ArticleNucleic acids research2011
Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 35 citations in OpenAlex.
- Modular determinants of cleavage preference in GIY-YIG nucleases revealed by block-based DNA shuffling and directed evolution.Nucleic acids research · 2026Article
- Functional dissection of the conserved C. elegans LEM-3/ANKLE1 nuclease reveals a crucial requirement for the LEM-like and GIY-YIG domains for DNA bridge processing.Nucleic acids research · 2025Article
- Plant Organellar MSH1 Is a Displacement Loop-Specific Endonuclease.Plant & cell physiology · 2024Article
- Characterization of winged helix domain fusion endonucleases as N6-methyladenine-dependent type IV restriction systems.Frontiers in microbiology · 2024Article
- Biochemical and mechanistic analysis of the cleavage of branched DNA by human ANKLE1.Nucleic acids research · 2023Article
- Holliday junction resolution by At-HIGLE: an SLX1 lineage endonuclease from Arabidopsis thaliana with a novel in-built regulatory mechanism.Nucleic acids research · 2022Article
- Structure specific DNA recognition by the SLX1-SLX4 endonuclease complex.Nucleic acids research · 2021Article
- Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli.Scientific reports · 2021Article
- Exploring the Structures and Functions of Macromolecular SLX4-Nuclease Complexes in Genome Stability.Frontiers in genetics · 2021Review
- Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI.Nucleic acids research · 2020Article
- Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease.Nucleic acids research · 2019Article
- Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA.Scientific reports · 2016Article
- Perpetuating the homing endonuclease life cycle: identification of mutations that modulate and change I-TevI cleavage preference.Nucleic acids research · 2016Article
- Structural and Mechanistic Analysis of the Slx1-Slx4 Endonuclease.Cell reports · 2015Article
- Type II restriction endonucleases--a historical perspective and more.Nucleic acids research · 2014Review
- Homing endonucleases: from genetic anomalies to programmable genomic clippers.Methods in molecular biology (Clifton, N.J.) · 2014Review
- Highlights of the DNA cutters: a short history of the restriction enzymes.Nucleic acids research · 2014Article
- The monomeric GIY-YIG homing endonuclease I-BmoI uses a molecular anchor and a flexible tether to sequentially nick DNA.Nucleic acids research · 2013Article
- Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI.Nucleic acids research · 2012Article
- Structural, functional and evolutionary relationships between homing endonucleases and proteins from their host organisms.Nucleic acids research · 2012Review
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 3 countries.
Funding
Abstract
The GIY-YIG nuclease domain is present in all kingdoms of life and has diverse functions. It is found in the eukaryotic flap endonuclease and Holliday junction resolvase Slx1-Slx4, the prokaryotic nucleotide excision repair proteins UvrC and Cho, and in proteins of 'selfish' genetic elements. Here we present the structures of the ternary pre- and post-cleavage complexes of the type II GIY-YIG restriction endonuclease Hpy188I with DNA and a surrogate or catalytic metal ion, respectively. Our structures suggest that GIY-YIG nucleases catalyze DNA hydrolysis by a single substitution reaction. They are consistent with a previous proposal that a tyrosine residue (which we expect to occur in its phenolate form) acts as a general base for the attacking water molecule. In contrast to the earlier proposal, our data identify the general base with the GIY and not the YIG tyrosine. A conserved glutamate residue (Glu149 provided in trans in Hpy188I) anchors a single metal cation in the active site. This metal ion contacts the phosphate proS oxygen atom and the leaving group 3'-oxygen atom, presumably to facilitate its departure. Taken together, our data reveal striking analogy in the absence of homology between GIY-YIG and ββα-Me nucleases.
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