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.

Základní údaje

Originální název

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

Autoři

MAZUR, Andrii (203 Česká republika), Tanyana PRUDNIKOVA (112 Bělorusko), Pavel GRINKEVICH (203 Česká republika), Jeroen R. MESTERS (276 Německo), Daria MRAZOVA (203 Česká republika), Radka CHALOUPKOVÁ (203 Česká republika, domácí), Jiří DAMBORSKÝ (203 Česká republika, garant, domácí), Michal KUTY (203 Česká republika), Petr KOLENKO (203 Česká republika) a Ivana KUTA SMATANOVA (203 Česká republika)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10609 Biochemical research methods

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.699

Kód RIV

RIV/00216224:14310/21:00119187

Organizační jednotka

Přírodovědecká fakulta

DOI

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

UT WoS

000625172500009

Klíčová slova anglicky

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

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 16. 2. 2023 12:41, Mgr. Michaela Hylsová, Ph.D.

Anotace

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.

Návaznosti

GA17-24321S, projekt VaV

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

Investor: Grantová agentura ČR, Studium hydratace a flexibility enzymů pomocí pokročilých strukturních a biofyzikálních metod

LM2015047, projekt VaV

Název: Česká národní infrastruktura pro biologická data (Akronym: ELIXIR-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Česká národní infrastruktura pro biologická data

LM2015055, projekt VaV

Název: Centrum pro systémovou biologii (Akronym: C4SYS)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, The national infrastructure C4SYS - Centre for Systems Biology

Citovat

MAZUR, Andrii, Tanyana PRUDNIKOVA, Pavel GRINKEVICH, Jeroen R. MESTERS, Daria MRAZOVA, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ, Michal KUTY, Petr KOLENKO a 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, roč. 77, March 2021, s. 347-356. ISSN 2059-7983. Dostupné z: 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 a 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, roč.~77, March 2021, s.~347-356. ISSN~2059-7983. Dostupné z: https://dx.doi.org/10.1107/S2059798321000486.

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