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Protein stability indicates divergent evolution of PD‐(D/E)XK type II restriction endonucleases
Author(s) -
Fuxreiter Monika,
Simon István
Publication year - 2002
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.4980102
Subject(s) - restriction enzyme , dna , recognition sequence , restriction site , active site , genetics , biology , base pair , enzyme , biochemistry
Type II restriction endonucleases recognize 4–8 base‐pair‐long DNA sequences and catalyze their cleavage with remarkable specificity. Crystal structures of the PD‐(DE)XK superfamily revealed a common α/β core motif and similar active site. In contrast, these enzymes show little sequence similarity and use different strategies to interact with their substrate DNA. The intriguing question is whether this enzyme family could have evolved from a common origin. In our present work, protein structure stability elements were analyzed and compared in three parts of PD‐(DE)XK type II restriction endonucleases: (1) core motif, (2) active‐site residues, and (3) residues playing role in DNA recognition. High correlation was found between the active‐site residues and those stabilization factors that contribute to preventing structural decay. DNA recognition sites were also observed to participate in stabilization centers. It indicates that recognition motifs and active sites in PD‐(DE)XK type II restriction endonucleases should have been evolutionary more conserved than other parts of the structure. Based on this observation it is proposed that PD‐(DE)XK type II restriction endonucleases have developed from a common ancestor with divergent evolution.