7JMV

Crystal structure of the pea pathogenicity protein 2 from Madurella mycetomatis complexed with 4-nitrocatechol

7JMV の概要

• エントリーDOI: 10.2210/pdb7jmv/pdb
• 分子名称: Pea pathogenicity protein 2, 4-NITROCATECHOL, POTASSIUM ION, ... (5 entities in total)
• 機能のキーワード: gallic acid decarboxylase, lyase
• 由来する生物種: Madurella mycetomatis
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 27681.16

構造登録者

Zeug, M.,Markovic, N.,Iancu, C.V.,Tripp, J.,Oreb, M.,Choe, J. (登録日: 2020-08-03, 公開日: 2021-02-17, 最終更新日: 2023-10-18)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.57 Å)