MODAMDH: identification of diverse Amine Dehydrogenases by screening biodiversity using sequence and structure-based approaches
Résumé
The current boom in environmental genomics data provides a huge resource of new sequences of potential biocatalysts. Through the MODAMDH project, we focus on one of the key biocatalysts named amine dehydrogenases (AmDHs) which enable the access to amines that are important entities in the chemical industry.
We started from a previously described NAD(P)H-dependent AmDH family from which several members were experimentally characterized. This family was first expanded, up to 27k sequences, by mining very large metagenomic databanks in search of the conserved catalytic domain. We then applied structural modelling and active site classification to define subfamilies. We also generated a pool of ~100k candidate families containing more than 20M NAD(P)-binding protein sequences from which we found, using HMM-HMM profile comparison, >30 families sharing distant homology with the reference AmDH family. Furthermore, catalophores (i.e. minimal active site topologies) will be designed from native AmDH structures and used to find active site analogs in the candidate NAD(P)-dependent families. Most interesting enzymes will be experimentally characterized through enzymatic and crystallographic assays.
This work is ongoing and the presented workflow could be applied to other enzyme families in the quest for new structures and activities.