The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional pre

Background: The PD-(D/E)XK nuclease superfamily, initially identified in type II restriction endonucleases and later in many enzymes involved in DNA recombination and repair, is one of the most challenging targets for protein sequence analysis and structure prediction. Typically, the sequence similarity between these proteins is so low, that most of the relationships between known members of the PD-(D/E)XK superfamily were identified only after the corresponding structures were determined experimentally. Thus, it is tempting to speculate that among the uncharacterized protein families, there are potential nucleases that remain to be discovered, but their identification requires more sensitive tools than traditional PSI-BLAST searches. Results: The low degree of amino acid conservation hampers the possibility of identification of new members of the PD-(D/E)XK superfamily based solely on sequence comparisons to known members. Therefore, we used a recently developed method HHsearch for s...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Jan Kosinski, Marcin Feder, Janusz M. Bujnicki
• Keywords: BMCBI 2005, Protein, Protein Families, Uncharacterized Protein Families