EzCatDB

R L C P
Hierarchic Classification of Catalytic Mechanisms


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

L 3.103.-.- : Phosphate group from Phosphate oxygen to Hydroxyl oxygen (Ligand group involved)


Catalytic mechanisms

  • 3.103.69900.- : 6-phosphofructokinase-like mechanism (Base/Modulator/Stabilizer); Base activates acceptor group; nucleophilic attack on transferred group by acceptor group; Inorganic-cofactor-assisted stabilization of transferred group and leaving group; SN2-like direct reacion
  • 3.103.69910.- : Deoxycytidine kinase-like mechanism (Base/Modulator-Stabilizer/Stabilizer); Modulator-assisted base activates acceptor group; nucleophilic attack on transferred group by acceptor group; Inorganic-cofactor-assisted stabilization of transferred group and leaving group; SN2-like direct reacion
  • 3.103.70000.- : Thymidine kinase-like mechanism (Base/Stabilizer); Base activation of acceptor group; nucleophilic attack on transferred group by acceptor group; Inorganic-cofactor-assisted stabilization of transferred group and leaving group; SN2-like direct reacion
  • 3.103.70020.- : N-acylneuraminate cytidylyltransferase-like mechanism (Base/Stabilizer); Base activates acceptor group through water; nucleophilic attack on transferred group by acceptor group; Inorganic-cofactor-assisted stabilization of leaving group; SN2-like direct reacion
  • 3.103.70035.- : Shikimate kinase-II-like mechanism (Base/Stabilizer); Nucleophilic attack of acceptor group activated by general base on transferred group; Inorganic-cofactor-assisted stabilization of transferred group and leaving group; SN2-like direct reaction
  • 3.103.70200.- : Poly(A) polymerase-alpha-like mechanism (Base); General base activates acceptor group; SN2-like nucleophilic attack on transferred group by acceptor group; Inorganic-cofactor interacting with acceptor/transferred/leaving groups
  • 3.103.70800.- : Adenylyl-sulfate kinase-like mechanism (Base/Proton_shuttle/Stabilizer); Base activation of acceptor group through proton_shuttle; Inorganic-cofactor-assisted nucleophilic attack on transferred group by acceptor group; Inorganic-cofactor-assisted transition-state stabilization; Inorganic-cofactor interacting with transferred group; SN2-like reaction
  • 3.103.70810.- : Glucokinase-like mechanism (Base/Stabilizer); Base activation of acceptor group; Nucleophilic attack on transferred group by acceptor group; Inorganic-cofactor-assisted transition-state stabilization; Inorganic-cofactor-coordinated water protonation to leaving group; SN2-like reaction
  • 3.103.75410.- : Gluconate kinase-like mechanism (Stabilizer); Substrate-assisted base/transferred group activation of acceptor group; Nucleophilic attack on transferred group by acceptor group; Inorganic-cofactor-assisted transition-state stabilization; Substrate-assisted acid/transferred group protonation to leaving group; Inorganic cofactor stabilization of both transferred group and leaving group; SN2-like reaction
  • 3.103.78000.- : HPP kinase-like mechanism (Stabilizer); Substrate-assisted base activation of acceptor group; Inorganic-cofactor-assisted nucleophilic attack by acceptor group on transferred group; SN2-like direct reaction; Inorganic-cofactor interacting with acceptor/transferred/leaving groups
  • 3.103.78010.- : Hydroxyethylthiazole-kinase-like mechanism (Stabilizer); Substrate-assisted base activation of nucleophile; Inorganic-cofactor-assisted nucleophilic attack by acceptor group on transferred group; stabilized transition state; SN2-like direct reaction; Inorganic-cofactor interacting with transferred/leaving groups
  • 3.103.78020.- : Pyridoxal kinase-like mechanism (Stabilizer); Substrate-assisted base activation of acceptor group by transferred group; Nucleophilic attack by acceptor group on transferred group; Inorganic-cofactor-assisted stabilization of transition-state; SN2-like direct reaction; Inorganic-cofactor interacting with leaving group
  • 3.103.80570.- : HMP kinase 1st reaction step-like mechanism (Stabilizer); Substrate-assisted base activation of acceptor group by transferred group; Nucleophilic attack by acceptor group on transferred group; Inorganic-cofactor-assisted stabilization of transition-state; SN2-like direct reaction; Inorganic-cofactor interacting with transferred/leaving groups
  • 3.103.90000.- : Gro-PCT-like mechanism (Stabilizer); Inorganic-cofactor-assisted nucleophilic attack by acceptor group on transferred group; SN2-like direct reaction; transition state stabilized by cofactor and stabilizer; inorganic-cofactor interacting with leaving group
  • 3.103.90020.- : DNA polymerase-like mechanism (Stabilizer); Inorganic-cofactor-assisted nucleophilic attack by acceptor group on transferred group; SN2-like direct reaction; Transition state stabilized by cofactor and stabilizer; Inorganic-cofactor interacting with acceptor/transferred/leaving groups
  • 3.103.90021.- : Reverse transcriptase-like mechanism (Stabilizer); Inorganic-cofactor-assisted nucleophilic attack by acceptor group on transferred group; SN2-like direct reaction; Transition state stabilized by cofactor; Inorganic-cofactor interacting with acceptor/transferred/leaving groups & Stabilization of leaving group
  • 3.103.106000.- : PI3-kinase-p110-like mechanism (Base/Stabilizer); Base activation of acceptor group; Nucleophilic attack on transferred group by acceptor group; Inorganic-cofactor-assisted stabilization of transition-state; Inorganic-cofactor interacting with transferred group and leaving group; SN1/SN2 unclear
  • 3.103.126600.- : Phosphorylase-kinase-like mechanism (Base-Acid/Stabilizer); Inorganic-cofactor-assisted SN1-like transition state between acceptor/transferred/leaving groups; Base deprotonation of acceptor group; Covalent bond formed between acceptor and transferred group; Acid protonation to transferred group; Inorganic-cofactor interacting with transferred/leaving groups
  • 3.103.130000.- : Insulin receptor-like mechanism (Base/Modulator); Inorganic-cofactor-assisted SN1-like transition state between acceptor/transferred/leaving groups; Base deprotonation of acceptor group; Covalent bond formed between acceptor and transferred group; Inorganic-cofactor interacting with transferred/leaving groups
  • 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 -)