Determinants of Catalytic Power and Ligand Binding in Glutamate Racemase

M. Ashley Spies; Joseph G. Reese; Dylan Dodd; Katherine L. Pankow; Steven R. Blanke; Jerome Baudry

doi:10.1021/ja809660g

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Journal article

Determinants of Catalytic Power and Ligand Binding in Glutamate Racemase

M. Ashley Spies, Joseph G. Reese, Dylan Dodd, Katherine L. Pankow, Steven R. Blanke and Jerome Baudry

Journal of the American Chemical Society, Vol.131(14), pp.5274-5284

04/15/2009

DOI: 10.1021/ja809660g

PMCID: PMC2882252

PMID: 19309142

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https://www.ncbi.nlm.nih.gov/pmc/articles/2882252View

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Abstract

Glutamate racemases (EC 5.1.1.3) catalyze the cofactor-independent stereoinversion of D- and L-glutamate and are important for viability in several Gram-negative and -positive bacteria. As the only enzyme involved in the stereoinversion Of L- to D-glutamate for peptidoglycan biosynthesis, glutamate racemase is an attractive target for the design of antibacterial agents. However, the development of competitive tight-binding inhibitors has been problematic and highly species specific. Despite a number of recent crystal structures of cofactor-independent epimerases and racemases, cocrystallized with substrates or substrate analogues, the source of these enzymes' catalytic power and their ability to acidify the C alpha of amino acids remains unknown. The present integrated computational and experimental study focuses on the glutamate racemase from Bacillus subtilis (RacE). A particular focus is placed on the interaction of the glutamate carbanion intermediate with RacE. Results suggest that the reactive form of the RacE-glutamate carbanion complex, vis-a-vis proton abstraction from Ca, is significantly different than the RacE-D-glutamate complex on the basis of the crystal structure and possesses dramatically stronger enzyme-ligand interaction energy. In silico and experimental site-directed mutagenesis indicates that the strength of the RacE-glutamate carbanion interaction energy is highly distributed among numerous electrostatic interactions in the active site, rather than being dominated by strong hydrogen bonds. Results from this study are important for laying the groundwork for discovery and design of high-affinity ligands to this class of cofactor-independent racemases.

Chemistry

Chemistry, Multidisciplinary

Physical Sciences

Science & Technology

Details

Title: Subtitle: Determinants of Catalytic Power and Ligand Binding in Glutamate Racemase
Creators: M. Ashley Spies - University of Tennessee at Knoxville
Joseph G. Reese - University of Tennessee at Knoxville
Dylan Dodd - University of Tennessee at Knoxville
Katherine L. Pankow - University of Tennessee at Knoxville
Steven R. Blanke - University of Tennessee at Knoxville
Jerome Baudry - University of Tennessee at Knoxville
Resource Type: Journal article
Publication Details: Journal of the American Chemical Society, Vol.131(14), pp.5274-5284
DOI: 10.1021/ja809660g
PMID: 19309142
PMCID: PMC2882252
NLM abbreviation: J Am Chem Soc
ISSN: 0002-7863
eISSN: 1520-5126
Publisher: Amer Chemical Soc
Number of pages: 11
Grant note: U54AI057156 / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) A1076830; A1057156 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA
Language: English
Date published: 04/15/2009
Academic Unit: Pharmaceutical Sciences and Experimental Therapeutics; Biochemistry and Molecular Biology; Medicinal and Natural Products Chemistry
Record Identifier: 9984293078002771

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