Mechanistic Insight into the Catalytic Activity of beta beta alpha-Metallonucleases from Computer Simulations: Vibrio vulnificus Periplasmic Nuclease as a Test Case

作者：Bueren Calabuig Juan A; Coderch Claire; Rico Eva; Jimenez Ruiz Antonio; Gago Federico^*

来源：ChemBioChem, 2011, 12(17): 2615-2622.

DOI：10.1002/cbic.201100485

• DNA cleavage
• enzyme catalysis
• molecular dynamics
• quantum chemistry
• water splitting

Using information from wild-type and mutant Vibrio vulnificus nuclease (Vvn) and I-PpoI homing endonuclease co-crystallized with different oligodeoxynucleotides, we have built the complex of Vvn with a DNA octamer and carried out a series of simulations to dissect the catalytic mechanism of this metallonuclease in a stepwise fashion. The distinct roles played in the reaction by individual active site residues, the metal cation and water molecules have been clarified by using a combination of classical molecular dynamics simulations and quantum mechanical calculations. Our results strongly support the most parsimonious catalytic mechanism, namely one in which a single water molecule from bulk solvent is used to cleave the phosphodiester bond and protonate the 3'-hydroxylate leaving group.

• 出版日期2011-11-25