3'-nucleases/nucleotidases of the S1-P1 family (EC 3.1.30.1) are single-strand-specific or non-specific zinc-dependent phosphoesterases present in plants, fungi, protozoan parasites, and in some bacteria. They participate in a wide variety of biological processes and their current biotechnological applications rely on their single-strand preference, nucleotide non-specificity, a broad range of catalytic conditions and high stability. We summarize the present and potential utilization of these enzymes in biotechnology and medicine in the context of their biochemical and structure-function properties. Explanation of unanswered questions for bacterial and trypanosomatid representatives could facilitate development of emerging applications in medicine.
- MeSH
- antitumorózní látky farmakologie MeSH
- biotechnologie metody MeSH
- cílená molekulární terapie metody MeSH
- endonukleasy specifické pro jednořetězcové nukleové kyseliny chemie genetika metabolismus farmakologie MeSH
- fungální proteiny chemie metabolismus MeSH
- interakce hostitele a patogenu MeSH
- lidé MeSH
- mutační analýza DNA metody MeSH
- nukleotidasy metabolismus MeSH
- substrátová specifita MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
The single-strand-specific S1 nuclease from Aspergillus oryzae is an archetypal enzyme of the S1-P1 family of nucleases with a widespread use for biochemical analyses of nucleic acids. We present the first X-ray structure of this nuclease along with a thorough analysis of the reaction and inhibition mechanisms and of its properties responsible for identification and binding of ligands. Seven structures of S1 nuclease, six of which are complexes with products and inhibitors, and characterization of catalytic properties of a wild type and mutants reveal unknown attributes of the S1-P1 family. The active site can bind phosphate, nucleosides, and nucleotides in several distinguished ways. The nucleoside binding site accepts bases in two binding modes-shallow and deep. It can also undergo remodeling and so adapt to different ligands. The amino acid residue Asp65 is critical for activity while Asn154 secures interaction with the sugar moiety, and Lys68 is involved in interactions with the phosphate and sugar moieties of ligands. An additional nucleobase binding site was identified on the surface, which explains the absence of the Tyr site known from P1 nuclease. For the first time ternary complexes with ligands enable modeling of ssDNA binding in the active site cleft. Interpretation of the results in the context of the whole S1-P1 nuclease family significantly broadens our knowledge regarding ligand interaction modes and the strategies of adjustment of the enzyme surface and binding sites to achieve particular specificity.
- MeSH
- aminokyseliny metabolismus MeSH
- Aspergillus oryzae enzymologie metabolismus MeSH
- endonukleasy specifické pro jednořetězcové nukleové kyseliny metabolismus MeSH
- fungální proteiny metabolismus MeSH
- katalytická doména fyziologie MeSH
- katalýza MeSH
- kinetika MeSH
- sekvence aminokyselin MeSH
- sekvenční seřazení MeSH
- substrátová specifita MeSH
- vazebná místa fyziologie MeSH
- Publikační typ
- časopisecké články MeSH
