EzCatDB

R L C P
Hierarchic Classification of Catalytic Mechanisms


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

L 1.15.-.- : Phosphoric Ester (Ligand group involved)


Catalytic mechanisms

  • 1.15.7590.- : PP2Calpha phosphtase-like mechanism (Acid/Base/Stabilizer); Cofactor-assisted water activation by base; SN2-like reaction; stabilized transition state; acid protonation to leaving group
  • 1.15.7910.- : Inositol-1-monophosphatase-like mechanism (Base/Proton_shuttle/Stabilizer); Cofactor-assisted water activation by base through proton shuttle; SN2-like reaction; Cofactor-assisted stabilization of transition state; Bond cleavage; Substrate-assisted water protonation to leaving group; Cofactor interaction with water/scissile bond/leaving group
  • 1.15.8000.- : Inorganic pyrophosphatase-like mechanism (Base/Stabilizer); Cofactor-asissted water activation by base; cofactor-assisted protonation by another water to leaving group; rather SN2 reaction
  • 1.15.8220.- : Thermophilus ADPribose pyrophosphatase Ndx4-like mechanism (Base/Stabilizer); Modulator-assisted cofactor binding; Cofactor-assisted water activation by base; Nucleophilic attack by activated water; Cofactor-assisted stabilization of transition-state; SN2 reaction; Cofactor-assisted stabilization of leaving group
  • 1.15.8230.- : DNA topoisomerase-II ATP hydrolysis mechanism (Base/Stabilizer); Water activation by base; Nucleophilic attack by water; Cofactor-assisted stabilization of transition-state; rather SN2 reaction
  • 1.15.8240.- : Nuclease P1-like mechanism (Base/Stabilizer); Cofactor-assisted water activation by base; Nucleophilic attack by activated water; Cofactor-assisted stabilization of transition-state; rather SN2 reaction
  • 1.15.8245.- : E.coli ADPribose pyrophosphatase-like mechanism (Base/Stabilizer); Cofactor-assisted water activation by base; Nucleophilic attack by activated water; Cofactor-assisted stabilization of transition-state; SN2 reaction; Cofactor-assisted stabilization of leaving group
  • 1.15.8300.- : BamHI-like mechanism (Base); Inorganic-cofactor-assisted water activation by base; SN2-like nucleophilic attack by water; Inorganic-cofactor-assisted stabilization of transition-state; Protonation to leaving group by another water bound to inorganic cofactor
  • 1.15.8310.- : Phosphotriesterase-like mechanism (Base); Inorganic-cofactor-assisted activation of scissile bond; Inorganic-cofactor-assisted water activation by base; SN2-like nucleophilic attack by water; Inorganic-cofactor-assisted stabilization of transition-state
  • 1.15.9400.- : Type-II restriction enzyme-like mechanism (Stabilizer); Two water molecules acting as base/acid; Substrate-assisted water activation for nucleophilic attack; Activated water stabilized; SN2-like nucleophilic attack by water; Cofactor-assisted stabilization of transition-state; Protonation to leaving group by another water bound to cofactor
  • 1.15.9500.- : Iron(III)-zinc(II) purple acid phosphatase-like mechanism (Acid/Stabilizer); Cofactor-asissted water activation; Nucleophilic attack by activated water; protonation to leaving group by acid; rather SN2 reaction
  • 1.15.9995.- : Human ADPribose pyrophosphatase NUDT9-like mechanism (Stabilizer/Modulator); Cofactor/Modulator-assisted water activation for SN2-like nucleophilic attack; Bond cleavage; cofactor-assisted stabilization of transition state
  • 1.15.10100.- : DNA-topoisomerase-I/3'-5' exonuclease-like mechanism (Modulator); Inorganic cofactor-assisted water activation; Inorganic cofactor-assisted stabilization of transition-state; Inorganic-cofactor interaction with water/atom adjacent to scissile bond/leaving group
  • 1.15.11200.- : Deoxyribonuclease-1-like mechanism (Acid/Base); Cofactor-assisted water activation by base; cofactor-assisted stabilization of transition-state; Protonation to leaving group by acid
  • 1.15.14410.- : Serine/threonine protein phosphatase 2B-like mechanism (Acid-Base/Modulator/Stabilizer); Cofactor-assisted water activation by base; SN1-like transition-state; Activated water attacks & acid protonation to leaving group
  • 1.15.30200.- : Prostatic acid phosphatase-like mechanism (Nucleophile/Acid-Base/Stabilizer); double-displacement; covalent bond formation between nucleophile and target atom; intermediate stablilized; protonation to 1st leaving group by acid; covalent bond attacked by base-activated water; intermediate stabilized; protonation to nucleophile
  • 1.15.32000.- : 3-phytase-like mechanism (Nucleophile/Acid); double-displacement; covalent bond formation between nucleophile and reactive atom; intermediate attacked by a water; leaving group protonated by acid
  • 1.15.33000.- : Adipocyte acid phosphatase-like mechanism (Nucleophile/Acid-Base/Stabilizer); double-displacement; covalent bond formation between nucleophile and target atom; intermediate stablilized; protonation to 1st leaving group by acid; covalent bond attacked by base-activated water; intermediate stabilized; protonation to nucleophile
  • 1.15.36030.- : Tyrosine-protein-phosphatase-like mechanism (Nucleophile/Acid-Base/Stabilizer/Modulator); 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
  • 1.15.36100.- : M-phase-inducer-phosphatase-1-like mechanism (Nucleophile/Acid-Base/Stabilizer); 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
  • 1.15.39000.- : SER Ca(2+)-ATPase-1-like mechanism (Nucleophile/Acid-Base/Stabilizer); Cofactor-assisted SN2-like nucleophilic attack; protonation to leaving group by acid; stabilized by cofactor and stabilizer; water activated by base
  • 1.15.60000.- : Ribonuclease-U2-like mechanism (Base-Acid/Acid-Base/Stabilizer); 1st base activation of substrate-assisted nucleophile; covalent bond formation between scissile bond and substrate-assisted nucleophile (SN2) & 1st acid protonation to leaving group; Intermediate stabilization; 2nd base activation of water; Hydrolysis assisted by 2nd acid protonation to substrate-nucleophile
  • 1.15.72000.- : Phosphoinositide phospholipase-C-delta-1-like mechanism (Base-Acid/Acid-Base/Stabilizer); Inorganic cofactor-assisted activation of substrate nucleophile by base; Intramolecular covalent bond within substrate induced by substrate-assisted nucleophilic attack & protonation to leaving group by general acid (SN2-like reaction); Inorganic cofactor-assisted stabilization of transition-state; 2nd base-activated water attacks on intermediate; Protonation to 2nd leaving group (1st nucleophile); 2nd leaving group 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 -)