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 1.13.30000.- : 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 (Catalytic mechanism)


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



Residues/Cofactors involved in Proteins

  • 1.13.30000.9 : Ser/His/Asp + Asn/Thr/mainchain amide
  • 1.13.30000.10 : Ser/His/Asp + mainchain amide
  • 1.13.30000.12 : Ser/Glu/Asp + Asp/mainchain amide
  • 1.13.30000.13 : Ser/Glu/Asp + Tyr/mainchain amide
  • 1.13.30000.16 : Ser/Tyr/Lys + mainchain amide
  • 1.13.30000.39 : Cys/His/Glu + Arg/mainchain amide
  • 1.13.30000.41 : Cys/His/Asp + mainchain amide
  • 1.13.30000.42 : Cys/His/Glu + mainchain amide
  • 1.13.30000.44 : Cys/His/Asn + Gln/mainchain amide
  • 1.13.30000.45 : Cys/His/Asp + Gln/mainchain amide
  • 1.13.30000.46 : Cys/His/Tyr + mainchain amide
  • 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 -)