PMID: 11324759Apr 28, 2001Paper

The herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: insight from molecular modeling and phylogenetic analysis

Virus Genes
Janusz M Bujnicki, Leszek Rychlewski

Abstract

The PD-(D/E)XK superfamily of deoxyribonucleases (ENases) comprises restriction endonucleases, exonucleases and nicking enzymes, which share a common fold and the architecture of the active site. Their extreme divergence generally hampers identification of novel members based solely on sequence comparisons. Here we report a remote similarity between the phage lambda exonuclease (lambda-exo), branching out early in the evolutionary history of ENases (3), with the family of alkaline exonucleases (AE) encoded by various viruses infecting higher Eukaryota. The predicted structural compatibility and the conservation of the functionally important residues between AE and ENases strongly suggest a distant evolutionary relationship between these proteins. According to the results of extensive sequence database mining, sequence/structure threading and molecular modeling it is plausible that the AE proteins with lambda-exo and some other putative phage-encoded exonucleases form a distinct subfamily of PD-(D/E)XK ENases. The phylogenetic history of this subfamily is inferred using sequence alignment and distance matrix methods.

Citations

Jul 27, 2004·Protein Science : a Publication of the Protein Society·Hua ChengNick V Grishin
Feb 14, 2006·Journal of Virology·Lukasz KnizewskiKrzysztof Ginalski
Jan 31, 2017·Nucleic Acids Research·Hyunah LeeTracey E Barrett
Sep 18, 2004·The Journal of Biological Chemistry·Siddamadappa ChandrashekaranValakunja Nagaraja
Jan 23, 2004·The Journal of Biological Chemistry·Victor S MikhailovGeorge F Rohrmann
Sep 9, 2011·The Journal of General Virology·Alison L KuchtaMichael A McVoy
Sep 16, 2004·Journal of Virology·Kazuhiro OkanoGeorge F Rohrmann
Feb 11, 2020·Frontiers in Genetics·Peng ZhangXuefeng Gu
Jun 23, 2009·Journal of Molecular Biology·Marlyse BuissonWim P Burmeister

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