ArticleNucleic acids research2011
DNA intercalation without flipping in the specific ThaI-DNA complex.
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 6 papers.
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Who cites it
6 citing papers in PubMed.
- Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI.Nucleic acids research · 2020Article
- Sequence specificity in DNA-drug intercalation: MD simulation and density functional theory approaches.Journal of computer-aided molecular design · 2020Article
- A novel transcriptional regulator of L-arabinose utilization in human gut bacteria.Nucleic acids research · 2015Article
- CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI.Nucleic acids research · 2012Article
- Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.Nucleic acids research · 2012Article
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Authors and funding
4 authors.
Funding
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Abstract
The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as the active site residues. This agrees with earlier bioinformatic predictions and implies that the PD and (D/E)XK motifs in the sequence are incidental. DNA recognition is very unusual: the two Met47 residues of the ThaI dimer intercalate symmetrically into the CG steps of the target sequence. They approach the DNA from the minor groove side and penetrate the base stack entirely. The DNA accommodates the intercalating residues without nucleotide flipping by a doubling of the CG step rise to twice its usual value, which is accompanied by drastic unwinding. Displacement of the Met47 side chains from the base pair midlines toward the downstream CG steps leads to large and compensating tilts of the first and second CG steps. DNA intercalation by ThaI is unlike intercalation by HincII, HinP1I or proteins that bend or repair DNA.
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