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Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases Jason Burke, James La Clair, Ryan Philippe, Anna Pabis, Marina Corbella, Joseph M. Jez, George Cortina, Miriam Kaltenbach, Marianne E Bowman, Gordon Louie, Katherine Woods, Andrew T Nelson, Dan S. Tawfik, Shina Kamerlin, and Joseph P. Noel ACS Catal., Just Accepted Manuscript • DOI: 10.1021/acscatal.9b01926 • Publication Date (Web): 30 Jul 2019 Downloaded from pubs.acs.org on July 30, 2019
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ACS Catalysis
Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases Jason R. Burke,†,# James J. La Clair,† Ryan N. Philippe,†,# Anna Pabis,‡ Marina Corbella,⊥ Joseph M. Jez,†,# George A. Cortina,§ Miriam Kaltenbach,|| Marianne E. Bowman,† Gordon V. Louie,† Katherine B. Woods,† Andrew T. Nelson,¶ Dan S. Tawfik,|| Shina C.L. Kamerlin,⊥ and Joseph P. Noel†,* †Howard
Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States ‡Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden ⊥Department of Chemistry – BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden §Department of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, VA 22903, United States ||Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel ¶Department of Chemistry, University of Texas at Austin, Austin, TX 78712, United States ABSTRACT: Chalcone isomerases are plant enzymes that perform enantioselective oxa-Michael cyclizations of 2hydroxychalcones into flavanones. An X-ray crystal structure of an enzyme-product complex and molecular dynamics simulations reveal an enzyme mechanism wherein the guanidinium ion of a conserved arginine positions the nucleophilic phenoxide and activates the electrophilic enone for cyclization through Brønsted and Lewis acid interactions. The reaction terminates by asymmetric protonation of the carbanion intermediate syn to the guanidinium. Interestingly, bifunctional guanidine- and urea-based chemical reagents, increasingly used for asymmetric organocatalytic applications, share mechanistic similarities with this natural system. Comparative protein crystal structures and molecular dynamics simulations further demonstrate how two active site water molecules coordinate a hydrogen bond network that enables expanded substrate reactivity for 6-deoxychalcones in more recently evolved type-2 chalcone isomerases. KEYWORDS: Michaelase , asymmetric biocatalysis arginine general acid catalytic water bifunctional guanidine catalysis enzyme evolution flavonoid biosynthesis
arginine for asymmetric addition reactions of aldehydes to nitroolefins.6 In this system, enzyme promiscuity has been exploited to engineer highly enantioselective “Michaelase” enzymes for more diverse applications.7,8 On several occasions, Lipases have been successfully engineered into “Michaelase” enzymes, although high reaction rates and good enantioselectivity are existing challenges.9,10 Therefore, a better understanding of biocatalytic principles is needed to guide efforts to engineer “Michaelase” enzymes. On the other hand, the Michael reaction is common in organic syntheses where it offers one of the most versatile and elegant means to combine fragments and install complex molecular frameworks.11,12 Recent advances in organocatalytic design have honed the use of guanidine- and urea-based templates for bifunctional asymmetric catalysts, which deploy hydrogen bonds and Lewis acids to activate and position electrophilic and nucleophilic moieties.13 Here we show that the natural plant enzyme, chalcone isomerase (CHI), employs such a
INTRODUCTION During plant transitions from aquatic to terrestrial ecosystems approximately 450 million years ago, critical chemo-adaptations emerged to attenuate exposure to UV radiation. In part, the biosynthesis of polyphenol-based sunscreens likely provided protection by efficiently absorbing UV light and mitigating associated damage from oxidative stress.1 Over time, plants evolved diverse biological roles for flavonoids in guarding against pathogenesis and herbivory, facilitating phytohormone transport and microbial symbiosis, and modulating floral pigmentation.2 In plants, polycyclic flavanones arise via enzymatic intramolecular Michael reactions. While additional examples of enantioselective Michael-type reactions have been characterized in natural product biosynthesis that efficiently construct C-C and C-O bonds (recently reviewed in reference 3), detailed mechanistic studies on enzymatic Michael reactions have been limited so far.4,5 In a recent study, an engineered "Michaelase" utilizes an
