Exploring sequence space: profile analysis and protein-ligand docking to screen omega-aminotransferases with expanded substrate specificity.
omega-Aminotransferase (omegaAT) is an interesting biocatalyst for the preparation of chiral amines, which are widely used as building blocks for pharmaceuticals, agrochemicals and fine chemicals. With the assumption that substrate and sequence spaces are in the process of co-evolution, we explored sequences space to screen the enzymes showing activity to new target compounds. Bacterial genome sequences (n=527) were analyzed by the profiles of subgroups in aminotransferase group II including ornithine aminotransferase (orAT), acetylornithine aminotransferase (aoAT), omegaAT, gamma-aminobutyrate aminotransferase (GABAAT) and 7,8-diaminopelargonate aminotransferase (DAPAAT). We selected the sequences having a Z score of 0-1.8 to guarantee the omegaAT reaction and to avoid the typical omegaAT sequences. Among the selected sequences, we filtered out the sequences with very low Z scores for the rest of four subgroups in aminotransferase group II to consider the diversity. For the selected sequences, we performed protein-ligand docking simulations to predict the docking pose of amino acceptor. Throughout all the analysis procedures, several candidate aminotransferase sequences for the asymmetric synthesis of chiral amines were obtained. An efficient procedure for virtual screening of novel enzymes was demonstrated.
Seo
Joo-Hyun
JH
School of Chemical and Biological Engineering and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea.
Park
Hyung-Yeon
HY
Kim
Juhan
J
Lee
Bon-Su
BS
Kim
Byung-Gee
BG
D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D004789:Enzyme Activation; D008024:Ligands; D008969:Molecular Sequence Data; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013379:Substrate Specificity; D000637:Transaminases / Q000737:chemistry*
D008024:Ligands; D000637:Transaminases