EzCatDB

R L C P
Hierarchic Classification of Catalytic Mechanisms


R 1.-.-.- : Hydrolysis (bond cleavage by water) (Reaction)

L 1.14.-.- : Thioester (One of Carbonyl Ester bonds) (Ligand group involved)


Catalytic mechanisms

  • 1.14.200.- : Pepsin-like mechanism (Acid-Base/Stabilizer); Water activation by base; SN2-like nucleophilic attack by activated water; Stabilization of transition-state; Protonation to leaving group by acid
  • 1.14.800.- : GDP mannose dehydrogenase final step-like mechanism (Base/Stabilizer); Base-activated water directly attacks on substrate; Stabilization of transition-state; Collapse of transition-state leads to release of leaving group
  • 1.14.10105.- : Glyoxalase-II-like mechanism (Modulator); Inorganic cofactor-assisted water activation; Inorganic cofactor-assisted stabilization of transition-state; Inorganic-cofactor interaction with water/intermediate (atom adjacent to scissile bond)
  • 1.14.30000.- : Trypsin-like mechanism (Nucleophile/Acid-Base/Modulator/Stabilizer); Modulator-assisted base activation of nucleophile; Nucleophilic attack on target bond; SN2-like reaction; covalent bond between enzyme and substrate; followed by protonation to leaving group; hydrolysis by base-activated water
  • 1.14.36110.- : 4-hydroxybenzoyl-CoA thioesterase-like mechanism (Nucleophile/Acid-Base/Stabilizer); SN1-like reaction induced by stabilizer; covalent bond formation between nucleophile and target atom; Acid protonation to leaving group; intermediate stablilized; covalent bond attacked by base-activated water; intermediate stabilized
  • 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 -)