Literature DB >> 18598058

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

Shonoi A Barnett1, Tina L Amyes, Bryant M Wood, John A Gerlt, John P Richard.   

Abstract

Kinetic analysis of decarboxylation catalyzed by S154A, Q215A, and S154A/Q215A mutant yeast orotidine 5'-monophosphate decarboxylases with orotidine 5'-monophosphate (OMP) and with a truncated nucleoside substrate (EO) activated by phosphite dianion shows (1) the side chain of Ser-154 stabilizes the transition state through interactions with the pyrimidine rings of OMP or EO, (2) the side chain of Gln-215 interacts with the phosphodianion group of OMP or with phosphite dianion, and (3) the interloop hydrogen bond between the side chains of Ser-154 and Gln-215 orients the amide side chain of Gln-215 to interact with the phosphodianion group of OMP or with phosphite dianion.

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Year:  2008        PMID： 18598058      PMCID： PMC2652672          DOI： 10.1021/bi800939k

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


  15 in total

1.  Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase.

Authors:  N Wu; Y Mo; J Gao; E F Pai
Journal:  Proc Natl Acad Sci U S A       Date:  2000-02-29       Impact factor: 11.205

2.  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

3.  The crystal structure and mechanism of orotidine 5'-monophosphate decarboxylase.

Authors:  T C Appleby; C Kinsland; T P Begley; S E Ealick
Journal:  Proc Natl Acad Sci U S A       Date:  2000-02-29       Impact factor: 11.205

4.  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

Review 5.  OMP decarboxylase--An enigma persists.

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

6.  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

7.  Strategy for analysing the co-operativity of intramolecular interactions in peptides and proteins.

Authors:  A Horovitz; A R Fersht
Journal:  J Mol Biol       Date:  1990-08-05       Impact factor: 5.469

8.  Yeast orotidine-5'-phosphate decarboxylase: steady-state and pre-steady-state analysis of the kinetic mechanism of substrate decarboxylation.

Authors:  D J Porter; S A Short
Journal:  Biochemistry       Date:  2000-09-26       Impact factor: 3.162

9.  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

10.  A substrate in pieces: allosteric activation of glycerol 3-phosphate dehydrogenase (NAD+) by phosphite dianion.

Authors:  Wing-Yin Tsang; Tina L Amyes; John P Richard
Journal:  Biochemistry       Date:  2008-04-01       Impact factor: 3.162
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  32 in total

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

Authors:  Tina L Amyes; Shonoi A Ming; Lawrence M Goldman; B McKay Wood; Bijoy J Desai; John A Gerlt; John P Richard
Journal:  Biochemistry       Date:  2012-05-31       Impact factor: 3.162

2.  Product deuterium isotope effects for orotidine 5'-monophosphate decarboxylase: effect of changing substrate and enzyme structure on the partitioning of the vinyl carbanion reaction intermediate.

Authors:  Krisztina Toth; Tina L Amyes; Bryant M Wood; Kui Chan; John A Gerlt; John P Richard
Journal:  J Am Chem Soc       Date:  2010-05-26       Impact factor: 15.419

3.  Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.

Authors:  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
Journal:  Biochemistry       Date:  2009-06-23       Impact factor: 3.162

4.  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

5.  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

6.  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

7.  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

8.  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

9.  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

10.  Uroporphyrinogen decarboxylation as a benchmark for the catalytic proficiency of enzymes.

Authors:  Charles A Lewis; Richard Wolfenden
Journal:  Proc Natl Acad Sci U S A       Date:  2008-11-06       Impact factor: 11.205
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