Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution

Abstract

Hydrogen bonds between backbone amide groups of enzymes and their substrates are often observed, but their importance in substrate binding and/or catalysis is not easy to investigate experimentally. We describe the generation and kinetic characterization of a backbone amide to ester substitution in the orotidine 5′-monophosphate (OMP) decarboxylase from Methanobacter thermoautotrophicum (MtOMPDC) to determine the importance of a backbone amide-substrate hydrogen bond. The MtOMPDC-catalyzed reaction is characterized by a rate enhancement (∼10 17 ) that is among the largest for enzyme-catalyzed reactions. The reaction proceeds through a vinyl anion intermediate that may be stabilized by hydrogen bonding interaction between the backbone amide of a conserved active site serine residue (Ser-127) and oxygen (O4) of the pyrimidine moiety and/or electrostatic interactions with the conserved general acidic lysine (Lys-72). In vitro translation in conjunction with amber suppression using an orthogonal amber tRNA charged with L-glycerate ( HO S) was used to generate the ester backbone substitution (S127 HO S). With 5-fluoro OMP (FOMP) as substrate, the amide to ester substitution increased the value of K m by ∼1.5-fold and decreased the value of k cat by ∼50-fold. We conclude that (i) the hydrogen bond between the backbone amide of Ser-127 and O4 of the pyrimidine moiety contributes a modest factor (∼10 2 ) to the 10 17 rate enhancement and (ii) the stabilization of the anionic intermediate is accomplished by electrostatic interactions, including its proximity of Lys-72. These conclusions are in good agreement with predictions obtained from hybrid quantum mechanical/molecular mechanical calculations.enzymology | cell-free translation | unnatural protein residue | flexible tRNA acylation ribozyme E lucidation of the structural strategies by which enzymes achieve their large rate enhancements is essential for understanding the evolution of enzymatic catalysis as well as facilitating the design of enzymes to catalyze novel reactions. Typically, the possible strategies are identified by high-resolution X-ray structural analyses, in which a stable mimic of a reactive intermediate or rate-determining transition state is bound in the active site. Then, site-directed mutagenesis is used to generate substitutions, in which the important interactions are removed or altered, with kinetic analyses and structural studies of the mutant enzymes allowing the importance of the interaction to be assessed. Indeed, for nearly 30 y, this approach has been used to evaluate the importance of interactions involving amino acid side chains. However, structural studies of many enzymes reveal the presence of hydrogen-bonding interactions between a backbone amide group donor and a heteroatom acceptor in the substrate. Such an interaction can contribute to catalysis by increasing in strength as the basicity/proton affinity of the acceptor is increased as the reaction coordinate is traversed (1). Perhaps the best known example of such an interactio...

Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5′-monophosphate decarboxylase catalysis

“…Apparently, OMPDC has evolved an effective transition-state stabilisation by an architecture that provides multiple favourable electrostatic interactions in a network of alternating charges as also supported by our quantum chemical calculations and mechanistic studies (Fig. 3d, e) [3][4][5][6][7][8][9][10]30 . The transition-state analog with the second highest affinity is 6-aza-UMP (K = 6 • 10 -8 M) and this high affinity has been attributed to a similar configuration as the genuine transition state owing to the lone pair at N6 3 .…”

New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition

“…Comparatively few decarboxylases have been shown to require no cofactor and, in these selected cases, catalysis involves non-oxidative decarboxylation of those substrates for which the corresponding carbanion species can be stabilised using simple acid-base chemistry. Examples include orotidine monophosphate decarboxylase14 and arylmalonate decarboxylase15.…”

Probing the role of the backbone carbonyl interaction with the CuA center in azurin by replacing the peptide bond with an ester linkage

“…[28][29][30] However, surprisingly, application of depsipeptides in deciphering protein function is limited primarily to the study of α-helical hydrogen bonding networks or hydrogen bonds to substrates in catalysis, since esters display different hydrogen bonding properties than their amide counterparts. [31][32][33] Depsipeptides are also known for their increased susceptibility to base hydrolysis compared to their peptide counterparts, and some studies have utilized this property within proteins. [34][35][36][37] Conversely, because of their lability most reported Fmoc-based solid phase peptide synthesis (SPPS) methods for depsipeptides typically involve extensive optimization to minimize hydrolysis and reduce racemization observed when the standard protocols are used for ester synthesis.…”