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 3.103.70035.- : 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 (Catalytic mechanism)


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

Residues/Cofactors involved in Proteins

  • 3.103.70035.351 : An acidic residue + Lys cluster + mainchain amide groups + magnesium ion bound to Asp/Ser
  • 3.103.70035.355 : An acidic residue + Arg/Lys cluster + magnesium ion bound to acidic residues
  • 3.103.70035.360 : An acidic residue + Arg/Lys cluster + mainchain amide groups + magnesium ion bound to [Ser or Thr]
  • 3.103.70035.364 : An acidic residue + Arg/Lys cluster + mainchain amide groups + magnesium ion bound to acidic residue and [Ser or Thr]
  • 3.103.70035.366 : An acidic residue + Lys (cluster) + mainchain amide groups + magnesium ion bound to [Asn or Gln] and [Ser or Thr]
  • 3.103.70035.456 : An acidic residue + mainchain amide groups + zinc ion bound + potassium ion bound to acidic residues/Ser or Thr/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 -)