7KD9

Crystal Structure of Gallic Acid Decarboxylase from Arxula adeninivorans

Summary for 7KD9

• Entry DOI: 10.2210/pdb7kd9/pdb
• Descriptor: Gallate decarboxylase, POTASSIUM ION (3 entities in total)
• Functional Keywords: decarboxylase, lyase
• Biological source: Blastobotrys adeninivorans (Yeast)
• Total number of polymer chains: 9
• Total formula weight: 245294.82

Authors

Zeug, M.,Markovic, N.,Iancu, C.V.,Tripp, J.,Oreb, M.,Choe, J. (deposition date: 2020-10-08, release date: 2021-02-17, Last modification date: 2023-10-18)

Primary citation

Zeug, M.,Markovic, N.,Iancu, C.V.,Tripp, J.,Oreb, M.,Choe, J.Y.
Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists.
Sci Rep, 11:3056-3056, 2021

PubMed Abstract: Hydroxybenzoic acids, like gallic acid and protocatechuic acid, are highly abundant natural compounds. In biotechnology, they serve as critical precursors for various molecules in heterologous production pathways, but a major bottleneck is these acids' non-oxidative decarboxylation to hydroxybenzenes. Optimizing this step by pathway and enzyme engineering is tedious, partly because of the complicating cofactor dependencies of the commonly used prFMN-dependent decarboxylases. Here, we report the crystal structures (1.5-1.9 Å) of two homologous fungal decarboxylases, AGDC1 from Arxula adenivorans, and PPP2 from Madurella mycetomatis. Remarkably, both decarboxylases are cofactor independent and are superior to prFMN-dependent decarboxylases when heterologously expressed in Saccharomyces cerevisiae. The organization of their active site, together with mutational studies, suggests a novel decarboxylation mechanism that combines acid-base catalysis and transition state stabilization. Both enzymes are trimers, with a central potassium binding site. In each monomer, potassium introduces a local twist in a β-sheet close to the active site, which primes the critical H86-D40 dyad for catalysis. A conserved pair of tryptophans, W35 and W61, acts like a clamp that destabilizes the substrate by twisting its carboxyl group relative to the phenol moiety. These findings reveal AGDC1 and PPP2 as founding members of a so far overlooked group of cofactor independent decarboxylases and suggest strategies to engineer their unique chemistry for a wide variety of biotechnological applications.

PubMed: 33542397
DOI: 10.1038/s41598-021-82660-z

Experimental method

X-RAY DIFFRACTION (1.94 Å)