Theoretical Study of the RNA Hydrolysis Mechanism of the Dinuclear Zinc Enzyme RNase Z

Abstract

RNase Z is a dinuclear zinc enzyme that catalyzes the removal of the tRNA 3Ј-end trailer. Density functional theory is used to investigate the phosphodiester hydrolysis mechanism of this enzyme with a model of the active site constructed on the basis of the crystal structure. The calculations imply that the reaction proceeds through two steps. The first step is a nucleophilic attack by a bridging hydroxide coupled with protonation of the leaving group by a Glu-His diad. Subsequently, a water molecule activated by the same Glu-His diad makes a reverse attack, regenerating the bridging hy-

Dipeptide hydrolysis by the dinuclear zinc enzyme human renal dipeptidase: Mechanistic insights from DFT calculations

“…This is similar to several other dinuclear zinc enzymes studied previously, such as, PTE [28], AAP [29], DHO [30], GlxII [31], AHL lactonase [32], and RNase Z [33].…”

“…The barrier is calculated to be 11.6 kcal/mol, which upon inclusion of solvation (e = 4) decreases somewhat to 9.7 kcal/mol. We notice that the nucleophilic attack occurs directly from the bridging position, similarly to other dinuclear zinc enzymes that we have studied previously, such as phosphotriesterase (PTE) [28], AAP [29], dihydroorotase (DHO) [30], glyoxalase II (GlxII) [31], acyl-homoserine lactone hydrolase (AHL lactonase) [32], and RNase Z [33]. At TS1, the nascent O l -C bond is 1.81 Å, which is decreased from 2.54 Å in React, and the peptide C-N and C-O bonds are elongated from 1.36 and 1.24 Å, to 1.41 and 1.29 Å, respectively.…”

“…We also consider the reaction of the cilastatin inhibitor and provide a rationalization for its low reactivity. This methodology has been successfully applied to study a wide array of enzymes, [22][23][24][25][26][27] including several related di-zinc enzymes [28][29][30][31][32][33].…”

How Can Methanol Dehydrogenase from Methylacidiphilum fumariolicum Work with the Alien CeIII Ion in the Active Center? A Theoretical Study

“…The reliability of cluster model in enzymatic catalysis has been largely explored in the last decades by different groups and for a huge number of enzymes …”

“…The solvation energies were obtained from single point calculations performed on the optimized geometries with the more extended basis set 6–311+G(2d,2p)|SDD. The choice of the dielectric constant ϵ =4 is usually considered to be a good representation of protein surrounding . For the potential energy surfaces (PESs), the final solvation energies reported include the ZPE corrections.…”