title: Phosphate mono- and diesterase activities of the trinuclear zinc enzyme nuclease P1--insights from quantum chemical calculations.
abstract: Nuclease P1 is a trinuclear zinc enzyme that catalyzes the hydrolysis of single-stranded DNA and RNA. Density functional calculations are used to elucidate the reaction mechanism of this enzyme with a model of the active site designed on the basis of the X-ray crystal structure. 2-Tetrahydrofuranyl phosphate and methyl 2-tetrahydrofuranyl phosphate substrates are used to explore the phosphomonoesterase and phosphodiesterase activities of this enzyme, respectively. The calculations reveal that for both activities, a bridging hydroxide performs an in-line attack on the phosphorus center, resulting in inversion of the configuration. Simultaneously, the P-O bond is cleaved, and Zn2 stabilizes the negative charge of the leaving alkoxide anion and assists its departure. All three zinc ions, together with Arg48, provide electrostatic stabilization to the penta-coordinated transition state, thereby lowering the reaction barrier.
authors.affiliation: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden.
authors.forename: Rong-Zhen
authors.initials: RZ
authors.lastname: Liao
authors.forename: Jian-Guo
authors.initials: JG
authors.lastname: Yu
authors.forename: Fahmi
authors.initials: F
authors.lastname: Himo
mesh_terms: D020134:Catalytic Domain; D004952:Esters; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism*; D006868:Hydrolysis; D006878:Hydroxides / Q000378:metabolism; D008958:Models, Molecular; D010710:Phosphates / Q000378:metabolism; D011789:Quantum Theory; D015719:Single-Strand Specific DNA and RNA Endonucleases / Q000737:chemistry / Q000378:metabolism*; D015032:Zinc
chemical_list: D004952:Esters; D005656:Fungal Proteins; D006878:Hydroxides; D010710:Phosphates; C526100:Nuclease P1, Penicillium citrinum; D015719:Single-Strand Specific DNA and RNA Endonucleases; D015032:Zinc