Paper Report for: Martinez-Martinez_2018_ACS.Chem.Biol_13_225 Reference
Title: Determinants and prediction of esterase substrate promiscuity patterns
Martinez-Martinez M , Coscolin C , Santiago G , Chow J , Stogios PJ , Bargiela R , Gertler C , Navarro-Fernandez J , Bollinger A and Ferrer M <32 more author(s)>
Martinez-Martinez M , Coscolin C , Santiago G , Chow J , Stogios PJ , Bargiela R , Gertler C , Navarro-Fernandez J , Bollinger A , Thies S , Mendez-Garcia C , Popovic A , Brown G , Chernikova TN , Garcia-Moyano A , Bjergah GE , Perez-Garcia P , Hai T , Del Pozo MV , Stokke R , Steen IH , Cui H , Xu X , Nocek BP , Alcaide M , Distaso M , Mesa V , Pelaez AI , Sanchez J , Buchholz PCF , Pleiss J , Fernandez-Guerra A , Glockner FO , Golyshina OV , Yakimov MM , Savchenko A , Jaeger KE , Yakunin AF , Streit WR , Golyshin PN , Guallar V , Ferrer M (- 32)
Ref: ACS Chemical Biology,
13 :225, 2018 :
PubMed Abstract PubMedSearch: Martinez-Martinez 2018 ACS.Chem.Biol 13 225 PubMedID: 29182315 Gene_locus related to this paper: 9zzzz-a0a2k8jn75 ,
9zzzz-a0a2k8jt94 ,
9zzzz-a0a0g3fj44 ,
9zzzz-a0a0g3fh10 ,
9zzzz-a0a0g3fh03 ,
9bact-a0a1s5qkj8 ,
9zzzz-a0a0g3feh5 ,
9zzzz-a0a0g3fkz4 ,
9zzzz-a0a0g3fh07 ,
9zzzz-a0a0g3fh34 ,
9zzzz-a0a0g3fh31 ,
9bact-KY458167 ,
alcbs-q0vqa3 ,
9bact-a0a1s5qki8 ,
9zzzz-a0a0g3feq8 ,
9zzzz-a0a0g3feh8 ,
9zzzz-a0a0g3fh19 ,
9bact-KY203037 ,
9bact-a0a1s5ql22 ,
9bact-a0a1s5qm34 ,
9bact-KY203034 ,
9bact-r9qzg0 ,
9bact-a0a1s5qly8 ,
9zzzz-a0a0g3fkz8 ,
9zzzz-a0a0g3feg9 ,
9zzzz-KY203033 ,
9zzzz-a0a0g3fes4 ,
9zzzz-a0a0g3fh42 ,
9bact-a0a1s5qlx2 ,
9zzzz-KY483651 ,
9bact-a0a1s5qmh4 ,
9zzzz-KY203032 ,
9zzzz-EH87 ,
9zzzz-a0a0g3fei1 ,
9zzzz-a0a0g3fet2 ,
9zzzz-KY483647 ,
9zzzz-EH82 ,
9zzzz-a0a0g3fe15 ,
9bact-KY203031 ,
9bact-t1w006 ,
9zzzz-a0a0g3fet6 ,
9bact-KY458164 ,
geoth-g8myf3 ,
9bact-a0a1s5ql04 ,
9gamm-a0a1y0ihk7 ,
9bact-a0a1s5qly6 ,
9bact-a0a1s5qkg4 ,
9bact-a0a1s5qkm4 ,
9gamm-s5tv80 ,
9gamm-a0a0c4zhg2 ,
9zzzz-t1b379 ,
9gamm-KY483646 ,
9bact-KY458160 ,
9zzzz-a0a0g3fj57 ,
9gamm-s5t8349 ,
9arch-KY203036 ,
9bact-KY458168 ,
9zzzz-a0a0g3fes0 ,
9zzzz-t1be47 ,
9bact-KY458159 ,
9zzzz-a0a0g3fh39 ,
9bact-t1vzd5 ,
9prot-EH41 ,
9bact-Lip114 ,
alcbs-q0vt77 ,
9bact-a0a1s5qke6 ,
9bact-a0a1s5qkf3 ,
9prot-SRP030024 ,
9gamm-s5t532 ,
9bact-a0a1s5qkl2 ,
9bact-a0a1s5qkk8 ,
9zzzz-KY203030 ,
9zzzz-t1d4I7 ,
9prot-KY019260 ,
9bact-a0a1s5qm38 ,
9arch-KY458161 ,
9prot-KY010302 ,
9zzzz-a0a0g3fl25 ,
9actn-KY010298 ,
9gamm-s5u059 ,
9bact-a0a1s5qmi7 ,
9bact-KY010297 ,
9bact-KY483642 ,
9bact-a0a1s5qkj1 ,
9bact-KY010299 ,
9bact-KY483648 ,
alcbs-q0vtl7 ,
9bact-a0a1s5qf1 ,
9bact-a0a1s5qkg0 ,
9bact-a0a0h4tgu6 ,
9bact-MilE3 ,
9bact-LAE6 ,
9alte-MGS-MT1 ,
9bact-r9qzf7 ,
9gamm-k0c6t6 ,
alcbs-q0vl36 ,
alcbs-q0vlq1 ,
alcbs-q0vq49 ,
bacsu-pnbae ,
canar-LipB ,
canan-lipasA ,
geost-lipas ,
marav-a1u5n0 ,
pseps-i7k8x5 ,
staep-GEHD ,
symth-q67mr3 ,
altma-s5cfn7 ,
cycsp-k0c2b8 ,
alcbs-q0vlk5 ,
9bact-k7qe48 ,
9bact-MGS-M1 ,
9bact-MGS-M2 ,
9bact-a0a0b5kns5 ,
9zzzz-a0a0g3fej4 ,
9zzzz-a0a0g3fj60 ,
9zzzz-a0a0g3fej0 ,
9zzzz-a0a0g3fj64 ,
9bact-a0a0b5kc16 ,
9zzzz-a0a0g3feg6 ,
9zzzz-a0a0g3feu6 Abstract
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.
