EzCatDB

R L C P
Hierarchic Classification of Catalytic Mechanisms


R 3.-.-.- : Transfer (bond cleavage and new bond formation) (Reaction)

L 3.100.-.- : Phosphate group from Hydroxyl oxygen to Hydroxyl oxygen (Ligand group involved)


Catalytic mechanisms

  • 3.100.790.- : Bacterial PI-PLC-like mechanism (Base/Acid/Modulator/Stabilizer); SN2-like reaction; Modulator-assisted base activation of acceptor group; Nucleophilic attack on transferred group by activated acceptor group; Stablization of transition state & Modulator-assisted acid protonation to leaving group
  • 3.100.219000.- : DNA topoisomerase III autotransfer mechanism (Nucleophile/Acid-Base/Modulator-Stabilizer); Modulator-assisted activation of nucleophile; SN2-like nucleophilic attack on transferred group by nucleophile; Transition state stabilized; protonation to leaving group by general acid; Base-activation of acceptor group; SN2-like nucleophilic attack on transferred group by acceptor group
  • 3.100.219010.- : DNA topoisomerase I autotransfer mechanism (Nucleophile/Acid-Base/Modulator/Modulator-Stabilizer); Modulator-assisted activation of nucleophile; SN2-like nucleophilic attack on transferred group by nucleophile; transition state stabilized; Another modulator activation of general acid; Acid protonation to leaving group; Base-activation of acceptor group; SN2-like nucleophilic attack on transferred group by acceptor group
  • 3.100.220195.- : Cofactor-dependent-phosphoglycerate-mutase-like mechanism (Nucleophile/Acid-Base/Modulator-Stabilizer/Stabilizer); Modulator-assisted activation of nucleophile; Nucleophilic attack on transferred group; SN2-like reaction; Stabilization of transition-state; covalent intermediate formed; followed by acid protonation to leaving group; Base activation of acceptor group; Nucleophilic attack of acceptor group on transferred group; SN2-like reaction
  • 3.100.305000.- : DNA topoisomerase II autotransfer mechanism (Nucleophile/Base/Stabilizer); Base activation of nucleophile; Nucleophilic attack on transferred group; Inroganic-cofactor-assisted stabilization of transition-state; followed by nucleophilic attack by acceptor group on transferred group
  • Copyright: Nozomi Nagano, JST & CBRC-AIST
    Funded by PRESTO/Japan Science and Technology Agency (JST) (December 2001 - November 2004)
    Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
    Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
    Funded by BIRD/Japan Science and Technology Agency (JST) (September 2005 - September 2008)
    Funded by BIRD/Japan Science and Technology Agency (JST) (October 2007 - September 2010)
    Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
    Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
    Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - March 2016)
    Funded by the project commissioned by the New Energy and Industrial Technology Development Organization (NEDO) (April 2016 -)