ArticleNucleic acids research2008
How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Base-excision restriction enzymes: expanding the world of epigenetic immune systems.DNA research : an international journal for rapid publication of reports on genes and genomes · 2023Article
- Type II restriction endonucleases--a historical perspective and more.Nucleic acids research · 2014Review
- Restriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats.Nucleic acids research · 2013Article
- DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme.Nucleic acids research · 2010Article
- Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes.Nucleic acids research · 2009Article
- Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.Nucleic acids research · 2009Article
- Article
- Central base pair flipping and discrimination by PspGI.Nucleic acids research · 2008Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Restriction endonucleases Ecl18kI and PspGI/catalytic domain of EcoRII recognize CCNGG and CCWGG sequences (W stands for A or T), respectively. The enzymes are structurally similar, interact identically with the palindromic CC:GG parts of their recognition sequences and flip the nucleotides at their centers. Specificity for the central nucleotides could be influenced by the strength/stability of the base pair to be disrupted and/or by direct interactions of the enzymes with the flipped bases. Here, we address the importance of these contributions. We demonstrate that wt Ecl18kI cleaves oligoduplexes containing canonical, mismatched and abasic sites in the central position of its target sequence CCNGG with equal efficiencies. In contrast, substitutions in the binding pocket for the extrahelical base alter the Ecl18kI preference for the target site: the W61Y mutant prefers only certain mismatched substrates, and the W61A variant cuts exclusively at abasic sites, suggesting that pocket interactions play a major role in base discrimination. PspGI and catalytic domain of EcoRII probe the stability of the central base pair and the identity of the flipped bases in the pockets. This 'double check' mechanism explains their extraordinary specificity for an A/T pair in the flipping position.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.