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Literature DB >> 22620855

Orotidine 5'-monophosphate decarboxylase: transition state stabilization from remote protein-phosphodianion interactions.

Tina L Amyes¹, Shonoi A Ming, Lawrence M Goldman, B McKay Wood, Bijoy J Desai, John A Gerlt, John P Richard.

Abstract

Mutants of orotidine 5'-monophosphate decarboxylase containing all possible single (Q215A, Y217F, and R235A), double, and triple substitutions of the side chains that interact with the phosphodianion group of the substrate orotidine 5'-monophosphate have been prepared. Essentially the entire effect of these mutations on the decarboxylation of the truncated neutral substrate 1-(β-d-erythrofuranosyl)orotic acid that lacks a phosphodianion group is expressed as a decrease in the third-order rate constant for activation by phosphite dianion. The results are consistent with a model in which phosphodianion binding interactions are utilized to stabilize a rare closed enzyme form that exhibits a high catalytic activity for decarboxylation.

Entities: Chemical Mutation Species

Mesh：

Substances：

Year: 2012 PMID： 22620855 PMCID： PMC3431445 DOI： 10.1021/bi300585e

Source DB: PubMed Journal: Biochemistry ISSN： 0006-2960 Impact factor: 3.162

18 in total

1. Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog.

Authors: B G Miller; A M Hassell; R Wolfenden; M V Milburn; S A Short
Journal: Proc Natl Acad Sci U S A Date: 2000-02-29 Impact factor: 11.205

Review 2. Binding energy, specificity, and enzymic catalysis: the circe effect.

Authors: W P Jencks
Journal: Adv Enzymol Relat Areas Mol Biol Date: 1975

Review 3. Catalysis by enzyme conformational change as illustrated by orotidine 5'-monophosphate decarboxylase.

Authors: Jiali Gao
Journal: Curr Opin Struct Biol Date: 2003-04 Impact factor: 6.809

4. Product deuterium isotope effect for orotidine 5'-monophosphate decarboxylase: evidence for the existence of a short-lived carbanion intermediate.

Authors: Krisztina Toth; Tina L Amyes; Bryant M Wood; Kui Chan; John A Gerlt; John P Richard
Journal: J Am Chem Soc Date: 2007-10-05 Impact factor: 15.419

5. 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.

Authors: Tina L Amyes; Bryant M Wood; Kui Chan; John A Gerlt; John P Richard
Journal: J Am Chem Soc Date: 2008-01-11 Impact factor: 15.419

6. Dissecting the total transition state stabilization provided by amino acid side chains at orotidine 5'-monophosphate decarboxylase: a two-part substrate approach.

Authors: Shonoi A Barnett; Tina L Amyes; Bryant M Wood; John A Gerlt; John P Richard
Journal: Biochemistry Date: 2008-07-04 Impact factor: 3.162

7. Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation.

Authors: B McKay Wood; Tina L Amyes; Alexander A Fedorov; Elena V Fedorov; Andrew Shabila; Steven C Almo; John P Richard; John A Gerlt
Journal: Biochemistry Date: 2010-05-04 Impact factor: 3.162

8. Activation of orotidine 5'-monophosphate decarboxylase by phosphite dianion: the whole substrate is the sum of two parts.

Authors: Tina L Amyes; John P Richard; James J Tait
Journal: J Am Chem Soc Date: 2005-11-16 Impact factor: 15.419

Review 9. On the importance of being zwitterionic: enzymatic catalysis of decarboxylation and deprotonation of cationic carbon.

Authors: John P Richard; Tina L Amyes
Journal: Bioorg Chem Date: 2004-10 Impact factor: 5.275

10. Activation of R235A mutant orotidine 5'-monophosphate decarboxylase by the guanidinium cation: effective molarity of the cationic side chain of Arg-235.

Authors: Shonoi A Barnett; Tina L Amyes; B McKay Wood; John A Gerlt; John P Richard
Journal: Biochemistry Date: 2010-02-09 Impact factor: 3.162

30 in total

1. The use of reaction timecourses to determine the level of minor contaminants in enzyme preparations.

Authors: Lawrence M Goldman; Tina L Amyes
Journal: Anal Biochem Date: 2014-01-03 Impact factor: 3.365

2. Catalysis by orotidine 5'-monophosphate decarboxylase: effect of 5-fluoro and 4'-substituents on the decarboxylation of two-part substrates.

Authors: Bogdana Goryanova; Krisztina Spong; Tina L Amyes; John P Richard
Journal: Biochemistry Date: 2013-01-11 Impact factor: 3.162

3. Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme.

Authors: Bijoy J Desai; B McKay Wood; Alexander A Fedorov; Elena V Fedorov; Bogdana Goryanova; Tina L Amyes; John P Richard; Steven C Almo; John A Gerlt
Journal: Biochemistry Date: 2012-10-17 Impact factor: 3.162

4. Proton transfer from C-6 of uridine 5'-monophosphate catalyzed by orotidine 5'-monophosphate decarboxylase: formation and stability of a vinyl carbanion intermediate and the effect of a 5-fluoro substituent.

Authors: Wing-Yin Tsang; B McKay Wood; Freeman M Wong; Weiming Wu; John A Gerlt; Tina L Amyes; John P Richard
Journal: J Am Chem Soc Date: 2012-08-21 Impact factor: 15.419

5. Atomic resolution structure of the orotidine 5'-monophosphate decarboxylase product complex combined with surface plasmon resonance analysis: implications for the catalytic mechanism.

Authors: Masahiro Fujihashi; Kazuya Mito; Emil F Pai; Kunio Miki
Journal: J Biol Chem Date: 2013-02-10 Impact factor: 5.157

6. Role of a guanidinium cation-phosphodianion pair in stabilizing the vinyl carbanion intermediate of orotidine 5'-phosphate decarboxylase-catalyzed reactions.

Authors: Bogdana Goryanova; Lawrence M Goldman; Tina L Amyes; John A Gerlt; John P Richard
Journal: Biochemistry Date: 2013-10-08 Impact factor: 3.162