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)

C 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 (Catalytic mechanism)


1st Nucleophile : an acceptor group in substrate
Catalytic groups : cofactor + groups in residue/substrate
General Base : non-existent
General Acid : non-existent

Residues/Cofactors involved in Proteins

  • 3.103.90020.1131 : Arg/Lys/Asn + two magnesium ions bound to acidic residues
  • 3.103.90020.1134 : Arg/Lys/Asn + two magnesium ions bound to acidic residues/Ser/mainchain carbonyl
  • 3.103.90020.1135 : Arg/Lys/His/Tyr + two magnesium ions bound to acidic residues/mainchain carbonyl
  • 3.103.90020.1136 : Arg/Lys + two magnesium ions bound to acidic residues/mainchain carbonyl
  • 3.103.90020.1140 : Arg/Lys + mainchain amide + magnesium ion bound to Thr + a divalent metal ion bound to His/Asp/Lys
  • 3.103.90020.1141 : Arg/Lys/His + mainchain amide groups + two divalent metal ions bound to acidic residues/mainchain carbonyl
  • 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 -)