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bifunctional strategy to direct the enantioselective cyclization of 2′-hydroxychalcones into flavanones. Two enzymatically distinct groups of CHIs guide the C-O bond forming oxa-Michael cyclization of flavanones in plants.14-18 Type-1 CHIs (CHI-1) are ubiquitous across the green plant lineage and catalyze the cyclization of 6′hydroxychalcones, such as 4,2′,4′,6′-tetrahydroxychalcone, to form chiral flavanones such as (2S)naringenin (Scheme 1). Type-2 CHIs (CHI-2) are more restricted throughout the plant kingdom and are most commonly found in Fabaceae (the Legume family). CHI2s possess comparable activity to CHI-1s for 6hydroxychalcones; however, CHI-2s also possess high activity for the more narrowly distributed 6deoxychalcones. The 6-deoxychalcones, such as 4,2,4trihydroxychalcone, contain a high energy intramolecular C=O--H-O bond, which prevents appreciable rates of auto-cyclization observed for 6-hydroxychalcones.19,20 These conformationally restrictive hydrogen bonds in 6deoxychalcones require CHI-2 catalytic activity for facile disruption and ensuing cyclization reactions.17,18 Here, we identify specific amino acid residues in CHI-2s that order active site waters to facilitate substrate reorganizations, enabling kinetically efficient ring closures of 6-deoxychalcones into reduced flavanones such as (2S)-liquiritigenin. O OH
H
RESULTS AND DISCUSSION To reveal the chemistry of the active site arginine and pinpoint the stereochemical differences that define substrate selectivity for CHI-1 versus CHI-2, we crystallized CHI-1 from Medicago truncatula (MtCHI-1), a close relative of the well-characterized CHI-2 from Medicago sativa (MsCHI-2).23-25 Protein crystals were transferred to a solution containing 4,2,4,6tetrahydroxychalcone and, over time, the crystalline proteins catalyzed the conversion of the substrate to (2S)-naringenin (Figure S1). The product-bound cocrystal structure was solved with eight fold protein molecules per asymmetric unit and electron density supporting (2S)-naringenin bound in five of the eight MtCHI-1 active sites (Figures 1a, S2, and Table S1). Crystallographic details of the MtCHI-1 • (2S)naringenin complex reveal multifunctional catalytic roles for the active site arginine (Arg37). Previous structures of MsCHI-2 • (2S)-naringenin show the catalytic arginine (Arg36) oriented away from the active site through a salt bridge interaction with Asp200 (Figure S3).18,19 However, mutation of Asp200 to Ala or Asn does not perturb enzyme activity, suggesting the crystallographic orientation of Arg36 in MsCHI-2 is non-productive (Table 1). In addition, differences in the positions and sterics of residues 196-202 in MtCHI-1 • (2S)-naringenin prohibit Arg37 from an orientation similar to that of Arg36 in MsCHI-2 (Figure S3). Instead, the MtCHI-1 • (2S)naringenin complex reveals that the carbocation center (C) of Arg37 resides within van der Waals radial distance of the product’s pyran oxygen (1O), supporting a role for Arg37 as a Lewis acid in stabilizing the nucleophilic 2′-oxoanion of the chalcone substrate (Figure 1b, Table S2). The guanidine of Arg37 forms a shared H-1O hydrogen bond with (2S)-naringenin, positing a mechanism in which Arg37 orients the substrate’s 2′-oxyanion for ring closure. Furthermore, the
O
6'
2 3
HO 4'
2
HO 4'
Although structures of CHIs have revealed an array of thermodynamically favored conformations for the active site arginine, evidence of its catalytic role has remained elusive.22-26 Protein X-ray crystal structures in conjunction with molecular dynamics simulations have further shaped our mechanistic understanding of the intramolecular oxaMichael reactions in both CHI-1s and CHI-2s.23-30 From a protein crystal structure of product-bound CHI-1, we here delineate the key catalytic roles of the conserved active site arginine in both aligning a nucleophilic Michael donor (2O-) and enhancing the electrophilicity of the enone Michael acceptor (C) through both Brønsted and Lewis acid interactions. Consistent with these observed structured interactions, the data presented support a model in which the reaction terminates upon the asymmetric transfer of a proton from the guanidinium moiety of the arginine to the substrate carbanion tautomer at C. The mechanistic details presented herein correlate features of this natural biocatalytic reaction with diverse, guanidine-based organocatalysts, developed for varied applications in asymmetric syntheses.13,31
