Nylon-Oligomer Hydrolase Promoting Cleavage Reactions in Unnatural Amide Compounds.
The active site of 6-aminohexanoate-dimer hydrolase, a nylon-6 byproduct-degrading enzyme with a β-lactamase fold, possesses a Ser112/Lys115/Tyr215 catalytic triad similar to the one of penicillin-recognizing family of serine-reactive hydrolases but includes a unique Tyr170 residue. By using a reactive quantum mechanics/molecular mechanics (QM/MM) approach, we work out its catalytic mechanism and related functional/structural specificities. At variance with other peptidases, we show that the involvement of Tyr170 in the enzyme-substrate interactions is responsible for a structural variation in the substrate-binding state. The acylation via a tetrahedral intermediate is the rate-limiting step, with a free-energy barrier of ∼21 kcal/mol, driven by the catalytic triad Ser112, Lys115, and Tyr215, acting as a nucleophile, general base, and general acid, respectively. The functional interaction of Tyr170 with this triad leads to an efficient disruption of the tetrahedral intermediate, promoting a conformational change of the substrate favorable for proton donation from the general acid.
†Center for Basic Education and Integrated Learning, Kanagawa Institute of Technology, 1030 Shimo-Ogino, Atsugi, Kanagawa 243-0292, Japan.
Katsumasa
K
Kamiya
‡Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.
Takeshi
T
Baba
§Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23 rue du Loess, 67034 Strasbourg, France.
Mauro
M
Boero
∥RIKEN, Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
Toru
T
Matsui
⊥Graduate School of Engineering, University of Hyogo, Himeji, Hyogo 671-2280, Japan.
Seiji
S
Negoro
‡Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.|#CREST, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012 Japan.
Yasuteru
Y
Shigeta
catalytic triad; enzymes; hydrolases; nylon-oligomer; peptidase