Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes

Abstract

Abstract:The 1994 structure of a transition state analog with AlF4 -and GDP complexed to G1α, a small G protein, heralded a new field of research into structure and mechanism of enzymes that manipulate transfer of the phosphoryl (PO3 -) group. The list of enzyme structures that embrace metal fluorides, MFx, as ligands that imitate either the phosphoryl group or a phosphate, is now growing at over 80 per triennium. They fall into three distinct geometrical classes: (i) Tetrahedral complexes, based on BeF3 -, mimic ground state phosphates; (ii) Octahedral complexes, primarily based on AlF4 -, mimic "in-line" anionic transition state for phosphoryl transfer; and (iii) Trigonal bipyramidal complexes, represented by MgF3 -and putative AlF3 0 moieties, additionally mimic the tbp geometry of the transition state. The interpretation of these structures provides a deeper mechanistic understanding of the behavior and manipulation of phosphate monoesters in molecular biology. This review provides a comprehensive overview of these structures, their uses, and their computational development. It questions the identification of AlF3 0 and MgF4 = as tbp species in protein complexes and discusses the relevance of physical organic chemistry and water-based model studies for understanding phosphoryl group transfer in enzymes. It describes two roles for amino acid side-chains that mediate proton transfers during phosphoryl transfer, based on the analysis of protein/MFx structures. First, they deploy hydrogen bonding to neutral oxygen nucleophiles so as to orientate them for correct orbital overlap with the electrophilic phosphorus center. Secondly, they behave as classical general acid/base catalysts.

A GAP‐GTPase‐GDP‐Pi Intermediate Crystal Structure Analyzed by DFT Shows GTP Hydrolysis Involves Serial Proton Transfers

“…This is a powerful example of phosphoryl transfer being suppressed by H-bonding between nucleophile and phosphoryl oxygen that denies bonding orbital overlap. [21] The above results establish the most favored location forthe migrating protons. H 1 is located on O4G and coordination to Gln63 is better than to Thr37.H 2 is preferentially bondedt o O3G giving as horter LBHB to O3B (2.43 )t han for the alternate situation (2.57 )t hought he Q DA scores are very close.…”

“…This angle changes to 1508 only on subsequent formation of the LBHB between O3G and O3B (Figure4c), conflicting with the need for "bending the formed PÀOb ond for optimal phosphoryl transfer",a dvocated elsewhere. [21] The 2nd computed structure leaves H 1 on O4G directed at Thr37 (C=O) with H 2 on O3G now coordinatingO 3B, ac hange that requires simple rotation of the PGÀO3B bond (Figure 4c). It has 9H-bonds with the strongestb eing aL BHB to O3B (2.45 )a nd as atisfactory mean Q DA 958 À1 (Figure S4c, Ta ble S2,e ntry 3, Supporting Information).…”

Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes

“…, from fluorine F 1 and the second carboxylate oxygen to give a near-planar six-membered ring ( Fig. 3a; all MF x structural data are tabulated in a recent review [27]). Because of its low electron density, the beryllium atom is difficult to locate by X-ray diffraction, resulting in uncertainty in its exact position, leading to considerable variation in attributed geometry (Fig.…”

“…and an Asp carboxylate fuse a 13-atom ring to the fluoroberyllate ring (rear). Octahedral coordination to Mg is completed by an additional aspartate (right), by 1-2 waters, and only twice by a histidine (top, magenta) (atom colors: fluorine, light blue; beryllium, lime; nitrogen, blue; oxygen, red; carbon, grey; 3-phosphoglycerate, cyan) (electron densities presented in CCP4MG from mtz data in EDS and contoured at 1r) (a adapted by the authors from [27] …”

“…The use of illustrations from Refs. [27] and [44] has been appreciatively acknowledged where appropriate.…”