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 1.15.9400.- : Type-II restriction enzyme-like mechanism (Stabilizer); Two water molecules acting as base/acid; Substrate-assisted water activation for nucleophilic attack; Activated water stabilized; SN2-like nucleophilic attack by water; Cofactor-assisted stabilization of transition-state; Protonation to leaving group by another water bound to cofactor (Catalytic mechanism)

P 1.15.9400.1180 : Lys + two magnesium ions bound to acidic residues (Residues/cofactors in Protein)


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



Related Enzymes

There are 7 entries in this class.
  • S00383 : 3.1.21.4; Type-2 restriction enzyme Cfr10I (Catalytic domain; 3.40.91.10)
  • S00390 : 3.1.21.4; Type-2 restriction enzyme PvuII (Catalytic domain; 3.40.210.10)
  • S00403 : 3.1.21.4; Type-2 restriction enzyme EcoRI (Catalytic domain; 3.40.580.10)
  • S00404 : 3.1.21.4; Type-2 restriction enzyme EcoRV (Catalytic domain; 3.40.600.10)
  • S00405 : 3.1.21.4; Type-2 restriction enzyme BglI (Catalytic domain; 3.40.600.20)
  • S00462 : 3.1.11.3; Exonuclease (Catalytic domain; 3.90.320.10)
  • T00055 : 3.1.21.4; Type-2 restriction enzyme FokI (Catalytic domain; 3.40.91.30)
  • 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 -)