Literature DB >> 19678695

Orotic acid decarboxylation in water and nonpolar solvents: a potential role for desolvation in the action of OMP decarboxylase.

Charles A Lewis1, Richard Wolfenden.   

Abstract

OMP decarboxylase (ODCase) generates a very large rate enhancement without the assistance of metals or other cofactors. The uncatalyzed decarboxylation of 1-methylorotate in water is shown to involve the monoanion, although uncharged 1-methylorotic acid is decarboxylated at a similar rate. To measure the extent to which the rate of the nonenzymatic decarboxylation of orotate derivatives might be enhanced by their removal from solvent water, the 1-phosphoribosyl moiety of OMP was replaced with 1-substituents that would allow it to enter less polar solvents. When the tetrabutylammonium salt of 1-cyclohexylorotate was transferred from water to a series of dipolar aprotic solvents, its rate of decarboxylation increased markedly, varying with the relative ability of each solvent to release the substrate in the ground state from stabilization by solvent water acting as a proton donor. These findings are consistent with the view that separation of the substrate from solvent water may contribute, at least to a limited extent, to the rate enhancement produced by ODCase. This enzyme's active site, like that of another cofactorless enzyme recently shown to produce a rate enhancement similar in magnitude (uroporphyrinogen decarboxylase), is equipped with an ammonium group positioned in such a way as to balance the electrostatic charge of the carboxylate group of the substrate and later supply a proton to the incipient carbanion in a relatively waterless environment.

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Year:  2009        PMID: 19678695      PMCID: PMC2746487          DOI: 10.1021/bi901085m

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


  30 in total

1.  The chemistry of the reaction determines the invariant amino acids during the evolution and divergence of orotidine 5'-monophosphate decarboxylase.

Authors:  T W Traut; B R Temple
Journal:  J Biol Chem       Date:  2000-09-15       Impact factor: 5.157

2.  Dissecting a charged network at the active site of orotidine-5'-phosphate decarboxylase.

Authors:  B G Miller; M J Snider; R Wolfenden; S A Short
Journal:  J Biol Chem       Date:  2001-01-30       Impact factor: 5.157

3.  Catalysis of decarboxylation by an adjacent negative charge: a theoretical approach.

Authors:  Ngoc Lien Tran; Michael E Colvin; Scott Gronert; Weiming Wu
Journal:  Bioorg Chem       Date:  2003-08       Impact factor: 5.275

4.  Modest catalysis of the decarboxylation of orotate by hydrogen bonding: a theoretical model for orotidine- 5' -monophosphate decarboxylase.

Authors:  Diana L Shem; Scott Gronert; Weiming Wu
Journal:  Bioorg Chem       Date:  2004-04       Impact factor: 5.275

5.  Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-A resolution: implications for catalysis.

Authors:  E Lolis; G A Petsko
Journal:  Biochemistry       Date:  1990-07-17       Impact factor: 3.162

6.  Mechanism of decarboxylation of 1,3-dimethylorotic acid. A model for orotidine 5'-phosphate decarboxylase.

Authors:  P Beak; B Siegel
Journal:  J Am Chem Soc       Date:  1976-06-09       Impact factor: 15.419

7.  Enzyme catalysis: conflicting requirements of substrate access and transition state affinity.

Authors:  R Wolfenden
Journal:  Mol Cell Biochem       Date:  1974-05-30       Impact factor: 3.396

8.  Letter: Mechanism of decarboxylation of 1,3-dimethylorotic acid. A possible role for orotate decarboxylase.

Authors:  B Beak; B Siegel
Journal:  J Am Chem Soc       Date:  1973-11-14       Impact factor: 15.419

9.  Mechanisms of thiamine-catalyzed reactions. A kinetic analysis of the decarboxylation of pyruvate by 3,4-dimethylthiazolium ion in water and ethanol.

Authors:  J Crosby; G E Lienhard
Journal:  J Am Chem Soc       Date:  1970-09-23       Impact factor: 15.419

10.  Changes in absorption spectrum and crystal structure of triose phosphate isomerase brought about by 2-phosphoglycollate, a potential transition state analogue.

Authors:  L N Johnson; R Wolfenden
Journal:  J Mol Biol       Date:  1970-01-14       Impact factor: 5.469

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  10 in total

1.  Convenient synthesis of N1-substituted orotic acid derivatives.

Authors:  Jeannette T Bowler; Caitlin R Clausen; Daniel J Blackburn; Weiming Wu
Journal:  Tetrahedron Lett       Date:  2014-11-19       Impact factor: 2.415

2.  Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site.

Authors:  Vanessa Iiams; Bijoy J Desai; Alexander A Fedorov; Elena V Fedorov; Steven C Almo; John A Gerlt
Journal:  Biochemistry       Date:  2011-09-06       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.  Stabilities of Uracil and Pyridone-Based Carbanions: A Systematic Study in the Gas Phase and Solution and Implications for the Mechanism of Orotidine-5'-Monophosphate Decarboxylase.

Authors:  Nicholas A Senger; Carly E Bliss; James R Keeffe; Scott Gronert; Weiming Wu
Journal:  Tetrahedron       Date:  2013-07-01       Impact factor: 2.457

5.  Three Pyrimidine Decarboxylations in the Absence of a Catalyst.

Authors:  Charles A Lewis; Lin Shen; Weitao Yang; Richard Wolfenden
Journal:  Biochemistry       Date:  2017-03-06       Impact factor: 3.162

6.  Implications for an imidazol-2-yl carbene intermediate in the rhodanase-catalyzed C-S bond formation reaction of anaerobic ergothioneine biosynthesis.

Authors:  Ronghai Cheng; Rui Lai; Chao Peng; Juan Lopez; Zhihong Li; Nathchar Naowarojna; Kelin Li; Christina Wong; Norman Lee; Stephen A Whelan; Lu Qiao; Mark W Grinstaff; Jiangyun Wang; Qiang Cui; Pinghua Liu
Journal:  ACS Catal       Date:  2021-03-01       Impact factor: 13.084

7.  Improved synthesis of N1-substituted orotic acid derivatives.

Authors:  Nicholas A Senger; Jeannette T Bowler; Rene S Mercado; Sidney Lin; Weiming Wu
Journal:  Tetrahedron Lett       Date:  2013-08-07       Impact factor: 2.415

8.  Origin of Free Energy Barriers of Decarboxylation and the Reverse Process of CO2 Capture in Dimethylformamide and in Water.

Authors:  Shaoyuan Zhou; Bach T Nguyen; John P Richard; Ronald Kluger; Jiali Gao
Journal:  J Am Chem Soc       Date:  2020-12-29       Impact factor: 15.419

Review 9.  Orotidine 5'-Monophosphate Decarboxylase: Probing the Limits of the Possible for Enzyme Catalysis.

Authors:  John P Richard; Tina L Amyes; Archie C Reyes
Journal:  Acc Chem Res       Date:  2018-03-29       Impact factor: 22.384

10.  Role of the Carboxylate in Enzyme-Catalyzed Decarboxylation of Orotidine 5'-Monophosphate: Transition State Stabilization Dominates Over Ground State Destabilization.

Authors:  Bogdana Goryanova; Tina L Amyes; John P Richard
Journal:  J Am Chem Soc       Date:  2019-08-14       Impact factor: 15.419

  10 in total

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