Stereochemical constraint in the evolution of pyridoxal-5'-phosphate-dependent enzymes. A hypothesis

Functional evolution of PLP-dependent enzymes based on active-site structural similarities

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5'-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS.

Structural Basis for D-Amino Acid Transamination by the Pyridoxal 5′-Phosphate-dependent Catalytic Antibody 15A9

Antibody 15A9, raised with 5'-phosphopyridoxyl (PPL)-N(epsilon)-acetyl-L-lysine as hapten, catalyzes the reversible transamination of hydrophobic D-amino acids with pyridoxal 5'-phosphate (PLP). The crystal structures of the complexes of Fab 15A9 with PPL-L-alanine, PPL-D-alanine, and the hapten were determined at 2.3, 2.3, and 2.5A resolution, respectively, and served for modeling the complexes with the corresponding planar imine adducts. The conformation of the PLP-amino acid adduct and its interactions with 15A9 are similar to those occurring in PLP-dependent enzymes, except that the amino acid substrate is only weakly bound, and, due to the immunization and selection strategy, the lysine residue that covalently binds PLP in these enzymes is missing. However, the N-acetyl-L-lysine moiety of the hapten appears to have selected for aromatic residues in hypervariable loop H3 (Trp-H100e and Tyr-H100b), which, together with Lys-H96, create an anion-binding environment in the active site. The structural situation and mutagenesis experiments indicate that two catalytic residues facilitate the transamination reaction of the PLP-D-alanine aldimine. The space vacated by the absent L-lysine side chain of the hapten can be filled, in both PLP-alanine aldimine complexes, by mobile Tyr-H100b. This group can stabilize a hydroxide ion, which, however, abstracts the C alpha proton only from D-alanine. Together with the absence of any residue capable of deprotonating C alpha of L-alanine, Tyr-H100b thus underlies the enantiomeric selectivity of 15A9. The reprotonation of C4' of PLP, the rate-limiting step of 15A9-catalyzed transamination, is most likely performed by a water molecule that, assisted by Lys-H96, produces a hydroxide ion stabilized by the anion-binding environment.

Pyridoxal-5'-phosphate-dependent catalytic antibodies

Strategies for expanding the catalytic scope of antibodies include the incorporation of inorganic or organic cofactors into their binding sites. An obvious choice is pyridoxal-5'-phosphate (PLP), which is probably the most versatile organic cofactor of enzymes. Monoclonal antibodies against the hapten N(alpha)-(5'-phosphopyridoxyl)-L-lysine, a stable analog of the covalent coenzyme-substrate adducts were screened by a competition ELISA for binding of the PLP-amino acid Schiff base adduct. The Schiff base with its C4'-N alpha double bond is, in contrast to the hapten, a planar compound and is an obligatory intermediate in all PLP-dependent reactions of amino acids. This highly discriminating screening step eliminated all but 5 of 24 hapten-binding antibodies. The five remaining antibodies were tested for catalysis of the PLP-dependent alpha,beta-elimination reaction of beta-chloroalanine. Antibody 15A9 complied with this selection criterion and catalyzed in addition 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). Homology modeling together with alanine scanning yielded a 3D model of Fab 15A9. The striking analogy between antibody 15A9 and PLP-dependent enzymes includes the following features: (1) The binding sites accommodate the planar coenzyme-amino acid adduct. (2) The bond at C alpha to be broken lies together with the C alpha-N bond in a plane orthogonal to the plane of coenzyme and imine bond. (3) The alpha-carboxylate group of the substrate is bound by an arginine residue. (4) The coenzyme-substrate adduct assumes a cisoid conformation. (5) PLP markedly contributes to catalytic efficiency, being a 10(4) times more efficient amino group acceptor than pyruvate. The protein moiety, however, ensures reaction as well as substrate specificity, and further accelerates the reaction (in 15A9 k(cat (Ab x PLP))'/k(cat (PLP))'=5 x 10(3)). The analogies of antibody 15A9 with PLP-dependent enzymes suggest that the selection criteria in the screening protocol were similar to those that have been operative in the molecular evolution of enzyme-assisted pyridoxal catalysis.

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.

The molecular evolution of pyridoxal-5'-phosphate-dependent enzymes

The pyridoxal-5-phosphate-dependent enzymes (B6 enzymes) that act on amino acid substrates are of multiple evolutionary origin. The numerous common mechanistic features of B6 enzymes thus are not historical traits passed on from a common ancestor enzyme but rather reflect evolutionary or chemical necessities. Family profile analysis of amino acid sequences supported by comparison of the available three-dimensional (3-D) crystal structures indicates that the B6 enzymes known to date belong to four independent evolutionary lineages of homologous (or more precisely paralogous) proteins, of which the alpha family is by far the largest. The alpha family (with aspartate aminotransferase as the prototype enzyme) includes enzymes that catalyze, with several exceptions, transformations of amino acids in which the covalency changes are limited to the same carbon atom that carries the amino group forming the imine linkage with the coenzyme (i.e., Calpha in most cases). Enzymes of the beta family (tryptophan synthase beta as the prototype enzyme) mainly catalyze replacement and elimination reactions at Cbeta. The D-alanine aminotransferase family and the alanine racemase family are the two other independent lineages, both with relatively few member enzymes. The primordial pyridoxal-5-phosphate-dependent enzymes apparently were regio-specific catalysts that first diverged into reaction-specific enzymes and then specialized for substrate specificity. Aminotransferases as well as amino acid decarboxylases are found in two different evolutionary lineages. Comparison of sequences from eukaryotic, archebacterial, and eubacterial species indicates that the functional specialization of most B6 enzymes has occurred already in the universal ancestor cell. The cofactor pyridoxal-5-phosphate must have emerged very early in biological evolution; conceivably, organic cofactors and metal ions were the first biological catalysts. In attempts to stimulate particular steps of molecular evolution, oligonucleotide-directed mutagenesis of active-site residues and directed molecular evolution have been applied to change both the substrate and reaction specificity of existent B6 enzymes. Pyridoxal-5-phosphate-dependent catalytic antibodies were elicited with a screening protocol that applied functional selection criteria as they might have been operative in the evolution of protein-assisted pyridoxal catalysis.

