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Identifying two ancient enzymes in Archaea using predicted secondary structure alignment

Nature Structural Biology volume 6, pages 750–754 (1999)Cite this article

Abstract

It is now possible to compare life forms at high levels of detail and completeness due to the increasing availability of whole genomes from all three domains. However, exploration of interesting hypotheses requires the ability to recognize a correspondence between proteins that may since have diverged beyond the threshold of detection by sequence-based methods. Since protein structure is far better conserved than protein sequence, structural information can enhance detection sensitivity, and this is the basis for the field of structural genomics. Demonstrating the effectiveness of this approach, we identify two important but previously elusive Archaeal enzymes: a homolog of dihydropteroate synthase and a thymidylate synthase. The former is especially noteworthy in that no Archaeal homolog of a bacterial folate biosynthetic enzyme has been found to date. Experimental confirmation of the deduced activity of both enzymes is described. Identification of two different proteins was attempted deliberately to help allay concern that predictive success is merely a lucky accident.

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Figure 1: Biosynthetic pathways.
Figure 2: Reaction proposed to be catalyzed by the thymidylate synthetase from Methanococcus jannaschii.

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Acknowledgements

Supported by a National Science Foundation grant to R.H.W. and a National Institutes of Health grant to G.D.R. We thank M.E. Rasche for running the experiments to trap the covalent complex between FdUMP and thymidylate synthase, K. Harich for preforming the GC-MS analyses, and D. Grahame for supplying the [methyl-3H]-methyl-tetrahydrosarcinapterin.

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Authors and Affiliations

  1. Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, 24061-0308, Virginia, USA

    Huimin Xu & Robert H. White

  2. Monsanto Company, Mail Zone AA3G, 700 Chesterfield Parkway North, St. Louis, 63198, Missouri, USA

    Rajeev Aurora

  3. Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, School of Medicine, 725 N. Wolfe Street, Baltimore, 21205, Maryland, USA

    George D. Rose

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  1. Huimin Xu
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Correspondence to Robert H. White.

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Xu, H., Aurora, R., Rose, G. et al. Identifying two ancient enzymes in Archaea using predicted secondary structure alignment. Nat Struct Mol Biol 6, 750–754 (1999). https://doi.org/10.1038/11525

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