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Deibert, M.; Gražulis, S.; Sasnauskas, Giedrius; Šikšnys, Virginijus; Huber, Robert

doi:10.1038/79032

Cited by 168 publications

(139 citation statements)

References 35 publications

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“…Such behavior of SgrAI resembles the mode of action of tetrameric endonuclease SfiI that binds two copies of its recognition sequence before cleaving concertedly at four phosphodiester bonds (9,10). Other examples of restriction endonucleases that cleave two recognition sites in a concerted fashion are Cfr10I and NgoMIV (11,12). The SgrAI recognition sequence (CPu2CCGGPyG) is a subset of the sequences cleaved by either Cfr10I (Pu2CCGGPy) or NgoMI V (G2CCGGC).…”

Section: Discussionmentioning

confidence: 99%

“…Recently, a similar reaction pathway has been shown to be characteristic for Sau3AI, except that it is a monomeric protein that dimerizes in the presence of DNA (8). SfiI (9,10), NgoMIV (11), and Cfr10I (12) are tetramers of identical subunits that need to bind to two recognition sites for catalysis, but in contrast to EcoRII or NaeI, they cleave four phosphodiester bonds in a concerted fashion (10)(11)(12). SgrAI, described here, is yet another example of the diverse mechanisms exhibited by restriction endonucleases.…”

mentioning

confidence: 99%

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Self-generated DNA termini relax the specificity of Sgr AI restriction endonuclease

Bitinaite

Schildkraut²

2002

Proc. Natl. Acad. Sci. U.S.A.

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The primary target of SgrAI restriction endonuclease is a multiple sequence of the form 5 -CPu2CCGGPyG. Previous work had indicated that SgrAI must bind two recognition sites simultaneously for catalysis [Bilcock, D. T., Daniels, L. E., Bath, A. J. & Halford, S. E. (1999) J. Biol. Chem. 274, 36379 -36386]. In the present study, SgrAI is shown to cleave not only its canonical sequences, but also the sequences 5 -CPuCCGGPy(A,T,C) and 5 -CPuCCGGGG, both referred to as secondary sequences. On plasmid pSK7, SgrAI cleaves secondary sites 26-fold slower than the canonical site. However, the same plasmid, but without the canonical site, is cleaved 200-fold slower. We show that DNA termini generated by cleaving the canonical site for SgrAI assist in the cleavage of secondary sites. The SgrAI-termini in cis with respect to secondary site are markedly preferred over those in trans. The SgrAI-termini provided in a form of oligonucleotide duplex are also shown to stimulate canonical site cleavage. At a 40-fold molar excess of the SgrAI-termini over substrate, the SgrAI specificity is shown to improve by two orders of magnitude, because of concurrent 10-fold increase in the cleavage of canonical site and 50-fold decrease in the cleavage of secondary sites. The unconventional reaction pathway by which SgrAI utilizes the self-generated DNA termini to cleave its DNA targets has not been observed hitherto among type II restriction endonucleases. Based on our work and previous reports, a pathway of DNA binding and cleavage by the SgrAI restriction endonuclease is proposed.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Self-generated DNA termini relax the specificity of Sgr AI restriction endonuclease

Bitinaite

Schildkraut²

2002

Proc. Natl. Acad. Sci. U.S.A.

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“…We have selected the pseudopalindrome cutter Ecl18kI (/CCNGG) and the related palindrome cutter NgoMIV (G/CCGGC) for a detailed comparison. A high resolution structure of NgoMIV with DNA has been reported previously [1]. We have now crystallized Ecl18kI with DNA and solved the structure at high resolution [2].…”

