Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking

Of the over 22 million protein sequences in the nonredundant TrEMBL database, fewer than 1% have experimentally confirmed functions. Structure-based methods have been used to predict enzyme activities from experimentally determined structures; however, for the vast majority of proteins, no such structures are available. Here, homology models of a functionally uncharacterized amidohydrolase from Agrobacterium radiobacter K84 (Arad3529) were computed on the basis of a remote template structure. The protein backbone of two loops near the active site was remodeled, resulting in four distinct active site conformations. Substrates of Arad3529 were predicted by docking of 57 672 high-energy intermediate (HEI) forms of 6440 metabolites against these four homology models. On the basis of docking ranks and geometries, a set of modified pterins were suggested as candidate substrates for Arad3529. The predictions were tested by enzymology experiments, and Arad3529 deaminated many pterin metabolites (substrate, k_cat/K_m [M^-1 s^-1]): formylpterin, 5.2 × 10⁶; pterin-6- carboxylate, 4.0 × 10⁶; pterin-7-carboxylate, 3.7 × 10⁶; pterin, 3.3 × 10⁶; hydroxymethylpterin, 1.2 × 10⁶; biopterin, 1.0 × 10⁶; d-(+)-neopterin, 3.1 × 10⁵; isoxanthopterin, 2.8 × 10⁵; sepiapterin, 1.3 × 10⁵; folate, 1.3 × 10⁵, xanthopterin, 1.17 × 10⁵; and 7,8-dihydrohydroxymethylpterin, 3.3 × 10⁴. While pterin is a ubiquitous oxidative product of folate degradation, genomic analysis suggests that the first step of an undescribed pterin degradation pathway is catalyzed by Arad3529. Homology model-based virtual screening, especially with modeling of protein backbone flexibility, may be broadly useful for enzyme function annotation and discovering new pathways and drug targets.