The tetrameric structure of the novel haloalkane dehalogenase
DpaA from Paraglaciecola agarilytica NO2

J 2021

The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2

MAZUR, Andrii, Tanyana PRUDNIKOVA, Pavel GRINKEVICH, Jeroen R. MESTERS, Daria MRAZOVA et. al.

Basic information

Original name

The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2

Authors

MAZUR, Andrii (203 Czech Republic), Tanyana PRUDNIKOVA (112 Belarus), Pavel GRINKEVICH (203 Czech Republic), Jeroen R. MESTERS (276 Germany), Daria MRAZOVA (203 Czech Republic), Radka CHALOUPKOVÁ (203 Czech Republic, belonging to the institution), Jiří DAMBORSKÝ (203 Czech Republic, guarantor, belonging to the institution), Michal KUTY (203 Czech Republic), Petr KOLENKO (203 Czech Republic) and Ivana KUTA SMATANOVA (203 Czech Republic)

Edition

Acta Crystallographica Section D: Structural Biology, Chester, International Union of Crystallography, 2021, 2059-7983

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10609 Biochemical research methods

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.699

RIV identification code

RIV/00216224:14310/21:00119187

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1107/S2059798321000486

UT WoS

000625172500009

Keywords in English

DpaA; crystallization; haloalkane dehalogenases; halogenated pollutants; tetrameric structure; oligomerization

Abstract

V originále

Haloalkane dehalogenases (EC 3.8.1.5) are microbial enzymes that catalyse the hydrolytic conversion of halogenated compounds, resulting in a halide ion, a proton and an alcohol. These enzymes are used in industrial biocatalysis, bioremediation and biosensing of environmental pollutants or for molecular tagging in cell biology. The novel haloalkane dehalogenase DpaA described here was isolated from the psychrophilic and halophilic bacterium Paraglaciecola agarilytica NO2, which was found in marine sediment collected from the East Sea near Korea. Gel-filtration experiments and size-exclusion chromatography provided information about the dimeric composition of the enzyme in solution. The DpaA enzyme was crystallized using the sitting-drop vapour-diffusion method, yielding rod-like crystals that diffracted X-rays to 2.0 angstrom resolution. Diffraction data analysis revealed a case of merohedral twinning, and subsequent structure modelling and refinement resulted in a tetrameric model of DpaA, highlighting an uncommon multimeric nature for a protein belonging to haloalkane dehalogenase subfamily I.

Links

GA17-24321S, research and development project

Name: Studium hydratace a flexibility enzymů pomocí pokročilých strukturních a biofyzikálních metod

Investor: Czech Science Foundation

LM2015047, research and development project

Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

MAZUR, Andrii, Tanyana PRUDNIKOVA, Pavel GRINKEVICH, Jeroen R. MESTERS, Daria MRAZOVA, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ, Michal KUTY, Petr KOLENKO and Ivana KUTA SMATANOVA. The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2. Acta Crystallographica Section D: Structural Biology. Chester: International Union of Crystallography, 2021, vol. 77, March 2021, p. 347-356. ISSN 2059-7983. Available from: https://dx.doi.org/10.1107/S2059798321000486.

@article{1790208,
   author = {Mazur, Andrii and Prudnikova, Tanyana and Grinkevich, Pavel and Mesters, Jeroen R. and Mrazova, Daria and Chaloupková, Radka and Damborský, Jiří and Kuty, Michal and Kolenko, Petr and Kuta Smatanova, Ivana},
   article_location = {Chester},
   article_number = {March 2021},
   doi = {http://dx.doi.org/10.1107/S2059798321000486},
   keywords = {DpaA; crystallization; haloalkane dehalogenases; halogenated pollutants; tetrameric structure; oligomerization},
   language = {eng},
   issn = {2059-7983},
   journal = {Acta Crystallographica Section D: Structural Biology},
   title = {The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2},
   url = {https://scripts.iucr.org/cgi-bin/paper?S2059798321000486},
   volume = {77},
   year = {2021}
}

TY  - JOUR
ID  - 1790208
AU  - Mazur, Andrii - Prudnikova, Tanyana - Grinkevich, Pavel - Mesters, Jeroen R. - Mrazova, Daria - Chaloupková, Radka - Damborský, Jiří - Kuty, Michal - Kolenko, Petr - Kuta Smatanova, Ivana
PY  - 2021
TI  - The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2
JF  - Acta Crystallographica Section D: Structural Biology
VL  - 77
IS  - March 2021
SP  - 347-356
EP  - 347-356
PB  - International Union of Crystallography
SN  - 20597983
KW  - DpaA
KW  - crystallization
KW  - haloalkane dehalogenases
KW  - halogenated pollutants
KW  - tetrameric structure
KW  - oligomerization
UR  - https://scripts.iucr.org/cgi-bin/paper?S2059798321000486
N2  - Haloalkane dehalogenases (EC 3.8.1.5) are microbial enzymes that catalyse the hydrolytic conversion of halogenated compounds, resulting in a halide ion, a proton and an alcohol. These enzymes are used in industrial biocatalysis, bioremediation and biosensing of environmental pollutants or for molecular tagging in cell biology. The novel haloalkane dehalogenase DpaA described here was isolated from the psychrophilic and halophilic bacterium Paraglaciecola agarilytica NO2, which was found in marine sediment collected from the East Sea near Korea. Gel-filtration experiments and size-exclusion chromatography provided information about the dimeric composition of the enzyme in solution. The DpaA enzyme was crystallized using the sitting-drop vapour-diffusion method, yielding rod-like crystals that diffracted X-rays to 2.0 angstrom resolution. Diffraction data analysis revealed a case of merohedral twinning, and subsequent structure modelling and refinement resulted in a tetrameric model of DpaA, highlighting an uncommon multimeric nature for a protein belonging to haloalkane dehalogenase subfamily I.
ER  -

MAZUR, Andrii, Tanyana PRUDNIKOVA, Pavel GRINKEVICH, Jeroen R. MESTERS, Daria MRAZOVA, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ, Michal KUTY, Petr KOLENKO and Ivana KUTA SMATANOVA. The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2. \textit{Acta Crystallographica Section D: Structural Biology}. Chester: International Union of Crystallography, 2021, vol.~77, March 2021, p.~347-356. ISSN~2059-7983. Available from: https://dx.doi.org/10.1107/S2059798321000486.

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