The use of biosensor technology for the engineering of antibodies and enzymes

Recently developed scientific instrumentation featuring surface plasmon resonance detection allows the detection of biomolecular interactions in real time and without chemical modification of the binding partners. These biosensors are proving invaluable tools in protein engineering, particularly in research aimed at the isolation and improvement of protein binders and catalysts from macromolecular repertoires containing billions of individual members. This article reviews the use of biosensor technology for the isolation and characterization of engineered antibodies and enzymes.

The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme

8-Amino-7-oxononanoate synthase (or 8-amino-7-ketopelargonate synthase; EC 2.3.1.47; AONS) catalyses the decarboxylative condensation of l-alanine and pimeloyl-CoA in the first committed step of biotin biosynthesis. We have cloned, over-expressed and purified AONS from Escherichia coli and determined the crystal structures of the apo and PLP-bound forms of the enzyme. The protein is a symmetrical homodimer with a tertiary structure and active site organisation similar to, but distinct from, those of other PLP-dependent enzymes whose three-dimensional structures are known. The critical PLP-binding lysine of AONS is located at the end of a deep cleft that allows access of the pantothenate arm of pimeloyl-CoA. A cluster of positively charged residues at the entrance to this cleft forms a putative diphosphate binding site for CoA. The structure of E. coli AONS enables identification of the key residues of the PLP-binding site and thus provides a framework with which to understand the biochemical mechanism, which is similar to that catalysed by 5-aminolevulinate synthase and two other alpha-oxoamine synthases. Although AONS has a low overall sequence similarity with the catalytic domains of other alpha-oxoamine synthases, the structure reveals the regions of significant identity to be functionally important. This suggests that the organisation of the conserved catalytic residues in the active site is similar for all enzymes of this sub-class of PLP-dependent enzymes and they share a common mechanism. Knowledge of the three-dimensional structure of AONS will enable characterisation of the structural features of this enzyme sub-family that are responsible for this important type of reaction.

The pyridoxal-5'-phosphate-dependent catalytic antibody 15A9: its efficiency and stereospecificity in catalysing the exchange of the alpha-protons of glycine

13C-NMR has been used to follow the exchange of the alpha-protons of [2-(13)C]glycine in the presence of pyridoxal-5'-phosphate and the catalytic antibody 15A9. In the presence of antibody 15A9 the 1st order exchange rates for the rapidly exchanged proton of [2-(13)C]glycine were only 25 and 150 times slower than those observed with tryptophan synthase (EC 4.2.1.20) and serine hydroxymethyltransferase (EC 2.1.2.1). The catalytic antibody increases the 1st order exchange rates of the alpha-protons of [2-(13)C]glycine by at least three orders of magnitude. We propose that this increase is largely due to an entropic mechanism which results from binding the glycine-pyridoxal-5'-phosphate Schiff base. The 1st and 2nd order exchange rates of the pro-2S proton have been determined but we were only able to determine the 2nd order exchange rate for the pro-2R proton of glycine. In the presence of 50 mM glycine the antibody preferentially catalyses the exchange of the pro-2S proton of glycine. The stereospecificity of the 2nd order exchange reaction was quantified and we discuss mechanisms which could account for the observed stereospecificity.

Monoclonal antibodies against Nalpha-(5'-phosphopyridoxyl)-L-lysine. Screening and spectrum of pyridoxal 5'-phosphate-dependent activities toward amino acids

Cofactors may be expected to expand the range of reactions amenable to antibody-assisted catalysis. The biological importance of pyridoxal 5'-phosphate (PLP) as enzymic cofactor in amino acid metabolism and its catalytic versatility make it an attractive candidate for the generation of cofactor-dependent abzymes. Here we report an efficient procedure to screen antibodies for PLP-dependent catalytic activity and detail the spectrum of catalytic activities found in monoclonal antibodies elicited against Nalpha-(5'-phosphopyridoxyl)-L-lysine. This hapten is a nonplanar analog of the planar, resonance-stabilized coenzyme-substrate adducts formed in the PLP-dependent reactions of amino acids. The hapten-binding antibodies were screened for binding of the planar Schiff base formed from PLP and D- or L-norleucine by competition enzyme-linked immunosorbent assay. The Schiff base (external aldimine) is an obligatory intermediate in all PLP-dependent reactions of amino acids. This simple, yet highly discriminating screening step eliminated most of the total 24 hapten-binding antibodies. Three positive clones bound the Schiff base with L-norleucine, two preferred that with the D-enantiomer. The positive clones were assayed for catalysis of Schiff base formation and of the alpha,beta-elimination reaction with the D- and L-enantiomers of beta-chloroalanine. Three antibodies were found to accelerate aldimine formation, and two of these catalyzed the PLP-dependent alpha,beta-elimination reaction. One of the alpha, beta-elimination-positive antibodies catalyzed the transamination reaction with hydrophobic D-amino acids and oxoacids (Gramatikova, S. I., and Christen, P. (1996) J. Biol. Chem. 271, 30583-30586). All catalytically active antibodies displayed continuous turnover. No PLP-dependent reactions other than aldimine formation, alpha, beta-elimination of beta-chloroalanine and transamination were detected. The successive screening steps plausibly simulate the functional selection pressures having been operative in the molecular evolution of primordial PLP-dependent protein catalysts to reaction- and substrate-specific enzymes.