TY - JOUR

T1 - Determinants and prediction of esterase substrate promiscuity patterns

AU - Martínez-Martínez, Mónica

AU - Coscolín, Cristina

AU - Santiago, Gerard

AU - Chow, Jennifer

AU - Stogios, Peter J.

AU - Bargiela, Rafael

AU - Gertler, Christoph

AU - Navarro-Fernández, J.

AU - Bollinger, Alexander

AU - Thies, Stephanie

AU - Méndez-García, Celia

AU - Popovic, Anna

AU - Brown, Greg

AU - Chernikova, Tatyana

AU - García-Moyano, Antonio

AU - Bjerga, Gro E.K.

AU - Perez-Garcia, Pablo

AU - Hai, Tran

AU - del Pozo, Mercedes V.

AU - Stokke, Runar

AU - Steen, Ida H.

AU - Cui, Hong

AU - Xu, Xiaohui

AU - Nocek, Boguslaw

AU - Alcaide, Maria

AU - Disasto, Marco

AU - Mesa, Victoria

AU - Pelaez, Ana I.

AU - Sanchez, Jesus

AU - Buchholz, Patrick C.F.

AU - Pleiss, Jurgen

AU - Fernández-Guerra, Antonio

AU - Glockner, Frank O.

AU - Golyshina, Olga

AU - Yakimov, Michail M.

AU - Savchenko, Alexei

AU - Jaeger, Karl-Erich

AU - Yakunin, A. F.

AU - Streit, Wolfgang R.

AU - Golyshin, Peter

AU - Guallar, Victor

AU - Ferrer, Manuel

PY - 2018

Y1 - 2018

N2 - Esterases receive special attention because their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others, remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps ranking (classifying) promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence datasets.

AB - Esterases receive special attention because their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others, remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps ranking (classifying) promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence datasets.

UR - https://pubs.acs.org/doi/abs/10.1021/acschembio.7b00996#notes1

U2 - 10.1021/acschembio.7b00996

DO - 10.1021/acschembio.7b00996

M3 - Article

VL - 13

SP - 225

EP - 234

JO - ACS Chemical Biology

JF - ACS Chemical Biology

SN - 1554-8929

IS - 1

ER -