Structure-function investigation of 3-methylaspartate ammonia lyase reveals substrate molecular determinants for the deamination reaction
Artikel i vetenskaplig tidskrift, 2020

The enzymatic reactions leading to the deamination of β-lysine, lysine, or 2-aminoadipic acid are of great interest for the metabolic conversion of lysine to adipic acid. Enzymes able to carry out these reactions are not known, however ammonia lyases (EC 4.3.1.-) perform deamination on a wide range of substrates. We have studied 3-methylaspartate ammonia lyase (MAL, EC 4.3.1.2) as a potential candidate for protein engineering to enable deamination towards β-lysine, that we have shown to be a competitive inhibitor of MAL. We have characterized MAL activity, binding and inhibition properties on six different compounds that would allow to define the molecular determinants necessary for MAL to deaminate our substrate of interest. Docking calculations showed that β-lysine as well as the other compounds investigated could fit spatially into MAL catalytic pocket, although they probably are weak or very transient binders and we identified molecular determinants involved in the binding of the substrate. The hydrophobic interactions formed by the methyl group of 3-methylaspartic acid, together with the presence of the amino group on carbon 2, play an essential role in the appropriate binding of the substrate. The results showed that β-lysine is able to fit and bind in MAL catalytic pocket and can be potentially converted from inhibitor to substrate of MAL upon enzyme engineering. The characterization of the binding and inhibition properties of the substrates tested here provide the foundation for future and more extensive studies on engineering MAL that could lead to a MAL variant able to catalyse this challenging deamination reaction.

Författare

Veronica Saez Jimenez

Chalmers, Biologi och bioteknik, Industriell bioteknik

Željka Sanader Maršić

Danish Cancer Research Society Center

Matteo Lambrughi

Danish Cancer Research Society Center

Jae Ho Shin

Chalmers, Biologi och bioteknik, Industriell bioteknik

Robin van Havere

Chalmers, Biologi och bioteknik, Industriell bioteknik

Elena Papaleo

Danish Cancer Research Society Center

Lisbeth Olsson

Chalmers, Biologi och bioteknik, Industriell bioteknik

Valeria Mapelli

Chalmers, Biologi och bioteknik, Industriell bioteknik

PLoS ONE

1932-6203 (ISSN)

Vol. 15 5 e0233467

Ämneskategorier

Strukturbiologi

Biokatalys och enzymteknik

Organisk kemi

DOI

10.1371/journal.pone.0233467

PubMed

32437404

Mer information

Senast uppdaterat

2020-06-18