EzCatDB

R L C P
Hierarchic Classification of Catalytic Mechanisms


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

L 3.133.-.- : Phosphate group from Phosphate oxygen to Phosphate oxygen (Ligand group involved)

C 3.133.300000.- : mRNA capping enzyme-like mechanism (Nucleophile/Acid-Base/Stabilizer); Base activation of nucleophile; Nucleophilic attack on transferred group; Inroganic-cofactor-assisted stabilization of transition-state; Intermediate stabilized; followed by nucleophilic attack by acceptor group on transferred group; Protonation to leaving nucleophile by acid; Inorganic-cofactor interacting with transferred group (Catalytic mechanism)


1st Nucleophile : a catalytic residue
Catalytic groups : cofactor + groups in residue/substrate
General Base : a catalytic residue
General Acid : a catalytic residue

Residues/Cofactors involved in Proteins

  • 3.133.300000.396 : Lys/Asp + Arg/Lys/Asn/Asp cluster + magnesium or manganese ion bound
  • 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 -)