Nucleases: diversity of structure, function and mechanism
Top Cited Papers
- 21 September 2010
- journal article
- review article
- Published by Cambridge University Press (CUP) in Quarterly Reviews of Biophysics
- Vol. 44 (1), 1-93
- https://doi.org/10.1017/s0033583510000181
Abstract
Nucleases cleave the phosphodiester bonds of nucleic acids and may be endo or exo, DNase or RNase, topoisomerases, recombinases, ribozymes, or RNA splicing enzymes. In this review, I survey nuclease activities with known structures and catalytic machinery and classify them by reaction mechanism and metal-ion dependence and by their biological function ranging from DNA replication, recombination, repair, RNA maturation, processing, interference, to defense, nutrient regeneration or cell death. Several general principles emerge from this analysis. There is little correlation between catalytic mechanism and biological function. A single catalytic mechanism can be adapted in a variety of reactions and biological pathways. Conversely, a single biological process can often be accomplished by multiple tertiary and quaternary folds and by more than one catalytic mechanism. Two-metal-ion-dependent nucleases comprise the largest number of different tertiary folds and mediate the most diverse set of biological functions. Metal-ion-dependent cleavage is exclusively associated with exonucleases producing mononucleotides and endonucleases that cleave double- or single-stranded substrates in helical and base-stacked conformations. All metal-ion-independent RNases generate 2′,3′-cyclic phosphate products, and all metal-ion-independent DNases form phospho-protein intermediates. I also find several previously unnoted relationships between different nucleases and shared catalytic configurations.This publication has 473 references indexed in Scilit:
- Molecular Architecture of the Mos1 Paired-End Complex: The Structural Basis of DNA Transposition in a EukaryoteCell, 2009
- Human SLX4 Is a Holliday Junction Resolvase Subunit that Binds Multiple DNA Repair/Recombination EndonucleasesCell, 2009
- Pre-mRNA Processing Reaches Back toTranscription and Ahead to TranslationCell, 2009
- Mre11 Dimers Coordinate DNA End Bridging and Nuclease Processing in Double-Strand-Break RepairCell, 2008
- Trex1 Prevents Cell-Intrinsic Initiation of AutoimmunityCell, 2008
- Mechanism of IS200/IS605 Family DNA Transposases: Activation and Transposon-Directed Target Site SelectionCell, 2008
- Structure of the Dual Enzyme Ire1 Reveals the Basis for Catalysis and Regulation in Nonconventional RNA SplicingCell, 2008
- Ribozyme Catalysis of Metabolism in the RNA WorldChemistry & Biodiversity, 2007
- Type II restriction endonucleases: structure and mechanismCellular and Molecular Life Sciences, 2005
- Crystal structure of the site-specific recombinase γδ resolvase complexed with a 34 by cleavage siteCell, 1995