMP are 3.6 kcal/mol and 10 cal K-1 mol -1 more positive, respectively, for MtOMPDC than for ScOMPDC. We suggest that these differences are related to the difference in the size of the active site loops at the mesophilic ScOMPDC and the thermophilic MtOMPDC. The greater enthalpic transition state stabilization available from the more extensive loop - substrate interactions for the ScOMPDC-catalyzed reaction is largely balanced by a larger entropic requirement for immobilization of the larger loop at this enzyme.

Original languageEnglish (US)
Pages (from-to)8006-8013
Number of pages8
JournalBiochemistry
Volume48
Issue number33
DOIs
StatePublished - Aug 25 2009

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Carboxy-Lyases
Thermodynamics
Decarboxylation
Catalytic Domain
Chemical activation
Grippers
Phosphates
Substrates
Methanobacteriaceae
Orotic Acid
Phosphites
Binding energy
Immobilization
Yeast
Saccharomyces cerevisiae
Stabilization
orotidylic acid
Enzymes

ASJC Scopus subject areas

  • Biochemistry

Cite this

An examination of the relationship between active site loop size and thermodynamic activation parameters for orotidine 5′-monophosphate decarboxylase from mesophilic and thermophilic organisms. / Toth, Krisztina; Amyes, Tina L.; Wood, B. McKay; Chan, Kui K.; Gerlt, John Alan; Richard, John P.

In: Biochemistry, Vol. 48, No. 33, 25.08.2009, p. 8006-8013.

Research output: Contribution to journalArticle

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abstract = "Closure of the active site phosphate gripper loop of orotidine 5′-monophosphate decarboxylase from Saccharomyces cerevisiae (ScOMPDC) over the bound substrate orotidine 5′-monophosphate (OMP) activates the bound substrate for decarboxylation by at least 104-fold [Amyes, T. L., Richard, J. P., and Tait, J. J. (2005) J. Am. Chem. Soc. 127, 15708-15709]. The 19-residue phosphate gripper loop of the mesophilic ScOMPDC is much larger than the nine-residue loop at the ortholog from the thermophile Methanothermobacter thermautotrophicus (MtOMPDC). This difference in loop size results in a small decrease in the total intrinsic phosphate binding energy of the phosphodianion group of OMP from 11.9 to 11.6 kcal/mol, along with a modest decrease in the extent of activation by phosphite dianion of decarboxylation of the truncated substrate 1-(β-D-erythrofuranosyl)orotic acid. The activation parameters ΔH‡ and ΔS‡ for kcat for decarboxylation of OMP are 3.6 kcal/mol and 10 cal K-1 mol -1 more positive, respectively, for MtOMPDC than for ScOMPDC. We suggest that these differences are related to the difference in the size of the active site loops at the mesophilic ScOMPDC and the thermophilic MtOMPDC. The greater enthalpic transition state stabilization available from the more extensive loop - substrate interactions for the ScOMPDC-catalyzed reaction is largely balanced by a larger entropic requirement for immobilization of the larger loop at this enzyme.",
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