Structural Insight into Catalysis by the Flavin-Dependent NADH
Oxidase (Pden_5119) of Paracoccus denitrificans

J 2023

Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans

KRYL, Martin, Vojtěch SEDLÁČEK and Igor KUČERA

Basic information

Original name

Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans

Authors

KRYL, Martin (203 Czech Republic, belonging to the institution), Vojtěch SEDLÁČEK (203 Czech Republic, belonging to the institution) and Igor KUČERA (203 Czech Republic, guarantor, belonging to the institution)

Edition

International Journal of Molecular Sciences, Basel, Multidisciplinary Digital Publishing Institute, 2023, 1422-0067

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.600 in 2022

RIV identification code

RIV/00216224:14310/23:00130493

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.3390/ijms24043732

UT WoS

000945013900001

Keywords in English

FMN; NADH; dioxygen reduction; Paracoccus denitrificans

Abstract

V originále

The Pden_5119 protein oxidizes NADH with oxygen under mediation by the bound flavin mononucleotide (FMN) and may be involved in the maintenance of the cellular redox pool. In biochemical characterization, the curve of the pH-rate dependence was bell-shaped with pK(a1) = 6.6 and pK(a2) = 9.2 at 2 mu M FMN while it contained only a descending limb pK(a) of 9.7 at 50 mu M FMN. The enzyme was found to undergo inactivation by reagents reactive with histidine, lysine, tyrosine, and arginine. In the first three cases, FMN exerted a protective effect against the inactivation. X-ray structural analysis coupled with site-directed mutagenesis identified three amino acid residues important to the catalysis. Structural and kinetic data suggest that His-117 plays a role in the binding and positioning of the isoalloxazine ring of FMN, Lys-82 fixes the nicotinamide ring of NADH to support the proS-hydride transfer, and Arg-116 with its positive charge promotes the reaction between dioxygen and reduced flavin.

Links

EF18_046/0015974, research and development project

Name: Modernizace České infrastruktury pro integrativní strukturní biologii

GA16-18476S, research and development project

Name: Oxidační stres u denitrifikačních baktérií: objasnění funkce zúčastněných proteinů a možných dopadů na životní prostředí

Investor: Czech Science Foundation

LM2023042, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii

Investor: Ministry of Education, Youth and Sports of the CR, CIISB - Czech Infrastructure for Integrative Structural Biology

MUNI/A/1313/2022, interní kód MU

Name: Podpora biochemického výzkumu v roce 2023

Investor: Masaryk University

MUNI/A/1604/2020, interní kód MU

Name: Podpora biochemického výzkumu v roce 2021

Investor: Masaryk University

Citovat

KRYL, Martin, Vojtěch SEDLÁČEK and Igor KUČERA. Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans. International Journal of Molecular Sciences. Basel: Multidisciplinary Digital Publishing Institute, 2023, vol. 24, No 4, p. 1-17. ISSN 1422-0067. Available from: https://dx.doi.org/10.3390/ijms24043732.

@article{2269877,
   author = {Kryl, Martin and Sedláček, Vojtěch and Kučera, Igor},
   article_location = {Basel},
   article_number = {4},
   doi = {http://dx.doi.org/10.3390/ijms24043732},
   keywords = {FMN; NADH; dioxygen reduction; Paracoccus denitrificans},
   language = {eng},
   issn = {1422-0067},
   journal = {International Journal of Molecular Sciences},
   title = {Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans},
   url = {https://www.mdpi.com/1422-0067/24/4/3732},
   volume = {24},
   year = {2023}
}

TY  - JOUR
ID  - 2269877
AU  - Kryl, Martin - Sedláček, Vojtěch - Kučera, Igor
PY  - 2023
TI  - Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans
JF  - International Journal of Molecular Sciences
VL  - 24
IS  - 4
SP  - 1-17
EP  - 1-17
PB  - Multidisciplinary Digital Publishing Institute
SN  - 14220067
KW  - FMN
KW  - NADH
KW  - dioxygen reduction
KW  - Paracoccus denitrificans
UR  - https://www.mdpi.com/1422-0067/24/4/3732
N2  - The Pden_5119 protein oxidizes NADH with oxygen under mediation by the bound flavin mononucleotide (FMN) and may be involved in the maintenance of the cellular redox pool. In biochemical characterization, the curve of the pH-rate dependence was bell-shaped with pK(a1) = 6.6 and pK(a2) = 9.2 at 2 mu M FMN while it contained only a descending limb pK(a) of 9.7 at 50 mu M FMN. The enzyme was found to undergo inactivation by reagents reactive with histidine, lysine, tyrosine, and arginine. In the first three cases, FMN exerted a protective effect against the inactivation. X-ray structural analysis coupled with site-directed mutagenesis identified three amino acid residues important to the catalysis. Structural and kinetic data suggest that His-117 plays a role in the binding and positioning of the isoalloxazine ring of FMN, Lys-82 fixes the nicotinamide ring of NADH to support the proS-hydride transfer, and Arg-116 with its positive charge promotes the reaction between dioxygen and reduced flavin.
ER  -

KRYL, Martin, Vojtěch SEDLÁČEK and Igor KUČERA. Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden\_{}5119) of Paracoccus denitrificans. \textit{International Journal of Molecular Sciences}. Basel: Multidisciplinary Digital Publishing Institute, 2023, vol.~24, No~4, p.~1-17. ISSN~1422-0067. Available from: https://dx.doi.org/10.3390/ijms24043732.

Detailed Information on Publication Record