Conformational changes allow processing of bulky substrates by
a haloalkane dehalogenase with a small and buried active site

J 2018

Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site

KOKKONEN, Piia Pauliina, David BEDNÁŘ, Veronika DOČKALOVÁ, Zbyněk PROKOP, Jiří DAMBORSKÝ et. al.

Základní údaje

Originální název

Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site

Autoři

KOKKONEN, Piia Pauliina (246 Finsko, domácí), David BEDNÁŘ (203 Česká republika, domácí), Veronika DOČKALOVÁ (203 Česká republika, domácí), Zbyněk PROKOP (203 Česká republika, domácí) a Jiří DAMBORSKÝ (203 Česká republika, garant, domácí)

Vydání

Journal of Biological Chemistry, Bethesda, USA, Amer. Soc. Biochem. Mol. Biol. 2018, 0021-9258

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.106

Kód RIV

RIV/00216224:14310/18:00106486

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1074/jbc.RA117.000328

UT WoS

000439449700020

Klíčová slova anglicky

enzyme kinetics; enzyme mechanism; protein conformation; molecular dynamics; molecular evolution; active site; conformational change; enzyme catalysis; haloalkane dehalogenase; dichloroethane degradation; ethylene dichloride;

Změněno: 23. 4. 2024 14:21, Mgr. Michal Petr

Anotace

V originále

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.

Návaznosti

LM2015085, projekt VaV

Název: CERIT Scientific Cloud (Akronym: CERIT-SC)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CERIT Scientific Cloud

Citovat

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. 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.

@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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