Journal:JMB:3

Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme

Moshe Ben-­David, Grzegorz Wieczorek, Mikael Elias, Israel Silman, Joel L. Sussman and Dan S. Tawfik ^[1]

Molecular Tour
Metal binding sites, especially those playing a catalytic role, exhibit high structural conservation (wildtype serum paraoxonase-1 (PON1) in the presence of either phosphate (PDB: 3sre) or the lactone-­analogue 2HQ (PDB: 3srg)). The location of the metal ion and of its ligating residues perfectly superpose, even in distant superfamily members that catalyze different chemical reactions. There exist, however, indications of changes in the configuration of catalytic metals, as part of the catalytic cycle, or upon binding different substrates. Such example is the case of the serum paraoxonase-1 (PON1), in which mutations in the H115 active site residue, induce a shift towards an alternative coordination mode of the catalytic Ca2+ (wildtype PON1 is in royalblue, H115W mutant is in magenta and H115Q/H134Q mutant is in salmon). PON1's native activity is the hydrolysis of lipophilic lactones, but it also promiscuously hydrolyzes organophosphates (OPs), particularly paraoxon. It uses different subsets of its catalytic machinery, and different active-site conformations, to catalyze these two reactions. However, the catalytic Ca2+, and its ligating residues are essential for both. H115 is playing a key role in the hydrolysis of lactones. Together with E53, it activates the hydrolytic water for the lactonase activity. Further, mutations to Gln or more drastically to Trp, reduce the lactonase activity significantly (up to 600-fold). The OP hydrolase activity is, however, enhanced. To gain insight for the structural and mechanistic changes that responsible for this functional transition, the crystal structure of two H115 mutants was determined, H115W and H115Q/H134Q. These crystal structures display major rearrangements of the catalytic metal and of its ligating residues. Specifically, the catalytic Ca2+ has moved a 1.8 Å upwards towards the enzyme’s surface, relative to its position in the WT structure. The position of the structural Ca2+, however, did not change. Further, the residues coordinating the catalytic Ca2+ are also altered in the mutant structure- the side-chains of N168, N224 and N270 do not interact directly with the catalytic Ca2+ as in the WT structure, but through waters that are absent in the native structure. The side-chain of N224 also exhibits a different orientation. For E53, which retains its direct interaction with the catalytic Ca2+, an alternative side-chain conformation was detected. Finally, the side-chains in the vicinity of the mutations also moved, for example for the H115W mutant, residues H134 and L69 moved in order to accommodate the bulkiness of the Trp in position 115. The structural strudies were also complimented with biochemical, mutational and computational analysis that were in good agreement with the structural observations. The computational simulations also suggest a general base catalysis mechanism in which E53, possibly together with H115 and/or D269, coordinates and activates the attacking water molecule. These findings, taken together, support the notion that PON1 can accommodate two (or more) alternative coordination modes for its catalytic Ca2+, and that these modes may be used to catalyze different reactions. PON1's native lactonase activity occurs within the canonical coordination scheme, with the location of the catalytic Ca2+ being similar in PON1 and in related enzymes that are highly diverged in their sequences. The promiscuous OPH activity, however, seems to utilize a fundamentally different Ca2+ mode, and a different mechanism. Alongside the conformational diversity of the protein's backbone and side-chains, metal repositioning may, therefore, contribute to the catalytic versatility of enzymes and to the ease by which new enzymatic functions diverge. The shift in the Ca2+ position, from a rarely populated metal state in the WT to a dominant state in H115W, follows a general model whereby evolution capitalizes on stochastic variations, be they atomic as with PON1's alternative location of the Ca2+, or cellular (e.g., transcriptional noise). Mutations do not create something from nothing. Rather, they shift the distribution such that a marginal, noise phenomenon becomes the norm.

PDB references: Serum paraoxonase-1 by directed evolution with the H115W mutation, 4hho; Serum paraoxonase-1 by directed evolution with the H115Q and H134Q mutations, 4hhq.