Octahedral Trifluoromagnesate, an Anomalous Metal Fluoride Species, Stabilizes the Transition State in a Biological Motor

Abstract

Isoelectronic metal fluoride transition state analogue (TSA) complexes, MgF 3 – and AlF 4 – , have proven to be immensely useful in understanding mechanisms of biological motors utilizing phosphoryl transfer. Here we report a previously unobserved octahedral TSA complex, MgF 3 (H 2 O) − , in a 1.5 Å resolution Zika virus NS3 helicase crystal structure. 19 F NMR provided independent validation and also the direct observation of conformational tightening resulting from ssRNA binding in solution. The TSA stabilizes the two conformations of motif V of the helicase that link ATP hydrolysis with mechanical work. DFT analysis further validated the MgF 3 (H 2 O) − species, indicating the significance of this TSA for studies of biological motors.

Conformational Changes and ATP Hydrolysis in Zika Helicase: The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations

“…The PDB structure contains two different conformations for motif V, A and B, which were selected to prepare the two initial structures of the system. These structures correspond to the RNA-free state, which seems to be an advantage to explore the conformational diversity of motif V, as far as the presence of RNA is known to constrict the active site . It must be noticed that the ZIKV helicase displays intrinsic ATPase activity, with a k cat = 1.18 s –1 ( T = 298 K) in the absence of RNA .…”

“…Structural analysis revealed two different conformations for motif V, one of the conserved sequences that connects the ATPase and RNase activities in NS3hel. , On the side of the RNA binding site, motif V contains a highly conserved threonine residue (Thr411) that forms a direct hydrogen bond contact with the nucleic acid . On the ATPase site, the same motif displays a hydrogen bond interaction between the backbone amide group of Gly415 and a water molecule, which is a candidate to perform the ATP hydrolysis reaction . Consequently, motif V may act as a communication channel between the ATPase and RNAase activities of NS3hel, facilitating the conversion of chemical energy into directed motion through conformational changes coupled to the ATPase cycle.…”

“…17 On the ATPase site, the same motif displays a hydrogen bond interaction between the backbone amide group of Gly415 and a water molecule, which is a candidate to perform the ATP hydrolysis reaction. 14 Consequently, motif V may act as a communication channel between the ATPase and RNAase activities of NS3hel, facilitating the conversion of chemical energy into directed motion through conformational changes coupled to the ATPase cycle. These structural observations make ZV-NS3hel an interesting model to study the coupling between the chemical energy released during ATP hydrolysis and conformational changes.…”

“…Around the two active sites, there are several conserved motifs, critical for ATP binding, interdomain communication, and RNA binding. Recently, ZIKV-NS3hel was crystallized with a transition state analogue (TSA) of ATP hydrolysis . Structural analysis revealed two different conformations for motif V, one of the conserved sequences that connects the ATPase and RNase activities in NS3hel. , On the side of the RNA binding site, motif V contains a highly conserved threonine residue (Thr411) that forms a direct hydrogen bond contact with the nucleic acid .…”

Mechanism of Triphosphate Hydrolysis by Human MAT2A at 1.07 Å Resolution

“…These bond orders define a loose, concerted nucleophilic PO 3 – transfer mechanism. This phosphoryl group geometry in MAT2A is similar to related members of the phosphohydrolase family when probed with metal fluorides. − …”