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@article{1503344, author = {Kokkonen, Piia Pauliina and Bednář, David and Dočkalová, Veronika and Prokop, Zbyněk and Damborský, Jiří}, article_location = {Bethesda, USA}, article_number = {29}, doi = {http://dx.doi.org/10.1074/jbc.RA117.000328}, keywords = {enzyme kinetics; enzyme mechanism; protein conformation; molecular dynamics; molecular evolution; active site; conformational change; enzyme catalysis; haloalkane dehalogenase; dichloroethane degradation; ethylene dichloride;}, language = {eng}, issn = {0021-9258}, journal = {Journal of Biological Chemistry}, title = {Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site}, url = {https://loschmidt.chemi.muni.cz/peg/category/publications/#2018}, volume = {293}, year = {2018} }
TY - JOUR ID - 1503344 AU - Kokkonen, Piia Pauliina - Bednář, David - Dočkalová, Veronika - Prokop, Zbyněk - Damborský, Jiří PY - 2018 TI - Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site JF - Journal of Biological Chemistry VL - 293 IS - 29 SP - 11505-11512 EP - 11505-11512 PB - Amer. Soc. Biochem. Mol. Biol. SN - 00219258 KW - enzyme kinetics KW - enzyme mechanism KW - protein conformation KW - molecular dynamics KW - molecular evolution KW - active site KW - conformational change KW - enzyme catalysis KW - haloalkane dehalogenase KW - dichloroethane degradation KW - ethylene dichloride; UR - https://loschmidt.chemi.muni.cz/peg/category/publications/#2018 N2 - Haloalkane dehalogenases catalyze the hydrolysis of halogen-carbon bonds in organic halogenated compounds and as such are of great utility as biocatalysts. The crystal structures of the haloalkane dehalogenase DhlA from the bacterium from Xanthobacter autotrophicus GJ10, specifically adapted for the conversion of the small 1,2-dichloroethane (DCE) molecule, display the smallest catalytic site (110 angstrom(3)) within this enzyme family. However, during a substrate-specificity screening, we noted that DhlA can catalyze the conversion of far bulkier substrates, such as the 4-(bromomethyl)-6,7-dimethoxy-coumarin (220 angstrom(3)). This large substrate cannot bind to DhlA without conformational alterations. These conformational changes have been previously inferred from kinetic analysis, but their structural basis has not been understood. Using molecular dynamic simulations, we demonstrate here the intrinsic flexibility of part of the cap domain that allows DhlA to accommodate bulky substrates. The simulations displayed two routes for transport of substrates to the active site, one of which requires the conformational change and is likely the route for bulky substrates. These results provide insights into the structure-dynamics function relationships in enzymes with deeply buried active sites. Moreover, understanding the structural basis for the molecular adaptation of DhlA to 1,2-dichloroethane introduced into the biosphere during the industrial revolution provides a valuable lesson in enzyme design by nature. ER -
KOKKONEN, Piia Pauliina, David BEDNÁŘ, Veronika DOČKALOVÁ, Zbyněk PROKOP a Jiří DAMBORSKÝ. Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site. \textit{Journal of Biological Chemistry}. Bethesda, USA: Amer. Soc. Biochem. Mol. Biol., 2018, roč.~293, č.~29, s.~11505-11512. ISSN~0021-9258. Dostupné z: https://dx.doi.org/10.1074/jbc.RA117.000328.
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