Markers of fitness in a successful enzyme superfamily

Abstract

Haloalkanoic acid dehalogenase (HAD) superfamily members serve as the predominant catalysts of metabolic phosphate ester hydrolysis in all three superkingdoms of life. Collectively, the known structural, bioinformatic, and mechanistic data offer a glimpse of the variety of HAD enzymes that have evolved in the service of metabolic expansion. Factors that have contributed to superfamily dominance include a chemically versatile nucleophile, stability of the core superfold, structural modularity of the chemistry and specificity domains, conformational coupling conferred by the topology of the inserted specificity elements, and retention of a conserved mold for stabilization of the trigonal bipyramidal transition state.

Figure 1

The general catalytic mechanism for phosphohydrolase members of the HADSF. Catalysis proceeds through an aspartylphosphate intermediate.

Figure 2

The catalytic motifs of the HADSF. A) Composite scheme of the residues involved in forming the phosphoryl-transfer catalytic site in the HADSF. Hydrogen bonds are depicted as dashed lines labeled with average bond lengths in Å(range of bond lengths in parenthesis) for the twelve liganded structures from which this is constructed. B) Position of the catalytic loops in the active site scaffolds (core in black, cap in grey) of C1, C2a and C2b members (coloring the same in A and B, substrate specificity loop in pink.

Figure 2

The catalytic motifs of the HADSF. A) Composite scheme of the residues involved in forming the phosphoryl-transfer catalytic site in the HADSF. Hydrogen bonds are depicted as dashed lines labeled with average bond lengths in Å(range of bond lengths in parenthesis) for the twelve liganded structures from which this is constructed. B) Position of the catalytic loops in the active site scaffolds (core in black, cap in grey) of C1, C2a and C2b members (coloring the same in A and B, substrate specificity loop in pink.

Figure 3

Topology diagram of the classic HADSF Rossmann core domain. The HAD C0/C1 and C2 cap insertion points are labeled. The signature single helical turn is in pink and β-hairpin is in green.

Figure 4

Schematic of the possible evolutionary path of C1 members from insertion and duplication of secondary structural elements into the β-hairpin of the Rossmann fold (PDB codes in bold).

Figure 5

Venn diagram of the substrate range of HADSF members. Capped proteins usually have small substrates (1) but may also work on termini of macromolecules (4); oligomerization can allow C0 members to utilize small substrates (3); capless members may utilize large molecule substrates (2) but can also utilize small substrates using the insert segment.

Figure 6

Stereo diagram of the catalytic motifs (colored as in Figure 2) of the HADSF member hexose phosphate phosphatase complexed with tungstate highlights the trigonal bipyramidal geometry supported by the phosphoryl transfer site.