From cofactor to enzymes. The molecular evolution of pyridoxal-5'-phosphate-dependent enzymes

The pyridoxal-5'-phosphate (vitamin B(6))-dependent enzymes that act on amino acid substrates have multiple evolutionary origins. Thus, the common mechanistic features of B(6) enzymes are not accidental historical traits but reflect evolutionary or chemical necessities. The B(6) enzymes belong to four independent evolutionary lineages of paralogous proteins, of which the alpha family (with aspartate aminotransferase as the prototype enzyme) is by far the largest and most diverse. The considerably smaller beta family (tryptophan synthase beta as the prototype enzyme) is structurally and functionally more homogenous. Both the D-alanine aminotransferase family and the alanine racemase family consist of only a few enzymes. The primordial pyridoxal-5'-phosphate-dependent protein catalysts apparently first diverged into reaction-specific protoenzymes, which then diverged further by specializing for substrate specificity. Aminotransferases as well as amino acid decarboxylases are found in two different evolutionary lineages, providing examples of convergent enzyme evolution. The functional specialization of most B(6) enzymes seems to have already occurred in the universal ancestor cell before the divergence of eukaryotes, archebacteria, and eubacteria 1500 million years ago. Pyridoxal-5'-phosphate must have emerged very early in biological evolution; conceivably, metal ions and organic cofactors were the first biological catalysts. To simulate particular steps of molecular evolution, both the substrate and reaction specificity of existent B(6) enzymes were changed by substitution of active-site residues, and monoclonal pyridoxal-5'-phosphate-dependent catalytic antibodies were produced with selection criteria that might have been operative in the evolution of protein-assisted pyridoxal catalysis.     

Pyridoxal-5'-phosphate-dependent catalytic antibodies

Cofactors--i.e., metal ions and coenzymes--extend the catalytic scope of enzymes and might have been among the first biological catalysts. They may be expected to efficiently extend the catalytic potential of antibodies. Monoclonal antibodies (MAbs) against Nalpha-phosphopyridoxyl-L-lysine were screened for 1) binding of 5'-phosphopyridoxyl amino acids, 2) binding of the planar Schiff base of pyridoxal-5'-phosphate (PLP) and amino acids, the first intermediate of all PLP-dependent reactions, and 3) catalysis of the PLP-dependent alpha, beta-elimination reaction with beta-chloro-D/L-alanine. Antibody 15A9 fulfilled all criteria and was also found to catalyze the cofactor-dependent transamination reaction of hydrophobic D-amino acids and oxo acids (k'cat = 0.42 min(-1) with D-alanine at 25 degrees C). No other reactions with either D- or L-amino acids were detected. PLP markedly contributes to catalytic efficacy-it is a 10(4) times more efficient acceptor of the amino group than pyruvate. The antibody ensures reaction specificity, stereospecificity, and substrate specificity, and further accelerates the transamination reaction (k'cat(Ab)/k'cat(PLP) = 5 x 10(3)). The successive screening steps simulate the selection criteria that might have been operative in the evolution of protein-assisted pyridoxal catalysis.     

Evolution of function in the crotonase superfamily: the stereochemical course of the reaction catalyzed by 2-ketocyclohexanecarboxyl-CoA hydrolase

Members of the mechanistically diverse enoyl-CoA hydratase (crotonase) superfamily catalyze reactions that involve stabilization of an enolate anion derived from an acyl thioester of coenzyme A. 2-Ketocyclohexanecarboxyl-CoA hydrolase (BadI), found in a pathway for anaerobic degradation of benzoate by Rhodopseudomonas palustris, is a member of the crotonase superfamily that catalyzes a reverse Dieckmann reaction in which the substrate is hydrolyzed to pimelyl-CoA. The substrate is the configurationally labile 2S-ketocyclohexanecarboxyl-CoA, and in 2H2O solvent hydrogen is incorporated into the 2-proS position of the pimelyl-CoA product. Therefore, the stereochemical course of the BadI-catalyzed reaction is inversion. This information is important for understanding the roles of active-site functional groups in the active site of BadI as well as in the active sites of the homologous 1,4-dihydroxynaphthoyl-CoA synthases that catalyze a forward Dieckmann reaction.     

