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Structure-Based Phylogenies of the Serine β-Lactamases

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Abstract

The serine β-lactamases present a special problem for phylogenetics because they have diverged so much that they fall into three classes that share no detectable sequence homology among themselves. Here we offer a solution to the problem in the form of two phylogenies that are based on a protein structure alignment. In the first, structural alignments were used as a guide for aligning amino acid sequences and in the second, the average root mean square distances between the alpha carbons of the proteins were used to create a pairwise distance matrix from which a neighbor-joining phylogeny was created. From those phylogenies, we show that the Class A and Class D β-lactamases are sister taxa and that the divergence of the Class C β-lactamases predated the divergence of the Class A and Class D β-lactamases.

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Acknowledgements

This study was supported by Grant GM60761 from the National Institutes of Health. We are grateful to Reviewer 1 for insightful comments on an earlier version of this paper.

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  1. Biology Department, Hutchison Hall, University of Rochester, Rochester, NY 14627-0211, USA

    Barry G. Hall & Miriam Barlow

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  1. Barry G. Hall
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  2. Miriam Barlow
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Correspondence to Barry G. Hall.

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Hall, B.G., Barlow, M. Structure-Based Phylogenies of the Serine β-Lactamases . J Mol Evol 57, 255–260 (2003). https://doi.org/10.1007/s00239-003-2473-y

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  • DOI: https://doi.org/10.1007/s00239-003-2473-y

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