title: Mechanistic insight into the catalytic activity of ββα-metallonucleases from computer simulations: Vibrio vulnificus periplasmic nuclease as a test case.
abstract: 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.
authors: Department of Pharmacology, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain.
authors: Juan A
authors: JA
authors: Bueren-Calabuig
authors: Claire
authors: C
authors: Coderch
authors: Eva
authors: E
authors: Rico
authors: Antonio
authors: A
authors: Jiménez-Ruiz
authors: Federico
authors: F
authors: Gago
mesh_terms: D055162:Biocatalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004706:Endodeoxyribonucleases / Q000737:chemistry / Q000378:metabolism; D004720:Endonucleases / Q000737:chemistry / Q000378:metabolism*; D007477:Ions / Q000737:chemistry; D008670:Metals / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D019897:Periplasm / Q000201:enzymology; D011789:Quantum Theory; D041261:Vibrio vulnificus / Q000201:enzymology*
chemical_list: D007477:Ions; D008670:Metals; D009838:Oligodeoxyribonucleotides; D004706:Endodeoxyribonucleases; D004720:Endonucleases; C064579:I-Ppo endonuclease