RLCP 1.30.-.- :EzCatDB EzCatDB

R L C P
Hierarchic Classification of Catalytic Mechanisms


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

L 1.30.-.- : C-O bond (O-glycoside bond) (Ligand group involved)

Catalytic mechanisms

  • 1.30.260.- : Endo-polygalacturonase-like mechanism (Acid/Base/Modulator); SN2-like reaction; Modulator-assisted activation of base; Water activation by base; Protonation to leaving group by acid leads to bond cleavage

  • 1.30.300.- : Exoglucanase-II-like mechanism (Acid/Base); Base-activated water directly attacks on substrate & hydrolysis assisted by proton donor (SN2)

  • 1.30.4920.- : Glucoamylase-like mechanism (Acid-Stabilizer/Stabilizer-Base/Modulator/Stabilizer-Modulator); Acid protonation to leaving group; Transition-state stabilization; Modulator-assisted Acid-Stabilizer; Stabilizer-Modulator-assisted base activation of water; Activated water attacks on transition-state to complete reaction

  • 1.30.4950.- : Goose-lysozyme-like mechanism (Acid-Base-Stabilizer); Protonation to leaving group by acid; Stabilization of SN1-like intermediate; Base-activated water attacks intermediate

  • 1.30.5050.- : Cellulase9A-like mechanism (Acid/Base/Modulator); Modulator-assisted base activation; SN1-like intermediate formation induced by protonation to leaving group; water activated by general base attacks on intermediate to complete reaction

  • 1.30.5100.- : beta-amylase-like mechanism (Acid/Base); SN1-like intermediate formation induced by protonation to leaving group; water activated by general base attacks on intermediate to complete reaction

  • 1.30.11370.- : ER-Man(9)-alpha-mannosidase-like mechanism (Acid/Base); Cofactor-assisted water activation by base; Protonation to leaving group through a water by acid

  • 1.30.33100.- : Lysozyme-C-like mechanism (Nucleophile/Acid-Base); covalent bond formation between substrate and nucleophile & protonation to leaving group by acid; nucleophilic attack of base-activated water

  • 1.30.35880.- : beta-galactanase-like mechanism (Nucleophile/Acid-Base/Modulator-Stabilizer/Modulator/Stabilizer); Modulation of nucleophile; Acid protonation to leaving group leads to transition-state; Stabilization of transition-state; Nucleophilic attack forms intermediate; Base deprotonation of water; Activated water attacks on intermediate; SN1-like reaction

  • 1.30.35885.- : beta-xylosidase-like mechanism (Nucleophile/Acid-Base/Modulator-Stabilizer/Modulator/Stabilizer); Modulation of nucleophile & acid-base; Acid protonation to leaving group leads to transition-state; Stabilization of transition-state; Nucleophilic attack forms intermediate; Base deprotonation of water; Activated water attacks on intermediate; SN1-like reaction

  • 1.30.35890.- : alpha-N-acetylgalactosaminidase-like mechanism (Nucleophile/Acid-Base/Stabilizer/Modulator); Modulation of nucleophile and acid-base; Acid protonation to leaving group leading to transition-state (SN1-like); Stabilization of transition-state; Nucleohilic attack forming intermediate; Base deprotonation of water; Activated water attack on intermediate completing reaction

  • 1.30.36000.- : alpha-amylase-like mechanism (Nucleophile/Acid-Base/Stabilizer-Modulator); Modulator-assisted acid; SN1-like reaction induced by protonation to 1st leaving group; Covalent bond formation between nucleophile and target atom; Intermediate stablilized; covalent bond attacked by base-activated water; Intermediate stabilized; protonation to nucleophile

  • 1.30.36010.- : Exoglucanase/xylanase-A-like mechanism (Nucleophile/Acid-Base/Stabilizer/Modulator); SN1-like reaction induced by protonation to 1st leaving group; covalent bond (intermediate) formation between nucleophile and target atom; covalent bond attacked by base-activated water; stabilization of leaving nucleophile

  • 1.30.36020.- : Gentiobiase-like mechanism (Nucleophile/Acid-Base/Stabilizer/Modulator); Modulation of nucleophile; SN1-like reaction induced by protonation to 1st leaving group; covalent bond formation between nucleophile and target atom;Stabilization of transition-state; covalent bond attacked by base-activated water

  • 1.30.36027.- : beta-mannanase26-like mechanism (Nucleophile/Acid-Base/Modulator/Modulator-Stabilizer/Stabilizer); Modulation of nucleophile and acid-base; SN1-like reaction induced by protonation to 1st leaving group; covalent bond formation between nucleophile and target atom; Stabilization of transition-state; covalent bond attacked by base-activated water

  • 1.30.36040.- : beta-D-glucan-exohydrolase-like mechanism (Nucleophile-Stabilizer/Acid-Base/Modulator); Modulator-assisted acid-base; SN1-like reaction induced by acid protonation to 1st leaving group; Stabilization of transition-state; Nucleophilic attack on target bond atom leading to covalent bonded intermediate formation; base-activated water makes a nucleophilic attack on intermediate completing hydrolysis

  • 1.30.36200.- : Lactase-like mechanism (Nucleophile/Acid/Base/Modulator); SN1-like reaction induced by protonation to 1st leaving group; Modulation of nucleophile; covalent bond (intermediate) formation between nucleophile and target atom; covalent bond attacked by base-activated water

  • 1.30.36210.- : Sialidase-like mechanism (Nucleophile/Acid-Base/Modulators); Modulation of nucleophile; SN1-like reaction induced by protonation to 1st leaving group; covalent bond (intermediate) formation between nucleophile and target atom; covalent bond attacked by base-activated water

  • 1.30.36211.- : Endoglucanase-E1-like mechanism (Nucleophile/Acid-Base/Modulators); Modulation of nucleophile & acid-base; SN1-like reaction induced by protonation to 1st leaving group; covalent bond (intermediate) formation between nucleophile and target atom; covalent bond attacked by base-activated water

  • 1.30.36300.- : Endo-beta-(1->3)-(1->4) glucanase-like mechanism (Nucleophile/Acid-Base); SN1-like transition state; covalent bond formation between substrate and nucleophile & protonation to leaving group by acid; followed by base-activated water

  • 1.30.46030.- : alpha-mannosidase-like mechanism (Nucleophile/Acid-Base/Modulator); Protonation to leaving group by acid leading to inorganic-cofactor stabilized transition-state; Modulator-assisted SN1-like nucleophilic attack forming covalent intermediate; intermediate stabilized by inorganic-cofactor; base-activated water attack on intermediate leading to transition-state stabilized by inorganic cofactor

    • 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 -)