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

Abstract

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 31P,1H 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. 19F and 27Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis translation state in which the phosphoryl unit is already detached from the arginine and lysine fingers.

Common patterns of hydrolysis initiation in P-loop fold nucleoside triphosphatases

“…Consequently, the common denominator of stimulatory patterns in diverse P-loop NTPases is the mechanistic interaction of stimulators with the γ-phosphate group in the transition state; this interaction is observed in all analyzed TS-like structures (Fig. 1C,D, 3-7, Table S1, S2) and can be inferred from many other structures, specifically those that can be related to post-transition states, see [113] and the accompanying paper [18].…”

“…While linking of O 2A and O 3G atoms by a stimulator enforces a counterclockwise twisting of γ-phosphate, it is not clear yet, what conformational changes are caused by stimulators that interact only with γ-phosphate. There is indirect evidence that γ-phosphate may be twisted clockwise in RecA NTPases, see [112, 113]. Also, in the structure of the ABC ATPase of the maltose transporter (PDB ID 3PUW, [93]) the AlF 4 − moiety is slightly twisted clockwise (Fig.…”

Common mechanism of activated catalysis in P-loop fold nucleoside triphosphatases -in varietate concordia

“…RecA recombinase of E. coli (PDB ID 3CMX, [129]) are available. However, the apical water molecule is absent from these structures, the possible reasons of which are discussed in [127].…”

Proton-phosphorous connectivities revealed by high-resolution proton-detected solid-state NMR

“…Next, we were interested in whether the H P protons can be selectively excited in spin-filtering experiments, in which two proton-phosphorus cross-polarization (CP) steps are applied (the experiment is denoted with hPH in the following; see Figure S7 for the pulse sequence). We have recently presented the first hPH correlation spectrum recorded at 100 kHz MAS in the context of a large motor protein coordinating to DNA and ADP to probe hydrogen bonding 11 .…”

“…Up to now, proton resonance lines at slow MAS frequencies (10-20 kHz) were typically rather broad which is often associated with an incomplete suppression of the homonuclear dipolar coupling network by magic-angle spinning (MAS) 6,7 . We herein introduce phosphorus-31 as an additional radiofrequency channel in proton-detected fast MAS experiments ( 100 kHz) 6-8 ≥ allowing the investigation of a variety of functionalized phosphorus-containing materials (for instance, heterogeneous catalysts, modified zeolites 9 or aluminophosphates 10 ), as well as the characterization of biomolecular protein-nucleotide complexes 11 . Compared to previously reported 31 P-detected 1 H- 31 P heteronuclear correlation experiments (HETCOR) combined with rather high-power 1 H homonuclear decoupling performed at relatively slow MAS frequencies 9,[12][13][14][15] , the herein proposed 1 H-detected 31 P-1 H correlation experiment at fast MAS benefits in particular from requiring small sample amounts (<0.5 mg) and low-power decoupling.…”