Description of Transport Tunnel in Haloalkane Dehalogenase
Variant LinB D147C+L177C from Sphingobium japonicum

J 2021

Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum

IERMAK, Iuliia, Oksana DEGTJARIK, Petra HAVLICKOVA, Michal KUTY, Radka CHALOUPKOVÁ et. al.

Základní údaje

Originální název

Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum

Autoři

IERMAK, Iuliia (276 Německo), Oksana DEGTJARIK (112 Bělorusko), Petra HAVLICKOVA (203 Česká republika), Michal KUTY (203 Česká republika), Radka CHALOUPKOVÁ (203 Česká republika, domácí), Jiří DAMBORSKÝ (203 Česká republika, garant, domácí), Tanyana PRUDNIKOVA (112 Bělorusko) a Ivana KUTA SMATANOVA (203 Česká republika)

Vydání

Catalysts, Basel, MDPI, 2021, 2073-4344

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Švýcarsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.501

Kód RIV

RIV/00216224:14310/21:00119186

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.3390/catal11010005

UT WoS

000609997300001

Klíčová slova anglicky

bacterial enzyme; haloalkane dehalogenase; mutant form; crystallization; tertiary structure; disulfide bond; protein engineering; molecular dynamics; access tunnel; substrate specificity

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 16. 2. 2023 12:37, Mgr. Michaela Hylsová, Ph.D.

Anotace

V originále

The activity of enzymes with active sites buried inside their protein core highly depends on the efficient transport of substrates and products between the active site and the bulk solvent. The engineering of access tunnels in order to increase or decrease catalytic activity and specificity in a rational way is a challenging task. Here, we describe a combined experimental and computational approach to characterize the structural basis of altered activity in the haloalkane dehalogenase LinB D147C+L177C variant. While the overall protein fold is similar to the wild type enzyme and the other LinB variants, the access tunnels have been altered by introduced cysteines that were expected to form a disulfide bond. Surprisingly, the mutations have allowed several conformations of the amino acid chain in their vicinity, interfering with the structural analysis of the mutant by X-ray crystallography. The duration required for the growing of protein crystals changed from days to 1.5 years by introducing the substitutions. The haloalkane dehalogenase LinB D147C+L177C variant crystal structure was solved to 1.15 angstrom resolution, characterized and deposited to Protein Data Bank under PDB ID 6s06.

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

LM2018121, projekt VaV

Název: Výzkumná infrastruktura RECETOX (Akronym: RECETOX RI)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, RECETOX RI

Citovat

IERMAK, Iuliia, Oksana DEGTJARIK, Petra HAVLICKOVA, Michal KUTY, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ, Tanyana PRUDNIKOVA a Ivana KUTA SMATANOVA. Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum. Catalysts. Basel: MDPI, 2021, roč. 11, č. 1, s. 1-15. ISSN 2073-4344. Dostupné z: https://dx.doi.org/10.3390/catal11010005.

@article{1790201,
   author = {Iermak, Iuliia and Degtjarik, Oksana and Havlickova, Petra and Kuty, Michal and Chaloupková, Radka and Damborský, Jiří and Prudnikova, Tanyana and Kuta Smatanova, Ivana},
   article_location = {Basel},
   article_number = {1},
   doi = {http://dx.doi.org/10.3390/catal11010005},
   keywords = {bacterial enzyme; haloalkane dehalogenase; mutant form; crystallization; tertiary structure; disulfide bond; protein engineering; molecular dynamics; access tunnel; substrate specificity},
   language = {eng},
   issn = {2073-4344},
   journal = {Catalysts},
   title = {Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum},
   url = {https://www.mdpi.com/2073-4344/11/1/5},
   volume = {11},
   year = {2021}
}

TY  - JOUR
ID  - 1790201
AU  - Iermak, Iuliia - Degtjarik, Oksana - Havlickova, Petra - Kuty, Michal - Chaloupková, Radka - Damborský, Jiří - Prudnikova, Tanyana - Kuta Smatanova, Ivana
PY  - 2021
TI  - Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum
JF  - Catalysts
VL  - 11
IS  - 1
SP  - 1-15
EP  - 1-15
PB  - MDPI
SN  - 20734344
KW  - bacterial enzyme
KW  - haloalkane dehalogenase
KW  - mutant form
KW  - crystallization
KW  - tertiary structure
KW  - disulfide bond
KW  - protein engineering
KW  - molecular dynamics
KW  - access tunnel
KW  - substrate specificity
UR  - https://www.mdpi.com/2073-4344/11/1/5
N2  - The activity of enzymes with active sites buried inside their protein core highly depends on the efficient transport of substrates and products between the active site and the bulk solvent. The engineering of access tunnels in order to increase or decrease catalytic activity and specificity in a rational way is a challenging task. Here, we describe a combined experimental and computational approach to characterize the structural basis of altered activity in the haloalkane dehalogenase LinB D147C+L177C variant. While the overall protein fold is similar to the wild type enzyme and the other LinB variants, the access tunnels have been altered by introduced cysteines that were expected to form a disulfide bond. Surprisingly, the mutations have allowed several conformations of the amino acid chain in their vicinity, interfering with the structural analysis of the mutant by X-ray crystallography. The duration required for the growing of protein crystals changed from days to 1.5 years by introducing the substitutions. The haloalkane dehalogenase LinB D147C+L177C variant crystal structure was solved to 1.15 angstrom resolution, characterized and deposited to Protein Data Bank under PDB ID 6s06.
ER  -

IERMAK, Iuliia, Oksana DEGTJARIK, Petra HAVLICKOVA, Michal KUTY, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ, Tanyana PRUDNIKOVA a Ivana KUTA SMATANOVA. Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum. \textit{Catalysts}. Basel: MDPI, 2021, roč.~11, č.~1, s.~1-15. ISSN~2073-4344. Dostupné z: https://dx.doi.org/10.3390/catal11010005.

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