Mechanistic diversity of fosfomycin resistance in pathogenic microorganisms

Microbial resistance to the antibiotic fosfomycin [(1R,2S)-epoxypropylphosphonic acid, 1] is known to be mediated by thiol transferase enzymes FosA and FosB, which catalyze the addition of glutathione and l-cysteine to C1 of the oxirane, respectively. A probe of the microbial genome database reveals a related group of enzymes (FosX). The genes mlr3345 from Mesorhizobium loti and lmo1702 from Listeria monocytogenes were cloned and the proteins expressed. This heretofore unrecognized group of enzymes is shown to catalyze the Mn(II)-dependent addition of water to C1 of the oxirane. The ability of each enzyme to confer resistance in Escherichia coli is correlated with their catalytic efficiency, such that the M. loti protein confers low resistance while the Listeria enzyme confers very robust resistance. The crystal structure of the FosX from M. loti was solved at a resolution of 1.83 A. The structure reveals an active-site carboxylate (E44) located about 5 A from the expected position of the substrate that appears to be poised to participate in catalysis. Single turnover experiments in H218O and kinetic analysis of the E44G mutant of the FosX enzymes indicate that the carboxylate of E44 acts as a general base in the direct addition of water to 1. The FosX from M. loti also catalyzes the addition of glutathione to the antibiotic. The catalytic promiscuity and low efficiency of the M. loti protein suggest that it may be an intermediate in the evolution of clinically relevant fosfomycin resistance proteins such as the FosX from Listeria monocytogenese.     

ETUDE PAR FLUORESCENCE DE BASES DE SCHIFF DU PYRIDOXAL, COMPARAISON AVEC LA L ASPARTATE-AMINOTRANSFERASE

Abstract— –Absorption and emission spectra of Schiff bases of pyridoxal-HCI or pyridoxal-5-phosphate with L-valine, n -butylamine or N-α-acetyl-L-lysine-N-methylamide have been studied as a function of pH. We can write the complete ionization diagram and equilibria. The results of Martell[6] are confirmed: the forms analogous to the coenzyme in aspartate aminotransferase, which absorb at 410 nm and 360 nm (or 340 nm for the Schiff base with n-butyl-amine) have the phenol OH ionized; the imine nitrogen is protonated for species absorbing at 410nm (in the enzyme: inactive form and complex with aminoacid) and unprotonated for species absorbing at 360 nm (in the enzyme, active form). Their fluorescence wavelengths are respectively 500 nm and 430 nm. Protonation of the pyridine nitrogen of these forms does not shift the absorption band; the fluorescence intensity is 20-fold greater for the N-protonated forms.
The real pK of the imine nitrogen is 8.5 ±0.8 for species with pyridine N-protonated or 10.4 for the non-protonated forms. The observed pK 6.3 in the enzyme can be explained if the imine nitrogen is hydrogen bonded to an amino-acid side chain of the protein: lysine, tyrosine, serine, sulfhydryl.
The quantum yield of the coenzyme fluorescence in the enzyme has been compared to that of the analogous Schiff base (absorbing at the same wavelength). According to the results, we cannot deduce whether the pyridine nitrogen is protonated in pyridoxal form of the enzyme.
If it is protonated, as in the pyridoxamine form, the coenzyme environment is not the same in the two forms. If the pyridine nitrogen is unprotonated in the pyridoxal form and protonated in the pyridoxamine form, the environment of the coenzyme is the same in these two forms of the enzyme.     

Stereochemistry of reactions of the inhibitor/substrates L- and D-beta-chloroalanine with beta-mercaptoethanol catalysed by L-aspartate aminotransferase and D-amino acid aminotransferase respectively

Two members of the alpha-family of PLP-dependent enzymes, L-aspartate aminotransferase and D-amino acid aminotransferase, have been shown to catalyse beta-substitution of L- and D-beta-chloroalanine respectively with beta-mercaptoethanol, reactions typical of the beta-family of PLP-dependent enzymes. The reaction catalysed by L-aspartate aminotransferase has been shown to occur with retention of stereochemistry, a typical outcome for reactions catalysed by beta-family enzymes. There are also indications that the reaction catalysed by D-amino acid aminotransferase may involve retention of stereochemistry. Both enzymes have been shown to catalyse exchange at C-3 when the appropriate enantiomer of beta-chloroalanine is the substrate.     

