Hall Barry G, Barlow Miriam
Biology Department, Hutchison Hall, University of Rochester, Rochester, NY 14627-0211, USA.
J Mol Evol. 2003 Sep;57(3):255-60. doi: 10.1007/s00239-003-2473-y.
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.
丝氨酸β-内酰胺酶给系统发育学带来了一个特殊问题，因为它们分化程度极高，以至于分成了三个类别，而这三个类别之间不存在可检测到的序列同源性。在此，我们以基于蛋白质结构比对的两个系统发育树的形式为该问题提供了一个解决方案。在第一个系统发育树中，结构比对被用作氨基酸序列比对的指导，而在第二个系统发育树中，蛋白质α碳原子之间的平均均方根距离被用于创建一个成对距离矩阵，进而由此构建出一个邻接法系统发育树。从这些系统发育树中，我们表明A类和D类β-内酰胺酶是姐妹类群，并且C类β-内酰胺酶的分化早于A类和D类β-内酰胺酶的分化。
