DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI

@article{Flick1998DNABA,
  title={DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI},
  author={Karen E. Flick and Melissa S. Jurica and Raymond J. Monnat and Barry L. Stoddard},
  journal={Nature},
  year={1998},
  volume={394},
  pages={96-101}
}
Homing endonucleases are a diverse collection of proteins that are encoded by genes with mobile, self-splicing introns. They have also been identified in self-splicing inteins (protein introns). These enzymes promote the movement of the DNA sequences that encode them from one chromosome location to another; they do this by making a site-specific double-strand break at a target site in an allele that lacks the corresponding mobile intron. The target sites recognized by these small endonucleases… 
Homing endonuclease structure and function
  • B. Stoddard
  • Medicine, Biology
    Quarterly Reviews of Biophysics
  • 2005
TLDR
Homing endonucleases can be divided into several unique families that are remarkable in several respects: they display extremely high DNA-binding specificities which arise from long DNA target sites (14–40 bp), they are tolerant of a variety of sequence variations in these sites, and they display disparate DNA cleavage mechanisms.
Homing endonuclease structureand function
Homing endonucleases are encoded by open reading frames that are embedded within group I, group II and archael introns, as well as inteins (intervening sequences that are spliced and excised
Homing endonuclease I-TevIII: dimerization as a means to a double-strand break
TLDR
I-TevIII, the H–N–H endonuclease encoded by the RB3 nrdB intron, is described, which makes a double-strand break on the DNA homing site by acting as a dimer, and through deletion analysis, the dimerization interface was mapped to the DNA-binding domain.
Homing endonucleases from mobile group I introns: discovery to genome engineering
TLDR
Crystallographic analyses of representatives from all known homing endonuclease families have illustrated both their mechanisms of action and their evolutionary relationships to a wide range of host proteins.
I-NjaI, a nuclear intron-encoded homing endonuclease from Naegleria, generates a pentanucleotide 3' cleavage-overhang within a 19 base-pair partially symmetric DNA recognition site.
TLDR
The I-NjaI endonuclease was affinity purified, characterized in more detail, and found to generate five-nucleotide 3' staggered ends at the intron insertion site which differs from the ends generated by all other known homing endonucleases.
Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI.
TLDR
It is suggested that the cleavage of each strand is catalyzed by each of the two non-equivalent active sites of PI-PfuI.
Homing endonucleases: structure, function and evolution
TLDR
This paper presents a new strategy of flexible recognition of very long DNA target sites that allows these sequences to minimize nonspecific cleavage within the host genome, while maximizing the ability of the endonuclease to cleave closely related variants of the homing site.
Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor
TLDR
A model in which the flexibility in protein-DNA interactions allows I-TevI to bind variant intronless alleles to promote intron mobility while facilitating its function in autorepression, and thereby persistence in its host is presented.
DNA binding and cleavage by the HNH homing endonuclease I-HmuI.
TLDR
I-HmuI provides an unambiguous structural connection between the His-Cys box endonucleases and the bacterial colicins, supporting the hypothesis that these enzymes diverged from a common ancestral nuclease.
The evolution of homing endonuclease genes and group I introns in nuclear rDNA.
TLDR
Evidence is found for intron-independent HEG invasion into both homologous and heterologous introns in often distantly related lineages, as well as the "switching" of HEGs between different intron peripheral loops and between sense and antisense strands of intron DNA, which suggest that nuclear Hegs are frequently mobilized.
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References

SHOWING 1-10 OF 25 REFERENCES
Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site.
TLDR
The endonuclease protected most of the purines found in both the major and minor grooves of the DNA helix from modification by dimethyl sulfate (DMS), however, the reactivity to DMS was enhanced at some purines, suggesting that binding leads to a conformational change in the DNA.
The structure of I-Crel, a Group I intron-encoded homing endonuclease
TLDR
The structure of I-Crel provides the first view of a protein encoded by a gene within an intron and the conserved LAGLIDADG motif, found in many mobile intron endonucleases, maturases and inteins, forms a novel helical interface and contributes essential residues to the active site.
Crystallization and preliminary X‐ray studies of I‐PpoI: A nuclear, intron‐encoded homing endonuclease from Physarum polycephalum
TLDR
Initial X‐ray diffraction experiments indicate that the asymmetric unit contains an enzyme homodimer and one duplex DNA molecule, and that the unit cell has a specific volume of 3.4 Å3/dalton, and provide strong evidence that I‐PpoI contains several bound zinc ions as part of its structure.
Homing endonucleases: keeping the house in order.
TLDR
The evolution of homing endonucleases is considered, both at the structure-function level and in terms of their persistence in widely divergent biological systems.
A mobile group I intron in the nuclear rDNA of physarum polycephalum
TLDR
This is the first demonstration of the transposition of a nuclear intron in an experimental setting, and provides a rare example of a protein encoded by an RNA polymerase I transcript.
Crystal Structure of PI-SceI, a Homing Endonuclease with Protein Splicing Activity
TLDR
This report presents prototypic structures of domains with single endonuclease and protein splicing active sites of PI-Scel, a bifunctional yeast protein that propagates its mobile gene by catalyzingprotein splicing and site-specific DNA double-strand cleavage.
Prokaryotic introns and inteins: a panoply of form and function
TLDR
It is illustrated that interrupted genes can no longer be considered the province of eukaryotes, but rather that many forms of IVSs are phylogenetically diverse, occurring also in bacterial and archaeal genomes.
A novel arrangement of zinc-binding residues and secondary structure in the C3HC4 motif of an alpha herpes virus protein family.
TLDR
A highly conserved, cysteine-rich region plays a crucial role in the function of a family of regulatory proteins encoded by alpha herpes viruses, and its secondary structure differs from that found in other characterized zinc-containing proteins.
DNA recognition by GAL4: structure of a protein-DNA complex
A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 Å resolution by X-ray crystallography. The protein binds as a
Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices.
The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A
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