RLCP 1.13.30185.- :EzCatDB 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)

C 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 (Catalytic mechanism)

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

Residues/Cofactors involved in Proteins

  • 1.13.30185.55 : Cys(N-terminal) + N-terminal alpha-amine + Asn/mainchain amide + Arg/Asp

    • 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 -)