You are here : Home > Research Centers and Units > Genoscope > UMR8030 > Organic Chemistry and Biocatalysis Laboratory (LCOB)

Laboratory

Organic Chemistry and Biocatalysis Laboratory (LCOB)

Research topics


​

Published on 20 November 2018
Thématiques de recherche 
There are several ways of accessing new enzymes. The approach developed at the UMR is based on investigation of the biodiversity of prokaryotic organisms (cf. Laboratory for the Screening of Bioconversion Activities).

A. Zaparucha, V. de Berardinis, C. Vergne-Vaxelaire "Genome mining for enzyme discovery", in "Modern Biocatalysis: Advances in Synthetic Biological Systems", editors: Gavin Williams and Mélanie Hall, the Royal Society of Chemistry, 2018, ISBN 978-1-78262-726-5.
https://pubs.rsc.org/en/content/ebook/978-1-78262-726-5


a-ketoglutarate dependent dioxygenases (a-KetoAcid Oxygenases, aKAO).

Oxidation reactions are among the most difficult to implement in chemistry but they are also among the most fundamental reactions. We have explored the catalytic capabilities of new aKAO, a family of enzymes catalyzing the hydroxylation reaction and an alternative to cytochromes P450.



      

We have identified aKAO active on lysine with regional selectivity for C3 or C4 (KDOs). The complementarity enables synthesis of lysine dihydroxylated by a cascade reaction.
To understand the selectivities observed, we performed a structural and computational analysis of the active sites based on the resolution of the structures of two of the enzymes discovered. We have extended our work to the Clavaminate Synthase Like (CSL) family to which our KDOs belong, to identify the structural elements responsible for substrate specificity and regioselectivity of the hydroxylation reaction of amino acids and derivatives.

  

D. Baud, P.-L. Saaidi, A. Monfleur, M. Harari, J. Cuccaro, A. Fossey, M. Besnard, A. Debard, A. Mariage, V. Pellouin, J.-L. Petit, M. Salanoubat, J. Weissenbach, V. de Berardinis, and A. Zaparucha Chem. Cat. Chem. 2014, 6, 3012-3017
K. Bastard, T. Isabet, E. A. Stura, P. Legrand, A. Zaparucha Sci. Rep. 2018
A. Zaparucha, V. de Berardinis, P.-L. Saaidi, D. Baud, WO2015078889

 

Amine dehydrogenases.

Access to β-amino acids, and more broadly to chiral amines from the corresponding ketones, is a reaction of great interest, particularly for the pharmaceutical industry. Few biocatalytic methods for the synthesis of optically pure β-amino acids and chiral amines have been explored. A class of enzymes can carry out this transformation: amines dehydrogenases (AmDH) catalysing the reductive amination of prochiral ketones into chiral amines. Among these oxidoreductases, only the amino acid dehydrogenases NAD(P)H-dependent known to convert α-keto acids have been well studied. 
We have discovered new AmDH s catalyzing the asymmetric reductive amination of various ketones and aldehydes. These are the first examples of wild AmDHs with related genes.

                        

Homology modelling based on the structural analysis of three new enzymes allowed the classification of active sites and revealed a superfamily of divergent proteins with specificities ranging from amino acid substrates to hydrophobic ketones (collaboration with Pr. G. Grogan, York University, UK).


 

O. Mayol, S. David, E. Darii, A. Debard, A. Mariage,V. Pellouin, J.-L. Petit, M. Salanoubat, V. de Berardinis, A. Zaparucha and C. Vergne-Vaxelaire Catal. Sci. Technol.2016, 6, 7421-7428.


Nitrilases.

Hydrolysis of nitriles to the corresponding carboxylic acids most frequently necessitates strong conditions, acidic or basic, which may give rise to undesirable byproducts. Enzymatic hydrolysis is an interesting alternative and spares fragile functional groups. Nitrilases are promiscuous enzymes; some of them are active on structurally very diverse substrates.


​                                        

During a large-scale study, we identified 125 new nitrilases and determined their substrate profiles. We are particularly interested in enzymes able to convert a-aminonitriles to a-amino acids thus providing the scope for access to non-natural amino acids. 

C. Vergne-Vaxelaire, F. Bordier, A. Fossey, M. Besnard-Gonnet, A. Debard, A. Mariage, V. Pellouin, A. Perret, J.-L. Petit, M. Stam, M. Salanoubat, J. Weissenbach, V. de Berardinis, A. Zaparucha Adv. Syn. Catal. 2013, 355, 1763-1779.
F. Bordier, M. Stam, E. Darii, S. Tricot, A. Fossey, J. Rohault, A. Debard, A. Mariage, V. Pellouin, J.-L. Petit, A. Perret, D. Vallenet, M. Salanoubat, J. Weissenbach, C. Vergne-Vaxelaire, V. de Berardinis, and A. Zaparucha J. Mol. Cat. B :enzymatic2014, 107, 79-88.



Enzymatic reaction cascades.

Various hydroxylated polyamines were synthesized from L-lysine by sequencing 1 or 2 stages of regiodivergent hydroxylation with decarboxylation. The synthesis, which is very short, enables access to chiral platform molecules.


A. Zaparucha, V. de Berardinis, P.-L. Saaidi, D. Baud, WO2015078889.
D. Baud, P.-L. Saaidi, A. Monfleur, M. Harari, J. Cuccaro, A. Fossey, M. Besnard, A. Debard, A. Mariage, V. Pellouin, J.-L. Petit, M. Salanoubat, J. Weissenbach, V. de Berardinis, and A. Zaparucha Chem. Cat. Chem. 2014, 6, 3012-3017