The mobility of the cap domain is essential for the substrate promiscuity of a family IV esterase from sorghum rhizosphere microbiome

Abstract

ABSTRACTMetagenomics offers the possibility to screen for versatile biocatalysts. In this study, the microbial community of theSorghum bicolorrhizosphere was spiked with technical cashew nut shell liquid, and after incubation, the eDNA was extracted and subsequently used to build a metagenomic library. We report the biochemical features and crystal structure of a novel esterase from the family IV, EH0, retrieved from an uncultured sphingomonad after a functional screen in tributyrin agar plates. EH0(Topt, 50 °C; Tm, 55.7 °C; pHopt, 9.5) was stable in the presence of 10-20% v/v organic solvents and exhibited hydrolytic activity againstp-nitrophenyl esters from acetate to palmitate, preferably butyrate (496 U mg−1), and a large battery of 69 structurally different esters (up to 30.2 U mg−1), including bis(2-hydroxyethyl)-terephthalate (0.16 ± 0.06 U mg−1). This broad substrate specificity contrasts with the fact that EH0showed a long and narrow catalytic tunnel, whose access appears to be hindered by a thigth folding of its cap domain. We propose that this cap domain is a highly flexible structure whose opening is mediated by unique structural elements, one of which is the presence of two contiguous proline residues likely acting as possible hinges, that altogether allow for the entrance of the substrates. Therefore, this work provides a new role for the cap domain, which until now was thought to be immobile elements that contain hydrophobic patches involved in substrate pre-recognition and in turn substrate specificity within family IV esterases.IMPORTANCEA better understanding of structure–function relationships of enzymes allows revealing key structural motifs or elements. Here, we studied the structural basis of the substrate promiscuity of EH0, a family IV esterase, isolated from a sample of theSorghum bicolorrhizosphere microbiome exposed to technical cashew nut shell liquid. The analysis of EH0revealed the potential of the sorghum rhizosphere microbiome as a source of enzymes with interesting properties, such as pH and solvent tolerance and remarkably broad substrate promiscuity. Its structure resembled those of homologous proteins from mesophilicParvibaculumandErythrobacterspp. and hyperthermophilicPyrobaculumandSulfolobusspp. and had a very narrow, single-entry access tunnel to the active site, access which is controlled by a capping domain that includes a number of not conserved proline residues. These structural markers, distinct from those of other substrate promiscuous esterases, can help tuning substrate profiles beyond tunnel and active site engineering.