        
Related information
Gene_Locus | 9zzzz-a0a2k8jn75 , 9zzzz-a0a2k8jt94 , 9zzzz-a0a0g3fj44 , 9zzzz-a0a0g3fh10 , 9zzzz-a0a0g3fh03 , 9bact-a0a1s5qkj8 , 9zzzz-a0a0g3feh5 , 9zzzz-a0a0g3fkz4 , 9zzzz-a0a0g3fh07 , 9zzzz-a0a0g3fh34 , 9zzzz-a0a0g3fh31 , 9bact-KY458167 , alcbs-q0vqa3 , 9bact-a0a1s5qki8 , 9zzzz-a0a0g3feq8 , 9zzzz-a0a0g3feh8 , 9zzzz-a0a0g3fh19 , 9bact-KY203037 , 9bact-a0a1s5ql22 , 9bact-a0a1s5qm34 , 9bact-KY203034 , 9bact-r9qzg0 , 9bact-a0a1s5qly8 , 9zzzz-a0a0g3fkz8 , 9zzzz-a0a0g3feg9 , 9zzzz-KY203033 , 9zzzz-a0a0g3fes4 , 9zzzz-a0a0g3fh42 , 9bact-a0a1s5qlx2 , 9zzzz-KY483651 , 9bact-a0a1s5qmh4 , 9zzzz-KY203032 , 9zzzz-EH87 , 9zzzz-a0a0g3fei1 , 9zzzz-a0a0g3fet2 , 9zzzz-KY483647 , 9zzzz-EH82 , 9zzzz-a0a0g3fe15 , 9bact-KY203031 , 9bact-t1w006 , 9zzzz-a0a0g3fet6 , 9bact-KY458164 , geoth-g8myf3 , 9bact-a0a1s5ql04 , 9gamm-a0a1y0ihk7 , 9bact-a0a1s5qly6 , 9bact-a0a1s5qkg4 , 9bact-a0a1s5qkm4 , 9gamm-s5tv80 , 9gamm-a0a0c4zhg2 , 9zzzz-t1b379 , 9gamm-KY483646 , 9bact-KY458160 , 9zzzz-a0a0g3fj57 , 9gamm-s5t8349 , 9arch-KY203036 , 9bact-KY458168 , 9zzzz-a0a0g3fes0 , 9zzzz-t1be47 , 9bact-KY458159 , 9zzzz-a0a0g3fh39 , 9bact-t1vzd5 , 9prot-EH41 , 9bact-Lip114 , alcbs-q0vt77 , 9bact-a0a1s5qke6 , 9bact-a0a1s5qkf3 , 9prot-SRP030024 , 9gamm-s5t532 , 9bact-a0a1s5qkl2 , 9bact-a0a1s5qkk8 , 9zzzz-KY203030 , 9zzzz-t1d4I7 , 9prot-KY019260 , 9bact-a0a1s5qm38 , 9arch-KY458161 , 9prot-KY010302 , 9zzzz-a0a0g3fl25 , 9actn-KY010298 , 9gamm-s5u059 , 9bact-a0a1s5qmi7 , 9bact-KY010297 , 9bact-KY483642 , 9bact-a0a1s5qkj1 , 9bact-KY010299 , 9bact-KY483648 , alcbs-q0vtl7 , 9bact-a0a1s5qf1 , 9bact-a0a1s5qkg0 , 9bact-a0a0h4tgu6 , 9bact-MilE3 , 9bact-LAE6 , 9alte-MGS-MT1 , 9bact-r9qzf7 , 9gamm-k0c6t6 , alcbs-q0vl36 , alcbs-q0vlq1 , alcbs-q0vq49 , bacsu-pnbae , canar-LipB , canan-lipasA , geost-lipas , marav-a1u5n0 , pseps-i7k8x5 , staep-GEHD , symth-q67mr3 , altma-s5cfn7 , cycsp-k0c2b8 , alcbs-q0vlk5 , 9bact-k7qe48 , 9bact-MGS-M1 , 9bact-MGS-M2 , 9bact-a0a0b5kns5 , 9zzzz-a0a0g3fej4 , 9zzzz-a0a0g3fj60 , 9zzzz-a0a0g3fej0 , 9zzzz-a0a0g3fj64 , 9bact-a0a0b5kc16 , 9zzzz-a0a0g3feg6 , 9zzzz-a0a0g3feu6
Substrate | Menthol , Glucose-pentaacetate , Methyl-salicylate , Methyl-ferulate , 1-Naphtylbutyrate , Pentadecylacetate , Dodecylacetate , Octylacetate , Hexylacetate , 1-Naphtylacetate , Methyl-cinnamate , Methyl-2,5-dihydroxycinnamate , Isobutyl-cinnamate , Phenethyl-cinnamate , Propyl-hexanoate , Propyl-butyrate , Propyl-propionate , Methyl-oleate , Methyl-decanoate , Benzyl-2-hydroxy-3-phenylpropanoate , Methyl-3-hydroxypentanoate , Diethyl-phthalate , Methyl-3-hydroxybenzoate , Benzylparaben , Butylparaben , Propylparaben , Menthylacetate , BFPME , Methyl(S)-3-hydroxybutyrate , Ethyl-lactate , Ethyl-4-chloro-3-hydroxybutanoate , Methyl-mandelate , N-Benzyl-D-proline-ethylester , N-Benzyl-L-proline-ethylester , (1S)-(-)-Menthylacetate , (1R)-(-)-Menthylacetate , Methylbenzoate , Ethylbenzoate , Ethylmyristate , Ethyldodecanoate , Ethyldecanoate , Ethyloctanoate , Ethylbutyrate , Ethylpropionate , Ethylacetate , Methyl-octanoate , Methyl-myristate , Methyl-dodecanoate , Methyl-hexanoate , Methyl-butyrate , Phenylpropionate , Phenylacetate , Tributyrin , Tripropionin , Triacetin , Trilaurin , Triolein , Trioctanoin , Methyl-L-lactate , Methyl-D-lactate , DDPDPDC , 2,4-Dichlorobenzyl-2,4-dichlorobenzoate , 2,4-Dichlorophenyl-2,4-dichlorobenzoate , Pentyl-benzoate , Cyclohexyl-butyrate , Ethyl-2-chlorobenzoate , D-Pantolactone , L-Pantolactone , Methyl-glycolate , gamma-Valerolactone , Ethyl-propionylacetate , Ethyl-acetoacetate , Ethyl-3-oxohexanoate , Ethyl-2-methylacetoacetate , Ethyl-2-ethylacetoacetate , 3-Methyl-3-butenyl-acetate , Geranyl-acetate , Vinyl-acrylate , Vinyl-crotonate , Vinyl-benzoate , Vinyl-oleate , Vinyl-palmitate , Vinyl-myristate , Vinyl-laurate , Vinyl-propionate , Vinyl-acetate , Vinyl-butyrate ,
Citations formats
Martinez-Martinez M, Coscolin C, Santiago G, Chow J, Stogios PJ, Bargiela R, Gertler C, Navarro-Fernandez J, Bollinger A, Thies S, Mendez-Garcia C, Popovic A, Brown G, Chernikova TN, Garcia-Moyano A, Bjergah GE, Perez-Garcia P, Hai T, Del Pozo MV, Stokke R, Steen IH, Cui H, Xu X, Nocek BP, Alcaide M, Distaso M, Mesa V, Pelaez AI, Sanchez J, Buchholz PCF, Pleiss J, Fernandez-Guerra A, Glockner FO, Golyshina OV, Yakimov MM, Savchenko A, Jaeger KE, Yakunin AF, Streit WR, Golyshin PN, Guallar V, Ferrer M (2018) Determinants and prediction of esterase substrate promiscuity patternsACS Chemical Biology 13 : 225-234 Martinez-Martinez M, Coscolin C, Santiago G, Chow J, Stogios PJ, Bargiela R, Gertler C, Navarro-Fernandez J, Bollinger A, Thies S, Mendez-Garcia C, Popovic A, Brown G, Chernikova TN, Garcia-Moyano A, Bjergah GE, Perez-Garcia P, Hai T, Del Pozo MV, Stokke R, Steen IH, Cui H, Xu X, Nocek BP, Alcaide M, Distaso M, Mesa V, Pelaez AI, Sanchez J, Buchholz PCF, Pleiss J, Fernandez-Guerra A, Glockner FO, Golyshina OV, Yakimov MM, Savchenko A, Jaeger KE, Yakunin AF, Streit WR, Golyshin PN, Guallar V, Ferrer M (2018) ACS Chemical Biology 13 : 225-234