5TH3

Restriction/modification system-Type II R.SwaI cleaved DNA complex

Summary for 5TH3

• Entry DOI: 10.2210/pdb5th3/pdb
• Related: 5TGQ 5TGX
• Descriptor: R-SwaI protein, DNA (cleaved 25-MER, portion 1), DNA (cleaved 25-MER, portion 2), ... (9 entities in total)
• Functional Keywords: i-swai, cleaved dna complex, r/m system, dna binding protein
• Biological source: Staphylococcus warneri; More
• Total number of polymer chains: 12
• Total formula weight: 141947.04

Authors

Shen, B.W.,Stoddard, B.L. (deposition date: 2016-09-29, release date: 2016-12-21, Last modification date: 2024-10-30)

Primary citation

Shen, B.W.,Heiter, D.F.,Lunnen, K.D.,Wilson, G.G.,Stoddard, B.L.
DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target.
Nucleic Acids Res., 45:1516-1528, 2017

PubMed Abstract: R.SwaI, a Type IIP restriction endonuclease, recognizes a palindromic eight base pair (bp) symmetric sequence, 5΄-ATTTAAAT-3΄, and cleaves that target at its center to generate blunt-ended DNA fragments. Here, we report three crystal structures of SwaI: unbound enzyme, a DNA-bound complex with calcium ions; and a DNA-bound, fully cleaved complex with magnesium ions. We compare these structures to two structurally similar ‘PD-D/ExK’ restriction endonucleases (EcoRV and HincII) that also generate blunt-ended products, and to a structurally distinct enzyme (the HNH endonuclease PacI) that also recognizes an 8-bp target site consisting solely of A:T base pairs. Binding by SwaI induces an extreme bend in the target sequence accompanied by un-pairing and re-ordering of its central A:T base pairs. This result is reminiscent of a more dramatic target deformation previously described for PacI, implying that long A:T-rich target sites might display structural or dynamic behaviors that play a significant role in endonuclease recognition and cleavage.

PubMed: 28180307
DOI: 10.1093/nar/gkw1200

Experimental method

X-RAY DIFFRACTION (2.33 Å)