Sequence, structure, and function relationships in the aldolase and tautomerase superfamilies

Studying the structure of an enzyme and how it relates to its function has been a goal of enzymologists for decades. Although informative and useful, classical techniques, such as BLAST searches or manual analysis of multisequence alignments may be too focused. These techniques tend to rely on comparing a manageable quantity of sequences. As a result, patterns in conservation of certain residues across a limited number of sequences carry more weight in the study. In the first section, we present a study that used these classical approaches to compare only 3 sequences of Aldolase Superfamily members as described below.
NahE is a hydratase-aldolase that converts o-substituted trans-benzylidenepyruvates (where the ortho-substituent is H, OH, or CO₂⁻) to benzaldehyde, salicylaldehyde, or 2-carboxybenzaldehyde, respectively, and pyruvate. The enzyme is part of a bacterial pathway for the degradation of naphthalene, which is a toxic and persistent environmental contaminant. Sequence, crystallographic, and mutagenic analysis identified the enzyme as a member of the N-acetylneuraminate lyase (NAL) subgroup in the aldolase superfamily. As such, it has a conserved lysine (Lys183) and tyrosine (Tyr155), for Schiff base formation, as well as a GXXGE motif for binding of the pyruvoyl carboxylate group. NahE crystal structures show these core active site elements along with other nearby residues that might be involved in the mechanism and/or specificity. Mutations of five active site amino acids (Thr65, Trp128, Tyr155, Asn157, and Asn281) were constructed and kinetic parameters measured in order to assess the effect(s) on binding, catalysis, and/or the reaction step (hydration vs aldol cleavage). The results show that the two Trp128 mutants (Phe and Tyr) have the least effect on catalysis, whereas amino acids with bulky side chains at Thr65 (Val) and Asn281 (Leu) have the greatest effect. The Y155F mutation also significantly hinders catalysis and falls in between these extremes. These observations are put into a structural context. Finally, trapping experiments were carried out with substrate, NaCNBH₃, and wild type and selected mutations. The mass spectral analysis is consistent with the observed activities and suggests that pyruvate is released quickly from the active site, but salicylaldehyde is not. In the second section, we utilize a more modern technique of sequence analysis. We present studies done to analyze trends observed within the Tautomerase Superfamily (TSF) that have been identified by a sequence similarity network (SSN). Hidden trends in sequences that appear insignificant at the small scale may be revealed on a larger scale, such as in the second section. The amino-terminal proline (Pro1) has long been thought to be a mechanistic imperative for tautomerase superfamily (TSF) enzymes, functioning as a general base or acid in all characterized reactions. However, a global examination of more than 11,000 nonredundant sequences of the TSF uncovered 346 sequences that lack Pro1. The majority (~85%) are found in the malonate semialdehyde decarboxylase (MSAD) subgroup where most of the 294 sequences form a separate cluster. Four sequences within this cluster retain Pro1. Because these four sequences might provide clues to assist in the identification and characterization of activities of nearby sequences without Pro1, they were examined by kinetic, inhibition, and crystallographic studies. The most promising of the four (from Calothrix sp. PCC 6303 designated 437) exhibited decarboxylase and tautomerase activities and was covalently modified at Pro1 by 3-bromopropiolate. A crystal structure was obtained for the apo enzyme (2.35 Å resolution). The formation of a 3-oxopropanoate adduct with Pro1 provides clues to build a molecular model for the bound ligand. The modeled ligand extends into a region that allows interactions with three residues (Lys37, Arg56, Glu98), suggesting that these residues could play roles in the observed decarboxylation and tautomerization activities. Moreover, these same residues are conserved in 16 nearby, non-Pro1 sequences in a sequence similarity network. Thus far, these residues have not been implicated in the mechanisms of any other TSF members. The collected observations provide starting points for the characterization of the non-Pro1 sequences. Five non-Pro1 sequences were studied in this section, as well, containing either glycine, alanine, valine, threonine, or serine at the N-terminus. The most promising was NJ7 (from Nostoc sp. strain PCC 7120/SAG 25.82/UTEX 2576 derived from the UniProt Accession code Q8YNJ7). Kinetic analysis showed that this enzyme with Val1 has tautomerization and decarboxylation activity. The introduction of Pro1 enhanced NJ7’s performance as a tautomerase and decarboxylase.