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How a purine salvage enzyme singles out the right base

Open AccessPublished:August 09, 2019DOI:https://doi.org/10.1074/jbc.H119.010025
      Two phosphoribosyltransferases in the purine salvage pathway exhibit exquisite substrate specificity despite the chemical similarity of their distinct substrates, but the basis for this discrimination was not fully understood. Ozeir et al. now employ a complementary biochemical, structural, and computational approach to deduce the chemical constraints governing binding and propose a distinct mechanism for catalysis in one of these enzymes, adenine phosphoribosyltransferase. These insights, built on data from an unexpected finding, finally provide direct answers to key questions regarding these enzymes and substrate recognition more generally.

      Introduction

      The fundamental understanding of enzyme–substrate specificity was introduced through the “Schlüssel-Schloss-Prinzip” (lock and key principle) by Emil Fischer in 1894. Mechanistic understanding of enzyme function has grown beyond this uncompromising theory beginning with Pauling’s seminal proposal of preferential binding of the transition state to the enzyme to today, where much is known about the determinants of substrate specificity and the mechanistic details of catalysis. This information adds to the knowledge base and is integral to the development of analogs that can serve as drugs with extensive implications in human health and disease, motivating continuing efforts even in well-trodden areas. For example, phosphoribosyltransferases have been studied extensively, yet critical questions still remain unanswered. This list of questions has just been shortened, however, by a new work from Ozeir et al. (
      • Ozeir M.
      • Huyet J.
      • Burgevin M.-C.
      • Pinson B.
      • Chesney F.
      • Remy J.-M.
      • Siddiqi A.R.
      • Lupoli R.
      • Pinon G.
      • Saint-Marc C.
      • Gibert J.-F.
      • Morales R.
      • Ceballos-Picot I.
      • Barouki R.
      • Daignan-Fornier B.
      • et al.
      Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction.
      ), in which a crystal structure that defied the odds has helped to demonstrate the specific chemical and conformation features that determine the substrate specificity and reaction mechanism of adenine phosphoribosyltransferase (APRT).
      The abbreviations used are: APRT
      adenine phosphoribosyltransferase
      hAPRT
      human APRT
      PRPP
      5-phospho-α-d-ribose 1-diphosphate
      HGPRT
      hypoxanthine-guanine phosphoribosyltransferase.
      Phosphoribosyltransferases reversibly catalyze the formation of a glycosidic bond, transferring a ribose phosphate moiety from 5-phospho-α-d-ribose 1-diphosphate (PRPP) to an acceptor molecule (purine, pyrimidine, ATP, quinolinate, nicotinamide, etc.). APRT and hypoxanthine-guanine phosphoribosyltransferase (HGPRT) are both involved in the purine salvage pathway, in which purines acquired from the environment are converted to mononucleotides that feed into the overall nucleotide pool. These enzymes are thus vital for actively metabolizing cells of protozoan parasites and cancer tissues, and their deficiencies are causative of physiological disorders such as Lesch–Nyhan syndrome, gouty arthritis, and urolithiasis. HGPRT and APRT have distinct specificities for either 6-oxopurines (i.e. guanine and hypoxanthine) or 6-aminopurine (i.e. adenine), respectively. However, as these purines differ only in the functional groups at the C2 and C6 carbons, the basis for selectivity is unclear. Moreover, the extensive literature available (
      • Goitein R.K.
      • Chelsky D.
      • Parsons S.M.
      Primary 14C and α secondary 3H substrate effects for some phosphoribosyltransferases.
      ,
      • Tao W.
      • Grubmeyer C.
      • Blanchard J.S.
      Transition state structure of Salmonella typhimurium orotate phosphoribosyltransferase.
      ,
      • Focia P.J.
      • Craig 3rd, S.P.
      • Eakin A.E.
      Approaching the transition state in the crystal structure of a phosphoribosyltransferase.
      ,
      • Héroux A.
      • White E.L.
      • Ross L.J.
      • Davis R.L.
      • Borhani D.W.
      Crystal structure of Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase with XMP, pyrophosphate, and two Mg2+ ions bound: insights into the catalytic mechanism.
      ,
      • Shi W.
      • Li C.M.
      • Tyler P.C.
      • Furneaux R.H.
      • Grubmeyer C.
      • Schramm V.L.
      • Almo S.C.