The structure of NADH in the enzyme dTDP-d-glucose dehydratase (RmlB)

The structure of Streptococcus suis serotype type 2 dTDP-d-glucose 4,6-dehydratase (RmlB) has been determined to 1.5 A resolution with its nicotinamide coenzyme and substrate analogue dTDP-xylose bound in an abortive complex. During enzyme turnover, NAD(+) abstracts a hydride from the C4' atom of dTDP-glucose-forming NADH. After elimination of water, hydride is then transferred back to the C6' atom of dTDP-4-keto-5,6-glucosene-regenerating NAD(+). Single-crystal spectroscopic studies unambiguously show that the coenzyme has been trapped as NADH in the crystal. Electron density clearly demonstrates that in contrast to native structures of RmlB where a flat nicotinamide ring is observed, the dihydropyridine ring of the reduced cofactor in this complex is found as a boat. The si face, from which the pro-S hydride is transferred, has a concave surface. Ab initio electronic structure calculations demonstrate that the presence of an internal hydrogen bond, between the amide NH on the nicotinamide ring and one of the oxygen atoms on a phosphate group, stabilizes this distorted conformation. Additionally, calculations show that the hydride donor ability of NADH is influenced by the degree of bending in the ring and may be influenced by an active-site tyrosine residue (Tyr 161). These results demonstrate the ability of dehydratase enzymes to fine-tune the redox potential of NADH through conformational changes in the nicotinamide ring.     

A 13C n.m.r. study of the B6 vitamins and of their aldimine derivatives

The vitamins, pyridoxine, pyridoxal, pyridoxamine, pyridoxal-5′-phosphate and pyridoxamine-5′-phosphate, have been studied in aqueous solution over a pH range of 2–12 by ¹³C nuclear magnetic resonance spectroscopy. Resonance assignments are made primarily by the spin–spin coupling constants of carbons with protons and with phosphorus. The proton–carbon coupling constants show a marked conformational dependence in the hemiacetal form of pyridoxal. Furthermore, the H-6? C-5 coupling constant in the vitamins is much smaller than the corresponding constant in pyridine. This may be due either to an effect of the C-5 substituent in vitamins or to a different electronic configuration of the zwitterionic hydroxypyridine ring. The addition of manganese to a solution of pyridoxal phosphate causes line broadenings consistent with the interaction of the metal ion with this vitamin at the formyl and phenolic oxygens. The chemical shifts of the aromatic carbons of pyridoxine have been calculated, as a function of pH, by summing shielding parameters which were estimated empirically from pyridine derivatives. The calculated shifts agree well with the experimental data for C-3, C-5 and C-6, less well for C-2, and poorly for C-4. The deviation from additivity for C-4 indicates a preferred orientation for the 4-hydroxymethyl substituent caused by internal hydrogen bonding between the substituents at C-3 and C-4. Evidence is presented for the existence of the free aldehyde form of pyridoxal at alkaline pH. Aldimine complexes of pyridoxal and pyridoxal phosphate with amines and amino acids have also been studied. Characteristic chemical shift changes caused by both pyridinium and aldimine nitrogen deprotonations are seen. Additionally, the chemical shifts of carbons of the pyridine ring are dependent upon the structure of the imine, especially when the aldimine nitrogen is protonated. We conclude that this dependency is due to steric effects in an aldimine complex which is constrained by internal hydrogen bonding. We also discuss the merits of carbons 3 and 4 as possible sites of cofactor labeling for enzymatic studies.     

Rapid photodynamics of vitamin B6 coenzyme pyridoxal 5'-phosphate and its Schiff bases in solution

The active form of vitamin B6, pyridoxal 5'-phosphate (PLP), is an important cofactor for numerous enzymes in amine and amino acid metabolism. Presented here is the first femtosecond transient absorption study of free PLP and two Schiff bases, PLP-valine and PLP-alpha-aminoisobutyric acid (AIB), in solution. Photoexcitation of free PLP leads to efficient triplet formation with an internal conversion rate that increases with increasing pH. The measured excited-state kinetics of the PLP-valine Schiff base exhibits a dramatic deuterium dependence as a result of excited-state proton transfer (ESPT) of the Calpha hydrogen in the amino acid substrate. This is consistent with formation of the key reaction carbanionic intermediate (quinonoid), which is resonance stabilized by the electron-deficient, conjugated pi system of the Schiff base/pyridine ring. The transient absorption signals of the PLP-Schiff base with alpha-methylalanine (2-aminoisobutyric acid), which does not have a Calpha proton, lack an observable deuterium effect, verifying ESPT formation of the quinonoid intermediate. In contrast to previous studies, no dependence on the excitation wavelength of the femtosecond kinetics is observed with PLP or PLP-valine, which suggests that a rapid (<250 fs) tautomerization occurs between the enolimine (absorbing at 330 nm) and ketoenamine (absorbing at 410 nm) tautomers in solution.     

