Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists

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 hydro...

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Autores principales:	Matthias Zeug, Nebojsa Markovic, Cristina V. Iancu, Joanna Tripp, Mislav Oreb, Jun-yong Choe
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/032368842d7f4b36972b7a1662d3f5a3
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spelling	oai:doaj.org-article:032368842d7f4b36972b7a1662d3f5a32021-12-02T10:44:08ZCrystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists10.1038/s41598-021-82660-z2045-2322https://doaj.org/article/032368842d7f4b36972b7a1662d3f5a32021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82660-zhttps://doaj.org/toc/2045-2322Abstract 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.Matthias ZeugNebojsa MarkovicCristina V. IancuJoanna TrippMislav OrebJun-yong ChoeNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Matthias Zeug Nebojsa Markovic Cristina V. Iancu Joanna Tripp Mislav Oreb Jun-yong Choe Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists
description	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.
format	article
author	Matthias Zeug Nebojsa Markovic Cristina V. Iancu Joanna Tripp Mislav Oreb Jun-yong Choe
author_facet	Matthias Zeug Nebojsa Markovic Cristina V. Iancu Joanna Tripp Mislav Oreb Jun-yong Choe
author_sort	Matthias Zeug
title	Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists
title_short	Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists
title_full	Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists
title_fullStr	Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists
title_full_unstemmed	Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists
title_sort	crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/032368842d7f4b36972b7a1662d3f5a3
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Crystal structures of non-oxidative decarboxylases reveal a new mechanism of action with a catalytic dyad and structural twists

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