Literature DB >> 21486036

OMP decarboxylase: phosphodianion binding energy is used to stabilize a vinyl carbanion intermediate.

Bogdana Goryanova1, Tina L Amyes, John A Gerlt, John P Richard.   

Abstract

Orotidine 5'-monophosphate decarboxylase (OMPDC) catalyzes the exchange for deuterium from solvent D(2)O of the C-6 proton of 1-(β-d-erythrofuranosyl)-5-fluorouracil (FEU), a phosphodianion truncated product analog. The deuterium exchange reaction of FEU is accelerated 1.8 × 10(4)-fold by 1 M phosphite dianion (HPO(3)(2-)). This corresponds to a 5.8 kcal/mol stabilization of the vinyl carbanion-like transition state, which is similar to the 7.8 kcal/mol stabilization of the transition state for OMPDC-catalyzed decarboxylation of a truncated substrate analog by bound HPO(3)(2-). These results show that the intrinsic binding energy of phosphite dianion is used in the stabilization of the vinyl carbanion-like transition state common to the decarboxylation and deuterium exchange reactions.
© 2011 American Chemical Society

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Year:  2011        PMID: 21486036      PMCID: PMC3099264          DOI: 10.1021/ja201734z

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  16 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

3.  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

Review 4.  OMP decarboxylase--An enigma persists.

Authors:  Brian P Callahan; Brian G Miller
Journal:  Bioorg Chem       Date:  2007-09-21       Impact factor: 5.275

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.  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

7.  A proficient enzyme.

Authors:  A Radzicka; R Wolfenden
Journal:  Science       Date:  1995-01-06       Impact factor: 47.728

Review 8.  Catalytic proficiency: the unusual case of OMP decarboxylase.

Authors:  Brian G Miller; Richard Wolfenden
Journal:  Annu Rev Biochem       Date:  2001-11-09       Impact factor: 23.643

9.  Phosphate binding energy and catalysis by small and large molecules.

Authors:  Janet R Morrow; Tina L Amyes; John P Richard
Journal:  Acc Chem Res       Date:  2008-02-23       Impact factor: 22.384

10.  Enzymatic catalysis of proton transfer at carbon: activation of triosephosphate isomerase by phosphite dianion.

Authors:  Tina L Amyes; John P Richard
Journal:  Biochemistry       Date:  2007-04-20       Impact factor: 3.162

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  31 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.  Isopentenyl diphosphate isomerase catalyzed reactions in D2O: product release limits the rate of this sluggish enzyme-catalyzed reaction.

Authors:  Venkatadurga Jonnalagadda; Krisztina Toth; John P Richard
Journal:  J Am Chem Soc       Date:  2012-04-05       Impact factor: 15.419

4.  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

Review 5.  A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer.

Authors:  Archie C Reyes; Tina L Amyes; John P Richard
Journal:  Org Biomol Chem       Date:  2017-10-31       Impact factor: 3.876

6.  Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase.

Authors:  Masahiro Fujihashi; Toyokazu Ishida; Shingo Kuroda; Lakshmi P Kotra; Emil F Pai; Kunio Miki
Journal:  J Am Chem Soc       Date:  2013-11-11       Impact factor: 15.419

7.  Reflections on the catalytic power of a TIM-barrel.

Authors:  John P Richard; Xiang Zhai; M Merced Malabanan
Journal:  Bioorg Chem       Date:  2014-07-11       Impact factor: 5.275

Review 8.  Specificity in transition state binding: the Pauling model revisited.

Authors:  Tina L Amyes; John P Richard
Journal:  Biochemistry       Date:  2013-02-04       Impact factor: 3.162

9.  Computational, structural, and kinetic evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase.

Authors:  Whitney F Kellett; Elizabeth Brunk; Bijoy J Desai; Alexander A Fedorov; Steven C Almo; John A Gerlt; Ursula Rothlisberger; Nigel G J Richards
Journal:  Biochemistry       Date:  2013-03-05       Impact factor: 3.162

10.  Using catalytic atom maps to predict the catalytic functions present in enzyme active sites.

Authors:  Geoffrey R Nosrati; K N Houk
Journal:  Biochemistry       Date:  2012-08-30       Impact factor: 3.162

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