6s58

AvaII restriction endonuclease in the absence of nucleic acids

spinqualitylabelsall models 6s58, resolution 2.32Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6s58 is a 4 chain structure with sequence from Nostoc sp. PCC 7120 = FACHB-418. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.32Å Ligands: CA, UNX Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q8YYB7_NOSS1 Publication Abstract from PubMed Restriction endonucleases naturally target DNA duplexes. Systematic screening has identified a small minority of these enzymes that can also cleave RNA/DNA heteroduplexes and that may therefore be useful as tools for RNA biochemistry. We have chosen AvaII (G downward arrowGWCC, where W stands for A or T) as a representative of this group of restriction endonucleases for detailed characterization. Here, we report crystal structures of AvaII alone, in specific complex with partially cleaved dsDNA, and in scanning complex with an RNA/DNA hybrid. The specific complex reveals a novel form of semi-specific dsDNA readout by a hexa-coordinated metal cation, most likely Ca2+ or Mg2+. Substitutions of residues anchoring this non-catalytic metal ion severely impair DNA binding and cleavage. The dsDNA in the AvaII complex is in the A-like form. This creates space for 2'-OH groups to be accommodated without intra-nucleic acid steric conflicts. PD-(D/E)XK restriction endonucleases of known structure that bind their dsDNA targets in the A-like form cluster into structurally similar groups. Most such enzymes, including some not previously studied in this respect, cleave RNA/DNA heteroduplexes. We conclude that A-form dsDNA binding is a good predictor for RNA/DNA cleavage activity. Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation.,Kisiala M, Kowalska M, Pastor M, Korza HJ, Czapinska H, Bochtler M Nucleic Acids Res. 2020 May 27. pii: 5847776. doi: 10.1093/nar/gkaa403. PMID:32459314 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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