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Mechanistic Insight into the Catalytic Activity of ββα‐Metallonucleases from Computer Simulations: Vibrio vulnificus Periplasmic Nuclease as a Test Case
Author(s) -
BuerenCalabuig Juan A.,
Coderch Claire,
Rico Eva,
JiménezRuiz Antonio,
Gago Federico
Publication year - 2011
Publication title -
chembiochem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.05
H-Index - 126
eISSN - 1439-7633
pISSN - 1439-4227
DOI - 10.1002/cbic.201100485
Subject(s) - phosphodiester bond , vibrio vulnificus , nuclease , cleave , molecular dynamics , chemistry , dna , catalysis , molecule , micrococcal nuclease , endonuclease , stereochemistry , active site , combinatorial chemistry , biophysics , biology , biochemistry , computational chemistry , bacteria , histone , rna , genetics , organic chemistry , nucleosome , gene
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.