6S58
AvaII restriction endonuclease in the absence of nucleic acids
Summary for 6S58
| Entry DOI | 10.2210/pdb6s58/pdb |
| Related | 6G3B 6S48 |
| Descriptor | Type II site-specific deoxyribonuclease, CALCIUM ION, UNKNOWN ATOM OR ION, ... (4 entities in total) |
| Functional Keywords | restriction endonuclease, apo, scanning, substrate, product complex, rna/dna hybrid, rna/dna heteroduplex, a-dna, hydrolase |
| Biological source | Nostoc sp. PCC 7120 = FACHB-418 |
| Total number of polymer chains | 4 |
| Total formula weight | 108883.03 |
| Authors | Kisiala, M.,Kowalska, M.,Korza, H.,Czapinska, H.,Bochtler, M. (deposition date: 2019-06-30, release date: 2020-05-20, Last modification date: 2024-01-24) |
| Primary citation | Kisiala, M.,Kowalska, M.,Pastor, M.,Korza, H.J.,Czapinska, H.,Bochtler, M. Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation. Nucleic Acids Res., 48:6954-6969, 2020 Cited by PubMed Abstract: 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↓GWCC, 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. PubMed: 32459314DOI: 10.1093/nar/gkaa403 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.32 Å) |
Structure validation
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