Section: Abstract: Crystallography Of Proteins and Nucleic Acids Resmentioning

confidence: 99%

Structural aspects of quadruplexes as potential therapeutic targets

Parkinson¹,

Neidle²

2006

Acta Cryst Sect A

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Structural investigations into quadruplexes, formed from guanine rich sequences found in the human chromosome, and development of small molecule ligands that can stabilize these structures have been the main focus of our research. The targeting of the telomere, a G-rich hexanucleotide repeat sequence TAGGGT, found at the end of all mammalian chromosomes has lead to the development of a series of ligands that can effectively inhibit the enzyme telomerase. Critically a 3' single stranded overhang, located at the end of the chromosome, is the substrate for the ribonucleoprotein telomerase. Folding of these telomeric repeats into higher order DNA structures inhibits access of telomerase and prevents telomere maintenance. Additionally, the binding of other associated proteins that form part of the telosome, are also disrupted leading rapidly to chromosomal damage, such as chromosomal fusions and apoptosis. We will discuss our research into the folding topologies that are available to these telomeric sequences and other target sequence found in the chromosome, and the design of selective ligands that target these novel topologies. This is of particular importance with the identification of quanine rich sequences that have been shown to form stable quadruplex structures within promotor regions of onogenes. The structural diversity of the quadruplex structures formed from these G-rich DNA sequences will also be reviewed. m04.o03

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“…Fig. 7 shows a secondary structure prediction for the catalytic domain of MboI in comparison with the secondary structure of EcoRII and NgoMIV, deduced from the crystal structures (31,33). The active site residues are indicated for all three enzymes, whereas the residues involved in DNA binding are only indicated for MboI (based on the mutational analysis) and NgoMIV (based on the co-crystal structure).…”

Section: Fig 3 Gel Electrophoretic Mobility Shift Experiments To Commentioning

confidence: 99%

“…(D/E)XK superfamily of Type II restriction endonucleases. In NgoMIV, for which a co-crystal structure is available (31), this region encompasses helices 3 and 7 and ␤-strands 2 and 3 that are involved in DNA recognition and cleavage. The involvement of this region in DNA binding and cleavage by Cfr10I and EcoRII is also apparent from crystal structures (32,33).…”

mentioning

confidence: 99%

Specificity Changes in the Evolution of Type II Restriction Endonucleases

Pingoud

Sudina

Geyer

et al. 2005

Journal of Biological Chemistry

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How restriction enzymes with their different specificities and mode of cleavage evolved has been a long standing question in evolutionary biology. We have recently shown that several Type II restriction endonucleases, namely SsoII (2CCNGG), PspGI (2CCWGG), Eco-RII (2CCWGG), NgoMIV (G2CCGGC), and Cfr10I (R2CCGGY), which recognize similar DNA sequences (as indicated, where the downward arrows denote cleavage position), share limited sequence similarity over an interrupted stretch of ϳ70 amino acid residues with MboI, a Type II restriction endonuclease from Moraxella bovis (Pingoud, V., Conzelmann, C., Kinzebach, S., Sudina, A., Metelev, V., Kubareva, E., Bujnicki, J. M., Lurz, R., Luder, G., Xu, S. Y., and Pingoud, A. (2003) J. Mol. Biol. 329, 913-929). Nevertheless, MboI has a dissimilar DNA specificity (2GATC) compared with these enzymes. In this study, we characterize MboI in detail to determine whether it utilizes a mechanism of DNA recognition similar to SsoII, PspGI, EcoRII, NgoMIV, and Cfr10I. Mutational analyses and photocross-linking experiments demonstrate that MboI exploits the stretch of ϳ70 amino acids for DNA recognition and cleavage. It is therefore likely that MboI shares a common evolutionary origin with SsoII, PspGI, EcoRII, NgoMIV, and Cfr10I. This is the first example of a relatively close evolutionary link between Type II restriction enzymes of widely different specificities.

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Untitled

Cited by 168 publications

References 35 publications

Self-generated DNA termini relax the specificity of Sgr AI restriction endonuclease

Self-generated DNA termini relax the specificity of Sgr AI restriction endonuclease

Structural aspects of quadruplexes as potential therapeutic targets

Specificity Changes in the Evolution of Type II Restriction Endonucleases

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