Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase.

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Abstrakt

Tytuł:: Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase.
Autorzy:: Malär AA; Physical Chemistry, ETH Zürich, Zürich, Switzerland.
Wili N; Physical Chemistry, ETH Zürich, Zürich, Switzerland.
Völker LA; Physical Chemistry, ETH Zürich, Zürich, Switzerland.
Kozlova MI; Department of Physics, Osnabrück University, Osnabrück, Germany.
Cadalbert R; Physical Chemistry, ETH Zürich, Zürich, Switzerland.
Däpp A; Physical Chemistry, ETH Zürich, Zürich, Switzerland.
Weber ME; Physical Chemistry, ETH Zürich, Zürich, Switzerland.
Zehnder J; Physical Chemistry, ETH Zürich, Zürich, Switzerland.
Jeschke G; Physical Chemistry, ETH Zürich, Zürich, Switzerland.
Eckert H; Institut für Physikalische Chemie, WWU Münster, Münster, Germany.; Instituto de Física de Sao Carlos, Universidade de Sao Paulo, Sao Carlos, SP, Brazil.
Böckmann A; Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS/Université de Lyon, Lyon, France.
Klose D; Physical Chemistry, ETH Zürich, Zürich, Switzerland. .
Mulkidjanian AY; Department of Physics, Osnabrück University, Osnabrück, Germany. .; School of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia. .
Meier BH; Physical Chemistry, ETH Zürich, Zürich, Switzerland. .
Wiegand T; Physical Chemistry, ETH Zürich, Zürich, Switzerland. .; Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany. .; Institute of Technical and Macromolecular Chemistry, RWTH Aachen, Aachen, Germany. .
Źródło:: Nature communications [Nat Commun] 2021 Sep 06; Vol. 12 (1), pp. 5293. Date of Electronic Publication: 2021 Sep 06.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
Język:: English
Imprint Name(s):: Original Publication: [London] : Nature Pub. Group
MeSH Terms:: Adenosine Diphosphate/*chemistry
Adenosine Triphosphate/*chemistry
Bacterial Proteins/*chemistry
DNA, Bacterial/*chemistry
DnaB Helicases/*chemistry
Helicobacter pylori/*enzymology
Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Aluminum Compounds/chemistry ; Aluminum Compounds/metabolism ; Arginine/chemistry ; Arginine/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Catalytic Domain ; Cloning, Molecular ; DNA, Bacterial/genetics ; DNA, Bacterial/metabolism ; DnaB Helicases/genetics ; DnaB Helicases/metabolism ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Fluorides/chemistry ; Fluorides/metabolism ; Gene Expression ; Helicobacter pylori/genetics ; Hydrolysis ; Lysine/chemistry ; Lysine/metabolism ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Substrate Specificity ; Thermodynamics
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Substance Nomenclature:: 0 (Aluminum Compounds)
0 (Bacterial Proteins)
0 (DNA, Bacterial)
0 (Recombinant Proteins)
61D2G4IYVH (Adenosine Diphosphate)
8L70Q75FXE (Adenosine Triphosphate)
94ZLA3W45F (Arginine)
EC 3.6.4.12 (DnaB Helicases)
K3Z4F929H6 (Lysine)
Q80VPU408O (Fluorides)
Z77H3IKW94 (aluminum fluoride)
Entry Date(s):: Date Created: 20210907 Date Completed: 20211005 Latest Revision: 20231107
Update Code:: 20240105
PubMed Central ID:: PMC8421360
DOI:: 10.1038/s41467-021-25599-z
PMID:: 34489448
: Czasopismo naukowe

Full Text Finder

The ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31 P, 1 H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19 F and 27 Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis transition state in which the phosphoryl unit is already detached from the arginine and lysine fingers.
(© 2021. The Author(s).)

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