      The 2.0 Å structure of human hypoxanthine-guanine phosphoribosyltransferase in complex with a transition-state analog inhibitor.
      ,
      • Shi W.
      • Li C.M.
      • Tyler P.C.
      • Furneaux R.H.
      • Cahill S.M.
      • Girvin M.E.
      • Grubmeyer C.
      • Schramm V.L.
      • Almo S.C.
      The 2.0 Å structure of malarial purine phosphoribosyltransferase in complex with a transition-state analogue inhibitor.
      ,
      • Thomas A.
      • Field M.J.
      A comparative QM/MM simulation study of the reaction mechanisms of human and Plasmodium falciparum HG(X)PRTases.
      ,
      • Moggré G.J.
      • Poulin M.B.
      • Tyler P.C.
      • Schramm V.L.
      • Parker E.J.
      Transition state analysis of adenosine triphosphate phosphoribosyltransferase.
      ) has demonstrated variations in reaction mechanism; for example, different HGPRTs have been shown to employ SN1 or SN2 mechanisms. The mechanism for APRT was not known.
      The new study from Ozeir et al. (
      • Ozeir M.
      • Huyet J.
      • Burgevin M.-C.
      • Pinson B.
      • Chesney F.
      • Remy J.-M.
      • Siddiqi A.R.
      • Lupoli R.
      • Pinon G.
      • Saint-Marc C.
      • Gibert J.-F.
      • Morales R.
      • Ceballos-Picot I.
      • Barouki R.
      • Daignan-Fornier B.
      • et al.
      Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction.
      ) takes on both of the mysteries surrounding APRT. The authors first report differential scanning fluorimetry data and biochemical assays that suggest hypoxanthine might not bind at all to hAPRT (
      • Ozeir M.
      • Huyet J.
      • Burgevin M.-C.
      • Pinson B.
      • Chesney F.
      • Remy J.-M.
      • Siddiqi A.R.
      • Lupoli R.
      • Pinon G.
      • Saint-Marc C.
      • Gibert J.-F.
      • Morales R.
      • Ceballos-Picot I.
      • Barouki R.
      • Daignan-Fornier B.
      • et al.
      Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction.
      ). Despite this information, they crystallize the protein in the presence of high concentrations of the purine, and remarkably, they get a crystal structure of the complex of human APRT (hAPRT) with hypoxanthine, PRPP, and Mg2+ in the active site. Similar experiments with guanine failed to trap this ligand in the active site. Comparing the hypoxanthine structure with a previous hAPRT–adenine–PRPP complex allowed them to determine molecular features responsible for conferring substrate specificity in this enzyme (Fig. 1). Compared with adenine, hypoxanthine shows relatively poorer electron density, as expected from its very weak affinity to the enzyme. Examination of the contacts of N1 and N3 of hypoxanthine with Arg-27 and Arg-67 in the ternary complex indicates that they are hydrogen bond acceptors, suggesting that the purine is present as the enol tautomer. The contact of C6O with the backbone carbonyl of Val-25 and the side chain of the catalytic base Glu-104 similarly points to the enol form. In contrast, in HGPRTs, the interaction with the side chain of an invariant lysyl residue ensures binding of the predominant keto form of the 6-oxopurine base (
      • Munagala N.R.
      • Wang C.C.
      Altering the purine specificity of hypoxanthine-guanine-xanthine phosphoribosyltransferase from Tritrichomonas foetus by structure-based point mutations in the enzyme protein.
      ) (Fig. 1A). The authors suggest that the destabilization effect of the enol form of hypoxanthine prevents phosphoribosylation. This may also suggest a general distinguishing principle for the two families of enzymes, one with specificity for oxopurines (keto form) and another with specificity for aminopurines.
      Figure thumbnail gr1
      Figure 1Structural basis of substrate selection in human APRT and reaction mechanism in phosphoribosyltransferases. A, contacts of hypoxanthine analog HPP with human HGPRT (PDB ID: 1D6N, left) and adenine with hAPRT (PDB ID: 6FCI, right). B, schematic of the basis of substrate selectivity in hAPRT. Among the purine bases, only adenine is turned over to give product AMP, whereas the weakly bound hypoxanthine in the active site remains uncatalyzed. Guanine does not bind to the enzyme active site.
      What about the reverse reaction? Unlike hypoxanthine and guanine, IMP and GMP do show moderate binding affinities with hAPRT, both in earlier inhibition studies and new differential scanning fluorimetry reported by Ozeir et al. (
      • Ozeir M.
      • Huyet J.
      • Burgevin M.-C.
      • Pinson B.
      • Chesney F.
      • Remy J.-M.
      • Siddiqi A.R.