Kinetic isotope effects of L-Dopa decarboxylase

A mixed centroid path integral and free energy perturbation method (PI-FEP/UM) has been used to investigate the primary carbon and secondary hydrogen kinetic isotope effects (KIEs) in the amino acid decarboxylation of L-Dopa catalyzed by the enzyme L-Dopa decarboxylase (DDC) along with the corresponding uncatalyzed reaction in water. DDC is a pyridoxal 5'-phosphate (PLP) dependent enzyme. The cofactor undergoes an internal proton transfer between the zwitterionic protonated Schiff base configuration and the neutral hydroxyimine tautomer. It was found that the cofactor PLP makes significant contributions to lowering the decarboxylation barrier, while the enzyme active site provides further stabilization of the transition state. Interestingly, the O-protonated configuration is preferred both in the Michaelis complex and at the decarboxylation transition state. The computed kinetic isotope effects (KIE) on the carboxylate C-13 are consistent with that observed on decarboxylation reactions of other PLP-dependent enzymes, whereas the KIEs on the α carbon and secondary proton, which can easily be validated experimentally, may be used as a possible identification for the active form of the PLP tautomer in the active site of DDC.     

Charge at the migrating hydrogen in the transition state of hydride transfer reactions from CH groups to hydride acceptors. Dynamics of the redox‐couple NADH‐NAD+

We consider the controversial conclusions of the charge at the migrating hydrogen in the transition state of hydride‐transfer reactions from CH‐groups to hydride acceptors. Quantum chemical calculations were performed on elementary organic reactions involving carbenium ions, which can be considered as hydride acceptors. We also discuss the biochemical hydride‐transfer reactions in which the coenzyme NADH‐NAD⁺ plays an important role. With the calculations and the experimental model systems, an answer is given for the stereospecificity of the hydride transfer. Generally, the hydride transfer occurs via a trigonal pyramidal geometry in which the transferred hydride of the CH‐group is located in the axial position. In the case of the coenzyme NADH‐NAD⁺, the hydride transfer is coupled with an out‐of‐plane orientation of the carboxamide group of the pyridinium moiety, resulting in an increased stereospecificity. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Plasma B-6 vitamer and plasma and urinary 4-pyridoxic acid concentrations in young women as determined using high performance liquid chromatography.

Plasma B-6 vitamer and plasma and urinary 4-pyridoxic acid concentrations of 21 young white women, 21-27 years, having radiomonitored pyridoxal 5'-phosphate and coenzyme stimulation of erythrocyte alanine aminotransferase activities indicative of adequate vitamin B-6 status were determined in an effort to establish normal ranges for plasma B-6 vitamers. B-6 vitamers and 4-pyridoxic acid were quantitated using reversed phase high performance liquid chromatography with fluorometric and ultraviolet detection. Pyridoxal phosphate values obtained by radioenzymatic and chromatographic, fluorometric and ultraviolet, assays were highly correlated as were pyridoxine phosphate values determined using both detectors. The B-6 vitamer and 4-pyridoxic acid values of these subjects should be of use in the establishment of normal ranges of these congeners in women.     

How an enzyme tames reactive intermediates: positioning of the active-site components of lysine 2,3-aminomutase during enzymatic turnover as determined by ENDOR spectroscopy

