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Bioinformatic analysis of fold-type III PLP-dependent enzymes discovers multimeric racemases

Pyridoxal-5′-phosphate (PLP)-dependent enzymes are ubiquitous in nature and catalyze a variety of important metabolic reactions. The fold-type III PLP-dependent enzyme family is primarily comprised of decarboxylases and alanine racemases. In the development of a multiple structural alignment databas...

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Published in:Applied microbiology and biotechnology 2017-02, Vol.101 (4), p.1499-1507
Main Authors: Knight, Anders M., Nobili, Alberto, van den Bergh, Tom, Genz, Maika, Joosten, Henk-Jan, Albrecht, Dirk, Riedel, Katharina, Pavlidis, Ioannis V., Bornscheuer, Uwe T.
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cited_by cdi_FETCH-LOGICAL-c543t-ef90d0635c1c9691fc11111711077c4adf9c2521426227cc85ec5e5e2c8d94953
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container_title Applied microbiology and biotechnology
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creator Knight, Anders M.
Nobili, Alberto
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Riedel, Katharina
Pavlidis, Ioannis V.
Bornscheuer, Uwe T.
description Pyridoxal-5′-phosphate (PLP)-dependent enzymes are ubiquitous in nature and catalyze a variety of important metabolic reactions. The fold-type III PLP-dependent enzyme family is primarily comprised of decarboxylases and alanine racemases. In the development of a multiple structural alignment database (3DM) for the enzyme family, a large subset of 5666 uncharacterized proteins with high structural, but low sequence similarity to alanine racemase and decarboxylases was found. Compared to these two classes of enzymes, the protein sequences being the object of this study completely lack the C-terminal domain, which has been reported important for the formation of the dimer interface in other fold-type III enzymes. The 5666 sequences cluster around four protein templates, which also share little sequence identity to each other. In this work, these four template proteins were solubly expressed in Escherichia coli , purified, and their substrate profiles were evaluated by HPLC analysis for racemase activity using a broader range of amino acids. They were found active only against alanine or serine, where they exhibited Michaelis constants within the range of typical bacterial alanine racemases, but with significantly lower turnover numbers. As the already described racemases were proposed to be active and appeared to be monomers as judged from their crystal structures, we also investigated this aspect for the four new enzymes. Here, size exclusion chromatography indicated the presence of oligomeric states of the enzymes and a native-PAGE in-gel assay showed that the racemase activity was present only in an oligomeric state but not as monomer. This suggests the likelihood of a different behavior of these enzymes in solution compared to the one observed in crystalline form.
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source ABI/INFORM Global; Springer Nature
subjects Amino acids
Analysis
Biochemistry
Bioinformatics
Biomedical and Life Sciences
Biosynthesis
Biotechnologically Relevant Enzymes and Proteins
Biotechnology
Carboxy-Lyases - chemistry
Carboxy-Lyases - metabolism
Cell cycle
Chemical reactions
Computational Biology - methods
Crystal structure
E coli
Enzymes
Escherichia coli
Life Sciences
Liquid chromatography
Microbial Genetics and Genomics
Microbiology
Polyamines
Protein Conformation
Proteins
Pyridoxal Phosphate - metabolism
Racemases and Epimerases - chemistry
Racemases and Epimerases - metabolism
Studies
title Bioinformatic analysis of fold-type III PLP-dependent enzymes discovers multimeric racemases
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