EzCatDB

R L C P
Hierarchic Classification of Catalytic Mechanisms


R 1.-.-.- : Hydrolysis (bond cleavage by water) (Reaction)

L 1.15.-.- : Phosphoric Ester (Ligand group involved)

C 1.15.8240.- : Nuclease P1-like mechanism (Base/Stabilizer); Cofactor-assisted water activation by base; Nucleophilic attack by activated water; Cofactor-assisted stabilization of transition-state; rather SN2 reaction (Catalytic mechanism)


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

Residues/Cofactors involved in Proteins

  • 1.15.8240.1166 : An acidic residue + Lys cluster + two magnesium ions bound to acidic residues/mainchain carbonyl + another magnesium ion bound to leaving group
  • 1.15.8240.1167 : An acidic residue + Arg/Lys + two magnesium ions bound to acidic residues/mainchain carbonyl + another magnesium ion bound to leaving group
  • 1.15.8240.2170 : Asp/Arg + two zinc ions bound to His/Asp cluster & mainchain (interacting throuhg a water) + zinc ion bound to His/Asp cluster
  • 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 -)