Mechanistic Strategies for Catalysis Adopted by Evolutionary Distinct Family 43 Arabinanases

Abstract

Background: Arabinanases are key enzymes involved in hemicellulose degradation. Results: Crystallographic, mutational, and biochemical assays of three arabinanases reveal the molecular mechanisms governing their catalysis and activation. Conclusion: Accessory domain and metal ion are essential for catalysis. Structural adaptations in the catalytic interface confer unique action modes to ruminal arabinanases. Significance: This work provides new molecular strategies for arabinan hydrolysis.

Structure‐guided design combined with evolutionary diversity led to the discovery of the xylose‐releasing exo‐xylanase activity in the glycoside hydrolase family 43

“…This study demonstrates the potential of combining rational design with evolutionary diversity to unravel new activities and modes of action and, in particular, the importance of the β‐propeller hollow properties for GH43 catalytic function as proposed in our previous work (Santos, Polo et al, ). In addition, these results expand our current mechanistic understanding about this fundamental GH family for most cellulolytic microorganisms.…”

“…Detailed structural analysis of the wt BlXynB revealed that the side chain of the catalytically relevant histidine (His 245 ) adopts an unusual rotameric conformation disrupting the hydrogen bond network supporting the catalytic residues. The His 245 side chain is supposed to adopt a perpendicular configuration in relation to the acidic catalytic residues, avoiding specific hydrogen bonds with these residues that could perturb the active‐site geometry (Santos, Polo et al, ). However, in the wt BlXynB structure, the adopted rotameric conformation of His 245 led to a direct interaction with the pKa modulator Asp 136 , which is critical for maintaining the general acid residue in a proper and productive orientation (Brüx et al, ; Figure c).…”

Three‐dimensional structures and functional studies of two GH43 arabinofuranosidases from Weissella sp. strain 142 and Lactobacillus brevis

“…The identity of the metal ion in W Araf43, however remains ambiguous, with Ca 2+ or Mg 2+ as most likely candidates. Other studies have shown that enzymes in GH43, such as ARN2 and ARN3 from a rumen metagenome (classified under subfamilies 4 and 5, respectively), present a calcium‐independent mechanism . In these enzymes, a sodium or magnesium ion may be a substituent for the calcium ion, and may have a related function.…”

Characterization of a furan aldehyde-tolerantβ-xylosidase/α-arabinosidase obtained through a synthetic metagenomics approach

“…; Santos et al . ). In contrast, Cu 2+ , Ni 2+ , Co 2+ and NH 4+ strongly inhibited the β ‐xylosidase activity of XylM1989.…”

“…Regarding the biochemical characterization, the three bivalent cations Ca 2+ , Mg 2+ and Mn 2+ clearly enhanced the activity of XylM1989, thus indicating that such cations are important as enzyme cofactors. A role in the enzymatic reaction, for example, by binding and stabilizing the substrate at the active site, may be invoked (Mora€ ıs et al 2012;Ahmed et al 2013;Santos et al 2014). In contrast, Cu 2+ , Ni 2+ , Co 2+ and NH 4+ strongly inhibited the b-xylosidase activity of XylM1989.…”