ArticleJournal of the American Chemical Society2013
Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 35 citations in OpenAlex.
- Enhancing Enzyme Activity With Mutation Combinations Guided by Few-Shot Learning and Causal Inference.Angewandte Chemie (International ed. in English) · 2026Article
- Structural and mechanistic insights into the divergence of pterin deaminase and sepiapterin deaminase.Applied microbiology and biotechnology · 2026Review
- A previously unappreciated class of metal-dependent bile salt hydrolases from the human gut microbiome.bioRxiv : the preprint server for biology · 2026Article
- Mechanism of soil bacteria (Cupriavidus sp. LA-1) for degrading natural pterin and lumazine pigments.Communications biology · 2025Article
- Carboxypeptidase G and pterin deaminase metabolic pathways degrade folic acid in Variovorax sp. F1.BMC microbiology · 2022Article
- Establishing pteridine metabolism in a progressive isogenic breast cancer cell model - part II.Metabolomics : Official journal of the Metabolomic Society · 2022Article
- Structural Determinants for Substrate Selectivity in Guanine Deaminase Enzymes of the Amidohydrolase Superfamily.Biochemistry · 2019Article
- Crius: A novel fragment-based algorithm of de novo substrate prediction for enzymes.Protein science : a publication of the Protein Society · 2018Article
- Article
- Confronting the catalytic dark matter encoded by sequenced genomes.Nucleic acids research · 2017Article
- Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions.Biochemistry · 2017Review
- Docking Screens for Novel Ligands Conferring New Biology.Journal of medicinal chemistry · 2016Review
- Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.Biochimica et biophysica acta · 2015Review
- Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases.Biochemistry · 2015Article
- Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach.PLoS computational biology · 2014Article
- Leveraging structure for enzyme function prediction: methods, opportunities, and challenges.Trends in biochemical sciences · 2014Review
- Functional annotation and structural characterization of a novel lactonase hydrolyzing D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate.Biochemistry · 2014Article
- Prediction of substrates for glutathione transferases by covalent docking.Journal of chemical information and modeling · 2014Article
- Substrate deconstruction and the nonadditivity of enzyme recognition.Journal of the American Chemical Society · 2014Article
- Structure-guided discovery of new deaminase enzymes.Journal of the American Chemical Society · 2013Article
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Authors and funding
9 authors at 5 institutions in 1 country.
Funding
Abstract
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 × 10(6); pterin-6-carboxylate, 4.0 × 10(6); pterin-7-carboxylate, 3.7 × 10(6); pterin, 3.3 × 10(6); hydroxymethylpterin, 1.2 × 10(6); biopterin, 1.0 × 10(6); d-(+)-neopterin, 3.1 × 10(5); isoxanthopterin, 2.8 × 10(5); sepiapterin, 1.3 × 10(5); folate, 1.3 × 10(5), xanthopterin, 1.17 × 10(5); and 7,8-dihydrohydroxymethylpterin, 3.3 × 10(4). 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.
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