London N, Farelli JD, Brown SD, Liu C, Huang H, Korczynska M, Al-Obaidi NF, Babbitt PC, Almo SC, Allen KN, Shoichet BK. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases.
Biochemistry 2015;
54:528-37. [PMID:
25513739 PMCID:
PMC4303301 DOI:
10.1021/bi501140k]
[Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
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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.
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