Lysine 2,3-aminomutase (LAM) utilizes a [4Fe-4S] cluster, S-adenosyl-L-methionine (SAM), and pyridoxal 5'-phosphate (PLP) to isomerize L-alpha-lysine to L-beta-lysine. LAM is a member of the radical-SAM enzyme superfamily in which a [4Fe-4S]+ cluster reductively cleaves SAM to produce the 5'-deoxyadenosyl radical, which abstracts an H-atom from substrate to form 5'-deoxyadenosine (5'-Ado) and the alpha-Lys* radical (state 3 (Lys*)). This radical isomerizes to the beta-Lys* radical (state 4(Lys*)), which then abstracts an H-atom from 5'-Ado to form beta-lysine and the 5'-deoxyadenosyl radical; the latter then regenerates SAM. We use 13C, 1,2H, 31P, and 14N ENDOR to characterize the active site of LAM in intermediate states that contain the isomeric substrate radicals or analogues. With L-alpha-lysine as substrate, we monitor the state with beta-Lys*. In parallel, we use two substrate analogues that generate stable analogues of the alpha-Lys* radical: trans-4,5-dehydro-L-lysine (DHLys) and 4-thia-L-lysine (SLys). This first glimpse of the motions of active-site components during catalytic turnover suggests a possible major movement of PLP during catalysis. However, the principal focus of this work is on the relative positions of the carbons involved in H-atom transfer. We conclude that the active site facilitates hydrogen atom transfer by enforcing van der Waals contact between radicals and their reacting partners. This constraint enables the enzyme to minimize and even eliminate side reactions of highly reactive species such as the 5'-deoxyadensosyl radical.     

Dual substrate recognition of aminotransferases

Pyridoxal 5'-phosphate-dependent aminotransferases reversibly catalyzes the transamination reaction in which the alpha-amino group of amino acid 1 is transferred to the 2-oxo acid of amino acid 2 (usually 2-oxoglutarate) to produce the 2-oxo acid of amino acid 1 and amino acid 2 (glutamate). An aminotransferase must thus be able to recognize and bind two kinds of amino acids (amino acids 1 and 2), the side chains of which are different in shape and properties, from among many other small molecules. The dual substrate recognition mechanism has been discovered based on three-dimensional structures of aromatic amino acids, histidinol phosphate, glutamine:phenylpyruvate, acetylornithine, and branched-chain amino acid aminotransferases. There are two representative strategies for dual substrate recognition. An aromatic amino acid aminotransferase prepares charged and neutral pockets for acidic and aromatic side chains, respectively, at the same place by a large-scale rearrangement of the hydrogen-bond network caused by the induced fit. In a branched-chain aminotransferase, the same hydrophobic cavity implanted with hydrophilic sites accommodates both hydrophobic and acidic side chains without side-chain rearrangements of the active-site residues, which is reminiscent of the lock and key mechanism. Dual substrate recognition in other aminotransferases is attained by combining the two representative methods.     

Theoretical studies on pyridoxal 5'-phosphate-dependent transamination of alpha-amino acids

Density functional methods have been applied to investigate the irreversible transamination between glyoxylic acid and pyridoxamine analog and the catalytic mechanism for the critical [1,3] proton transfer step in aspartate aminotransferase (AATase). The results indicate that the catalytic effect of pyridoxal 5'-phosphate (PLP) may be attributed to its ability to stabilize related transition states through structural resonance. Additionally, the PLP hydroxyl group and the carboxylic group of the amino acid can shuttle proton, thereby lowering the barrier. The rate-limiting step is the tautomeric conversion of the aldimine to ketimine by [1,3] proton transfer, with a barrier of 36.3 kcal/mol in water solvent. A quantum chemical model consisting 142 atoms was constructed based on the crystal structure of the native AATase complex with the product L-glutamate. The electron-withdrawing stabilization by various residues, involving Arg386, Tyr225, Asp222, Asn194, and peptide backbone, enhances the carbon acidity of 4'-C of PLP and Calpha of amino acid. The calculations support the proposed proton transfer mechanism in which Lys258 acts as a base to shuttle a proton from the 4'-C of PLP to Calpha of amino acid. The first step (proton transfer from 4'-C to lysine) is shown to be the rate-limiting step. Furthermore, we provided an explanation for the reversibility and specificity of the transamination in AATase.     

Enzymatic reduction of ribonucleotides: biosynthesis pathway of deoxyribonucleotides

Ribonucleotide reductases are enzymes that synthesize the deoxyribonucleotides required for the replication of DNA in dividing cells. They thus have a key function for the growth of microorganisms and of all plant and animal tissues. The enzymes reduce all four purine and pyrimidine ribonucleotides (as the 5′-diphosphates or triphosphates) with direct substitution of the 2′-hydroxyl group by hydrogen. The physiological reducing agents are the mercapto groups of thioredoxins, a group of small proteins, which are regenerated from the oxidized form by NADPH-dependent thioredoxin reductases. There are two known types of ribonucleotide reductases (I and II), which catalyze hydrogen transfer with the aid of protein-bound iron ions or of 5′-deoxyadenosylcobalamin (coenzyme B₁₂); free radicals can be detected in both cases. The enzymes are regulated by effector nucleotides. There may exist a homeostatic mechanism, which guarantees the supply of DNA precursors to the cell.     

