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- W2029230152 abstract "Enzyme function prediction remains an important open problem. Though structure-based modeling, such as metabolite docking, can identify substrates of some enzymes, it is ill-suited to reactions that progress through a covalent intermediate. Here we investigated the ability of covalent docking to identify substrates that pass through such a covalent intermediate, focusing particularly on the haloalkanoate dehalogenase superfamily. In retrospective assessments, covalent docking recapitulated substrate binding modes of known cocrystal structures and identified experimental substrates from a set of putative phosphorylated metabolites. In comparison, noncovalent docking of high-energy intermediates yielded nonproductive poses. In prospective predictions against seven enzymes, a substrate was identified for five. For one of those cases, a covalent docking prediction, confirmed by empirical screening, and combined with genomic context analysis, suggested the identity of the enzyme that catalyzes the orphan phosphatase reaction in the riboflavin biosynthetic pathway of Bacteroides." @default.
- W2029230152 created "2016-06-24" @default.
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- W2029230152 date "2015-01-05" @default.
- W2029230152 modified "2023-10-18" @default.
- W2029230152 title "Covalent Docking Predicts Substrates for Haloalkanoate Dehalogenase Superfamily Phosphatases" @default.
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- W2029230152 doi "https://doi.org/10.1021/bi501140k" @default.
- W2029230152 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/4303301" @default.
- W2029230152 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/25513739" @default.
- W2029230152 hasPublicationYear "2015" @default.
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