2'
O
3
2' OH
4 4
OH
OH O
4,2',4',6'-tetrahydroxychalcone
2
HO 4'
CHI-1 & CHI-2
3
2' OH
4
OH
4,2',4'-trihydroxychalcone
CHI-2 OH
O
5
O 3
3
2
HO
7
2
O
HO
1
(2S)-naringenin
4' OH
7
O 1
4'
(2S)-liquiritigenin
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OH
Scheme 1. CHI-2s catalyze the cyclization of 6hydroxychalcones and 6-deoxychalcones into (2S)flavanones; CHI-1s are selective for 6-hydroxychalcones. All plant CHI enzymes evolved from a larger family of non-enzymatic, Fatty Acid Binding Proteins (FAPs), present throughout green plants, fungi, and protists.21 The emergence and evolution of enzyme activity in the CHI-fold was enabled, in part, by a founder mutation that expands the dynamism and conformational space of an active site arginine.22 In non-catalytic FAPs, the same arginine plays a structural role in fatty-acid binding.21
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ACS Catalysis
guanidine of Arg37 is positioned to act asymmetrically as a Brønsted acid through a shared H bond with C3 of
(2S)-naringenin (C in 4,2,4,6-tetrahydroxychalcone). This Brønsted acid
Figure 1. Structural role of the arginine in CHI catalysis. (a) X-ray crystal structure of MtCHI-1 bound with (2S)-naringenin. (b) Enzyme-product interactions suggest how the guanidinium of Arg37 directs ring closure by positioning and activating the substrate through hydrogen bonds (yellow dotted lines) and a Lewis acid interaction (red dotted line). (c) The conformational space defined by six Arg37-substrate contacts (Hη2-2O-, Hε-Cα, Nη1-2O-, Nη2-2O-, Hε-2O-, Cζ-2O-) and reactive 2O--C distance observed in simulations of MtCHI-1 in complex with 4,2,4,6-tetrahydroxychalcone, support the existence of stable enzymesubstrate interactions that are favorable for catalysis.
simultaneously position and activate both a nucleophile and electrophile through Lewis acid and Brønsted acid interactions for conjugate addition.38 Together, the mechanistic similarity of these examples of guanidine based organocatalysts highlights the potential for chalcone isomerases to serve as proteinaceous catalysts in diverse enantioselective chemical applications, as direct, natural complements for synthetic catalyst design. Recent studies have identified alternatives to guanidinium-based asymmetric catalysis of flavanones from chalcones. Chiral thioureas derived from quinine/quinidine scaffolds have been adapted as synthetic mimetics of CHI enantioselective functionality.39,40 The human gut bacterium, Eubacterium ramulus, which evolved CHI activity from an unrelated protein fold, reverses the reaction for flavonoid catabolism.41,42 The bacterial CHI is similar to plant CHIs in its selectivity for (2S)-flavanones; however, for the bacterial CHI an active site histidine facilitates general acid/base catalysis. The active site arginine is essential for efficient catalysis in plant CHIs. Chalcone isomerases catalyze enantioselective cyclizations of 2′-hydroxychalcones into flavanones with remarkably high catalytic efficiencies for plant enzymes.14,22-26. For MsCHI-2, mutations of Arg36 (R36A, R36H, R36M and R36Q) result in approximately 104 to 105-fold reductions in catalytic turnover (kcat min1) of 4,2,4,6-tetrahydroxychalcone and 4,2,4trihydroxychalcone, respectively (Table 1). For both MsCHI-2 and MtCHI-1, substitutions of active site arginines with lysines also dramatically reduce catalytic turnover: approximately 103-fold for 4,2,4,6tetrahydroxychalcone, and >103-fold for 4,2,4trihydroxychalcone with MsCHI-2 (Table 1). For MsCHI-2 and MtCHI-1, these results support a role for the arginine residue in facilitating CHI catalysis by acting as more than a simple point charge, but instead carrying out delocalized, multidentate functions.