Promiscuous catalysis by the tetrahymena group I ribozyme

Catalytic promiscuity, the ability of an enzyme to catalyze alternative reactions, has been suggested to have played an important role in the evolution of new catalytic activities in protein enzymes. Similarly, promiscuous activities may have been advantageous in an earlier RNA world. The Tetrahymena Group I ribozyme naturally catalyzes the site-specific guanosine attack on an anionic phosphate diester and has been shown to also catalyze aminoacyl transfer to water, albeit with a small rate acceleration (<10-fold). This inefficient catalysis could be due to the differences in charge and/or geometry requirements for the two reactions. Herein, we describe a new promiscuous activity of this ribozyme, the site-specific guanosine attack on a neutral phosphonate diester. This alternative substrate lacks the negative charge at the reaction center but, in contrast to the aminoacyl substrate, can undergo nucleophilic attack with the same geometry as the natural substrate. Our results show that the neutral phosphonate reaction is catalyzed about 1 x 106-fold, substantially better than the acyl transfer but far below the normal anionic substrate. We conclude that both charge and geometry are important factors for catalysis of the normal reaction and that promiscuous catalytic activities of ribozymes could have been created or enhanced by reorienting and swapping RNA domains.     

Through the Looking Glass: Chiral Recognition of Substrates and Products at the Active Sites of Racemases and Epimerases

Unlike most enzymes, which exhibit stereospecific substrate binding, racemases and epimerases bind and catalyze the reversible interconversion of enantiomeric and epimeric pairs of substrates. Over the past 15 years, a growing number of racemase and epimerase structures have been solved, furnishing insights into the nature of chiral recognition of substrates by these enzymes. Those enzymes catalyzing stereoinversion of a carbon acid substrate through a direct 1,1-proton transfer mechanism all bind their substrates in a mirror-image packing orientation. This does not apply generally to racemases and epimerases that use other mechanisms, such as NADH-dependent epimerases that employ a “flipping” mechanism. In general, polar groups are bound and fixed at the three binding determinants on the protein defining a pseudo-mirror plane, while nonpolar groups may be mobile. The hydrogen atoms on each stereocenter are positioned antipodal with respect to the pseudo-mirror plane, making a two-base mechanism imperative. Recognition that mirror-image packing is the common binding mode for enantiomeric or epimeric substrates of these enzymes should inform modelling/docking studies and protein engineering.     

Molecular dynamics and density functional studies of substrate binding and catalysis of arginine deiminase

The active-site dynamics of arginine deiminase (ADI) complexed with the arginine substrate are investigated with ns molecular dynamics for the wildtype ADI and several mutants. It is shown that the substrate is held in the active site by an extensive hydrogen bond network, which may be weakened by substitution of active-site residues. In addition, the initial step of the catalysis is explored in several truncated active-site models with density functional theory. Evidence is presented in support of the hypothesis that the nucleophilic attack of the ADI Cys thiol at the guanidino carbon of the substrate is initiated by substrate-mediated proton transfer to a His residue in the catalytic triad (Cys-His-Glu). In addition, the active-site residues are found to strongly influence the reaction profile, consistent with their important role in catalysis.     

Aldolase Cascade Facilitated by Self‐Assembled Nanotubes from Short Peptide Amphiphiles

Early evolution benefited from a complex network of reactions involving multiple C?C bond forming and breaking events that were critical for primitive metabolism. Nature gradually chose highly evolved and complex enzymes such as lyases to efficiently facilitate C?C bond formation and cleavage with remarkable substrate selectivity. Reported here is a lipidated short peptide which accesses a homogenous nanotubular morphology to efficiently catalyze C?C bond cleavage and formation. This system shows morphology‐dependent catalytic rates, suggesting the formation of a binding pocket and registered enhancements in the presence of the hydrogen‐bond donor tyrosine, which is exploited by extant aldolases. These assemblies showed excellent substrate selectivity and templated the formation of a specific adduct from a pool of possible adducts. The ability to catalyze metabolically relevant cascade transformations suggests the importance of such systems in early evolution.