      • Lupoli R.
      • Pinon G.
      • Saint-Marc C.
      • Gibert J.-F.
      • Morales R.
      • Ceballos-Picot I.
      • Barouki R.
      • Daignan-Fornier B.
      • et al.
      Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction.
      ). To understand why hAPRT can bind but not turn over these substrates, the authors obtained structures bound to IMP and GMP and compared these with the AMP-bound structure. Interestingly, in both IMP and GMP complexes, the oxopurine base appears to be in the keto form, meaning that other factors have impeded the reverse reaction from proceeding. The keto tautomers alter key hydrogen bonds with the purine nitrogens, leading to different energetics and different conformations within the ligand binding site. The AMP N1 interacts with the Arg-27 amide NH, whereas the protonated IMP N1 interacts with the Arg-27 backbone carbonyl, resulting in the displacement of the oxopurine ring that in turn reorients the Arg-67 side chain into the diphosphate-binding region, thereby occluding it from binding and catalysis. This diphosphate occlusion was observed in the GMP structure as well. Also, the ribose rings of IMP and GMP display 4′ endo conformations as compared with the 3′ exo conformation of AMP. This alternative geometry blocks the Mg2+ coordination that facilitates intermediate formation, inhibiting the reaction. These structural differences in protein–ligand interactions comprehensively explain substrate specificity in hAPRT.
      Finally, the authors use QM/MM calculations to explore the mechanism of hAPRT's two reactions. Their approach provides a highly accurate description of the electronic structure of atoms in the QM region using hybrid density functionals. Similar QM/MM calculations were used to determine the mechanism of another phosphoribosyltransferase, HG(X)PRTase, as following the DNAN (SN1) route (
      • Thomas A.
      • Field M.J.
      A comparative QM/MM simulation study of the reaction mechanisms of human and Plasmodium falciparum HG(X)PRTases.
      ). The current work of Ozeir et al. (
      • Ozeir M.
      • Huyet J.
      • Burgevin M.-C.
      • Pinson B.
      • Chesney F.
      • Remy J.-M.
      • Siddiqi A.R.
      • Lupoli R.
      • Pinon G.
      • Saint-Marc C.
      • Gibert J.-F.
      • Morales R.
      • Ceballos-Picot I.
      • Barouki R.
      • Daignan-Fornier B.
      • et al.
      Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction.
      ) argues for a ANDN (SN2) mechanism for the same reaction in hAPRT, as the DNAN route is shown to involve an intermediate with a high energy of 100 kJ/mol over the reactant state, unlike the ANDN mechanism, whose intermediate is 7 kJ/mol more stable than the reactants.
      It will be interesting to see what new information can be obtained from additional calculations that explicitly consider changes in the configurational entropy along the reaction coordinate, although the unfavorable DNAN intermediate suggests that these methods would not significantly alter the mechanism from the one proposed. Similarly, corroboration of these QM/MM studies with investigations involving kinetic isotope effect and spectroscopic methods should be performed to confirm the SN2 type mechanism in human APRT as proposed in this paper. Finally, it will be exciting to see how these new insights into hAPRT and HGPRT discrimination inform inhibitor design strategies, with the hope of disrupting parasites and cancer and treating human disorders.

      Acknowledgment

      We acknowledge all of the researchers whose work could not be cited due to space constraints.

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      Linked Article

      • Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction
        Journal of Biological ChemistryVol. 294Issue 32
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          The reversible adenine phosphoribosyltransferase enzyme (APRT) is essential for purine homeostasis in prokaryotes and eukaryotes. In humans, APRT (hAPRT) is the only enzyme known to produce AMP in cells from dietary adenine. APRT can also process adenine analogs, which are involved in plant development or neuronal homeostasis. However, the molecular mechanism underlying substrate specificity of APRT and catalysis in both directions of the reaction remains poorly understood. Here we present the crystal structures of hAPRT complexed to three cellular nucleotide analogs (hypoxanthine, IMP, and GMP) that we compare with the phosphate-bound enzyme.
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