EzCatDB

R L C P
Hierarchic Classification of Catalytic Mechanisms


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

L 1.13.-.- : Amide bond (One of Carbonyl Ester bonds; including peptide bond) (Ligand group involved)


Catalytic mechanisms

  • 1.13.200.- : 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
  • 1.13.7495.- : E.coli N-Acetyl-D-glucosamine-6-phosphate deacetylase-like mechanism (Acid-Base/Modulator-Stabilizer); Inorganic cofactor-assisted activation of water and scissile bond; Modulator-assisted activation of scissile bond; Base deprotonation of water; Activated water attacks on scissile bond forming intermediate; Intermediate stabilized by inorganic cofactor and stabilizer; Acid protonation to leaving group; SN2-like reaction
  • 1.13.7500.- : One zinc beta-lactamase mechanism (Acid-Base/Stabilizer); Cofactor-assisted water activation by base; SN2-like reaction; Transition state stabilized by cofactor and stabilizer; Acid protonation to leaving group
  • 1.13.7630.- : N-Acetylglucosamine-6-phosphate deacetylase-like mechanism (Acid-Base); Cofactor-assisted water activation by base through proton shuttle; SN2-like reaction; Cofactor-assisted stabilization of transition state; Acid protonation to leaving group; Cofactor interaction with water/atom adjacent to scissile bond
  • 1.13.10000.- : Two zinc beta-lactamase mechanism (Stabilizer); Cofactor-assisted water activation for SN2-like nucleophilic attack; Bond cleavage; cofactor-assisted stabilization of transition state; Water protonation to leaving group
  • 1.13.10880.- : Muramoyl-pentapeptide-carboxypeptidase-like mechanism (Acid-Base/Modulator/Stabilizer); Modulator-assisted base; Inorganic-cofactor-assisted base activation of water; Activated water attacks on scissile bond; Inorganic-cofactor-assisted stabilization of intermediate; Modulator-assisted acid protonation to leaving group
  • 1.13.10900.- : Thermolysin-like mechanism (Acid-Base/Stabilizer); Inorganic cofactor-assisted water activated by base; Activated water attacks on target bond; Inorganic cofactor-assisted stabilization of intermediate (bond & leaving group); Protonation to leaving group by acid leading to cleavage of bond; SN1/SN2 unclear
  • 1.13.11100.- : Serralysin-like mechanism (Acid-Base/Stabilizer); Cofactor-assisted water activated by base; Cofactor-assisted stabilization of transition-state; Protonation to leaving group by acid; SN1/SN2 unclear
  • 1.13.11110.- : Carboxypeptidase A-like mechanism (Acid-Base-Stabilizer/Stabilizer); Cofactor-assisted water activated by base; Cofactor-assisted stabilization of transition-state; Protonation to leaving group by acid; SN1/SN2 unclear
  • 1.13.11400.- : Adamalysin-II-like mechanism (Acid-Base); Cofactor-assisted water activation by base; cofactor-assisted stabilization of transition-state; Protonation to leaving group by acid
  • 1.13.13000.- : Matrilysin-like mechanism (Acid-Stabilizer); Water activated by inorganic cofactor; Trasition state stabilized by cofactor and stabilizer; Acid protonation to leaving group
  • 1.13.29990.- : beta-lactamase OXA10 mechanism (Nucleophile/Acid-Base/Modulator/Stabilizer); double-displacement; Modulator-assisted base activation of nucleophile; covalent bond formation between nucleophile and target atom; Acid protonation to 1st leaving group; Intermediate stablilized; Base activation of water; Covalent bond attacked by water; Acid protonation to nucleophile
  • 1.13.30000.- : 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
  • 1.13.30005.- : DmpA-like mechanism (Nucleophile/Acid-Base/Modulator/Stabilizer); Modulator-assisted base activation of nucleophile; Modulator-assisted nucleophilic attack on target bond; SN2-like reaction; Stabilization of transision-state; covalent bond between enzyme and substrate; followed by protonation to leaving group; hydrolysis by base-activated water
  • 1.13.30010.- : 20S-proteasome-like mechanism (Nucleophile/Acid-Base/Stabilizer/Modulator); Base-activation of nucleophile through a water; covalent bond formation between nucleophile and target atom; intermediate stablilized; protonation to 1st leaving group; covalent bond attacked by base-activated water
  • 1.13.30015.- : DD-carboxypeptidase-like mechanism (Nucleophile/Base-Modulator/Acid-Base/Modulator/Stabilizer); Modulator-assisted 1st base-activation of nucleophile; Nucleophilic attack on target atom; Intermediate stablilized; Acid protonation to 1st leaving group; Modulator-assisted 2nd base activation of water; Intermediate attacked by activated water leading to hydrolysis
  • 1.13.30020.- : Tricorn protease-like mechanism (Nucleophile/Acid-Base/Modulator/Proton shuttle/Stabilizer); Modulator assists acid-base through proton shuttle; 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
  • 1.13.30100.- : Caspase-1-like mechanism (Nucleophile/Acid-Base/Stabilizer); Base-activation of nucleophile; covalent bond formation between nucleophile and target atom; intermediate stablilized; protonation to 1st leaving group; covalent bond attacked by base-activated water; intermediate stabilized; protonation to nucleophile
  • 1.13.30110.- : Asparagine-synthetase-B glutamine hydrolysis mechanism (Nucleophile/Acid-Base/Stabilizer); double-displacement; Base-activation of nucleophile through a water; covalent bond formation between nucleophile and target atom; intermediate stablilized; protonation to 1st leaving group through a water; covalent bond attacked by base-activated water; intermediate stabilized; protonation to nucleophile thorugh a water
  • 1.13.30120.- : Plasminogen-like mechanism (Nucleophile/Acid-Base/Modulator); covalent bond between enzyme and substrate; followed by protonation to leaving group; hydrolysis by base-activated water
  • 1.13.30185.- : Penicillin acylase-like mechanism (Nucleophile-Base-Acid/Stabilizer/Modulator); double-displacement; Base activation of nucleophile through water; Nucleophilic attack & acid protonation to leaving group through water leading to covalent bond formation between nucleophile and target atom; intermediate stablilized; covalent bond attacked by water; intermediate stabilized; protonation to nucleophile through water
  • 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 -)