Decoding Essential Amino Acid Residues in the Substrate Groove of a Non-Specific Nuclease from Pseudomonas syringae

Lynn Sophie Schwardmann,Volker Nölle,Skander Elleuche,Sarah Schmitz

doi:10.3390/catal9110941

Abstract

Non-specific nucleases (NSN) are of interest for biotechnological applications, including industrial downstream processing of crude protein extracts or cell-sorting approaches in microfabricated channels. Bacterial nucleases belonging to the superfamily of phospholipase D (PLD) are featured for their ability to catalyze the hydrolysis of nucleic acids in a metal-ion-independent manner. In order to gain a deeper insight into the composition of the substrate groove of a NSN from Pseudomonas syringae, semi-rational mutagenesis based on a structure homology model was applied to identify amino acid residues on the protein’s surface adjacent to the catalytic region. A collection of 12 mutant enzymes each with a substitution to a positively charged amino acid (arginine or lysine) was produced in recombinant form and biochemically characterized. Mutations in close proximity to the catalytic region (inner ring) either dramatically impaired or completely abolished the enzymatic performance, while amino acid residues located at the border of the substrate groove (outer ring) only had limited or no effects. A K119R substitution mutant displayed a relative turnover rate of 112% compared to the original nuclease. In conclusion, the well-defined outer ring of the substrate groove is a potential target for modulation of the enzymatic performance of NSNs belonging to the PLD superfamily.

Highlights

Non-specific nucleases (NSN) are a group of enzymes that hydrolyze deoxyribonucleic acid (DNA)and ribonucleic acid (RNA) in all conformations, including single-stranded and double-stranded or linear and circularized substrates, without sequence specificity [1]
The well-defined outer ring of the substrate groove is a potential target for modulation of the enzymatic performance of NSNs belonging to the Keywords: DNase; kinetic profiles; RNase; semi-rational mutagenesis; substrate specificity
A semi-rational approach was used to select suitable mutation sites within the substrate groove of an NSN from Pseudomonas syringae, which were substituted by site-directed mutagenesis against positively charged amino acid residues to modulate the affinity for negatively charged substrates

Summary

Introduction

Non-specific nucleases (NSN) are a group of enzymes that hydrolyze deoxyribonucleic acid (DNA)and ribonucleic acid (RNA) in all conformations, including single-stranded and double-stranded or linear and circularized substrates, without sequence specificity [1]. Non-specific nucleases (NSN) are a group of enzymes that hydrolyze deoxyribonucleic acid (DNA). NSNs are ubiquitously distributed among all organisms and are of great potential for versatile biotechnological and clinical applications [2,3,4]. Enzymes that are highly indiscriminate towards different substrates are generally considered as potential evolutionary starting points for developing novel or more specific catalytic activities [5,6,7]. PLDs act as important key players in various physiological processes, including cell migration and membrane trafficking [10]. This family of enzymes usually encodes two copies of the conserved HxK(x) D(x) GSxN motif in one gene

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