interaction may increase the electrophilicity of the olefin at C further favoring the approach to a catalytically productive substrate conformation. Molecular dynamics of MtCHI-1 in complex with 4,2,4,6-tetrahydroxychalcone indicate a clear preference for substrate conformations approaching cyclization. In these simulations, the nucleophilic Michael donor is stabilized by the guanidinium ion of Arg37, primarily through simultaneous interaction with the N and N atoms of the arginine side chain, as well as the carbocationic center of the ion (C) (Figure 1c and Table S3). At the same time, the mutual orientation of Arg37 and the substrate in the simulated Michaelis complex, and the proximity of the N group to the C atom supports the posited role of the guanidinium ion acting as a Brønsted acid in the enantioselective cyclization of 4,2,4,6-tetrahydroxychalcone. Furthermore, analysis of the joint distribution of the χ1 and χ3 dihedral angles, sampled by the Arg36/37 side chains of MsCHI-2 and MtCHI-1 in our molecular dynamic simulations, highlights that the catalytically optimal conformation for this residue is also a stable conformation (Figure S4). Together with the structures, these results highlight how the positioning, electrostatics and hydrogen bond geometry of arginine’s natural guanidine work to simultaneously stabilize, organize and activate multiple moieties involved in conjugate addition reactions. Intriguingly, these structural details correlate features of this biocatalytic reaction with asymmetric organocatalysts developed for the Strecker reaction,32 Michael reactions,33-35 and Claisen rearrangements,36,37 among others.38 For example, Lewis acid and Brønsted acid interactions, mediated through the guanidinium moiety of a chiral, triazabicyclo[4.4.0]dec-5-ene (TBD)based catalyst, direct a tandem thiol Michael addition toward a particular stereochemical outcome.33 Further, an X-ray crystal structure of the TBD catalyst clearly demonstrates the capacity of the guanidinium to
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MsCHI-2 D200N 2,730 ± 161 12.6 ± 2.3 3,610,000 MtCHI-1 0.15 ± 0.13 44 ± 48 56 AtCHI-1 0.064 ±0.005 16.8 ± 3.5 42 AtCHI-1 V106G 0.16 ±0.02 31.9 ± 8.5 603 aWhere saturation was not observed, k /K values were estimated cat M using kcat/[S]
Stereochemistry of the proton transfer step. The orientation and proximity of the guanidinium NH bond to the 3C carbon of (2S)-naringenin suggest that Arg37 delivers H to the carbanion tautomer of the substrate’s enolate intermediate (Figure 1b). Using fractionated lysates from the Fabaceae, Vigna radiata (Mung Bean), an early investigation reported CHImediated protonation of C consistent with the formation of the H-C bond syn to the O-C bond of 4,2′,4′-trihydroxychalcone.43,44 However, ambiguities were noted in the interpretation of these NMR spectra due to unresolved heterogeneities. In light of the catalytic role and positioning of Arg37 in the structure of MtCHI-1, we evaluated the stereochemistry of the proton transfer, and expanded the scope of the study to include homogenously purified MtCHI-1, MsCHI-2, and the ubiquitous substrate, 4,2,4,6-tetrahydroxychalcone.
