Structure-based phylogenies of the serine beta-lactamases.
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.
Hall
Barry G
BG
Biology Department, Hutchison Hall, University of Rochester, Rochester, NY 14627-0211, USA. drbh@mail.rochester.edu
Barlow
Miriam
M
D001419:Bacteria / Q000201:enzymology / Q000235:genetics; D001499:Bayes Theorem; D008957:Models, Genetic; D015394:Molecular Structure; D010802:Phylogeny; D001618:beta-Lactamases / Q000737:chemistry / Q000145:classification* / Q000235:genetics*
D001618:beta-Lactamases