Abstract
With many genomes sequenced, a pressing challenge in biology is predicting the function of the proteins that the genes encode. When proteins are unrelated to others of known activity, bioinformatics inference for function becomes problematic. It would thus be useful to interrogate protein structures for function directly. Here, we predict the function of an enzyme of unknown activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate forms of thousands of candidate metabolites. The docking hit list was dominated by adenine analogues, which appeared to undergo C6-deamination. Four of these, including 5-methylthioadenosine and S-adenosylhomocysteine (SAH), were tested as substrates, and three had substantial catalytic rate constants (105 M-1s-1). The X-ray crystal structure of the complex between Tm0936 and the product resulting from the deamination of SAH, S-inosylhomocysteine, was determined, and it corresponded closely to the predicted structure. The deaminated products can be further metabolized by T. maritima in a previously uncharacterized SAH degradation pathway. Structure-based docking with high-energy forms of potential substrates may be a useful tool to annotate enzymes for function.
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Acknowledgements
This work was supported by grants from the National Institutes of Health, supporting docking analyses (to B.K.S.), large scale structural analysis (to S.C.A.), and function prediction (to F.M.R., B.K.S. and S.C.A.). F.M.R. thanks the Robert A. Welch Foundation for support. J.C.H. thanks the Deutsche Akademie der Naturforscher Leopoldina for a fellowship. We thank J. Irwin, V. Thomas and K. Babaoglu for reading this manuscript. The clone for Tm0172 was kindly supplied by the Joint Center for Structural Genomics.
Author Contributions J.C.H designed the docking database, performed the docking runs, and analysed the docking results. F.M.R. and R.M.-A. performed the enzymatic characterization of Tm0936 and Tm0172, including cloning and purification of the proteins. S.C.A., E.F. and A.A.F. determined the X-ray structure of Tm0936 with S-inosyl-homocysteine. J.C.H. and B.K.S. largely wrote the paper. All authors discussed the results and commented on the manuscript.
The complex structure of Tm0936 with SIH has been deposited in the PDB (accession code 2PLM).
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Hermann, J., Marti-Arbona, R., Fedorov, A. et al. Structure-based activity prediction for an enzyme of unknown function. Nature 448, 775–779 (2007). https://doi.org/10.1038/nature05981
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DOI: https://doi.org/10.1038/nature05981
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