Flavanones formed by MtCHI-1 and MsCHI-2 in the presence of water exhibit two doublets of doublets by proton NMR, characteristic of equatorial and axial protons at the C atoms in these products (Figures 2a-b and S5). When the enzyme reactions are run in D2O, the flavanone proton peaks corresponding to H-ax are absent and the H-eq peaks occur as doublets with small J-coupling constants indicative of gauche orientations relative to H-ax protons. These data unequivocally demonstrate that H-ax derives from enzyme-mediated protonation of the si (pro-S) face of the carbanion tautomer intermediate for both CHI-1 and CHI-2. Nonenzymatic cyclization of 4,2,4,6-tetrahydroxychalcone into naringenin in D2O results in deuterium incorporation at both the H-ax and H-eq positions equivalently (Figure 2c). Together, these results are consistent with a structural model in which the H proton of the guanidinium is transferred to the carbanion tautomer of the enolate intermediate during enzymatic cyclization of (2S)-flavanones. While arginine is often considered an unlikely candidate to function as a general acid/base in enzymatic reactions because of the apparent high pKa of its guanidinium group (pKa 13.8),45 exceptions have been described for citrate synthase,46 serine recombinase,47 IMP dehydrogenase,48 endoribonuclease,49-51 and fumarate reductase52-54. Current hypotheses that posit the role of arginines as general acids/bases in enzyme catalysis depend upon: (1) pKa values of substrates, (2) geometric constraints of the guanidinium cations in the postulated enzyme transition states,55,56 (3) burial of side chain charges in hydrophobic environments,57 and (4) in the case of fumarate reductase, proton shuttling via a Grotthus-like mechanism.54,58 It is probable that CHI enzymes share mechanistic features with these studied systems. For example, similar to Grotthus-like mechanisms, and mechanisms in which proximal charges affect pKa values, a buried, active site Lys97-Zundel cation feature in CHI-2 may serve to reduce the effective pKa of the catalytic arginine, priming it as a Brønsted base to deprotonate the substrate 2′OH.23,34 Strong kinetic isotope effects for CHI-2, which are dependent upon the water-coordinating side chains of Thr48 and Tyr106, suggest proton transfer along the Lys97-linked water chain is rate limiting.25 Proton transfer can frequently be the rate limiting step of enzyme catalysis, as recently demonstrated for a catalytic arginine in the heme biosynthesis enzyme, uroporphyrinogen III decarboxylase.59 Finally, there is growing evidence that flavonoid biosynthesis occurs within endoplasmic reticulum-anchored metabolons which contain chalcone isomerases.60,61 Membrane environments, such as these, have been estimated to reduce the pKa of arginine’s guanidinium greater than 4 units, providing an
Table 1. Michaelis Menten Kinetics 4,2′,4′,6′-tetrahydroxychalcone kcat (min-1) MsCHI-2 MsCHI-2 R36Aa MsCHI-2 R36H MsCHI-2 R36K MsCHI-2 R36Ma MsCHI-2 R36Qa MsCHI-2 G95S MsCHI-2 G95T MsCHI-2 G95V MsCHI-2 K97A MsCHI-2 K97E MsCHI-2 K97M MsCHI-2 K97Q MsCHI-2 K109M MsCHI-2 D200A MsCHI-2 D200N MtCHI-1 MtCHI-1 R37K MtCHI-1 T49A MtCHI-1 Y107F MtCHI-1 K110M MtCHI-1 S193A AtCHI-1 AtCHI-1 V106G
MsCHI-2 MsCHI-2 R36Aa MsCHI-2 R36H MsCHI-2 R36K MsCHI-2 R36Ma MsCHI-2 R36Qa MsCHI-2 G95S MsCHI-2 G95T MsCHI-2 G95V MsCHI-2 K97A MsCHI-2 K97E MsCHI-2 K97M MsCHI-2 K97Q MsCHI-2 K109M MsCHI-2 D200A
KM (M)
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kcat/KM (s-1 M-1)
11,180 ± 1,380 112 ± 28 1,660,000 2.1
