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J Mol Evol. 2003 Sep;57(3):255-60.

Structure-based phylogenies of the serine beta-lactamases.

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


The serine beta-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 beta-lactamases are sister taxa and that the divergence of the Class C beta-lactamases pre-dated the divergence of the Class A and Class D beta-lactamases.

[Indexed for MEDLINE]

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