spacer

Entry M0011    3.1.21.2    deoxyribonuclease IV (phage-T4-induced)

Next Step

Step 01

Zinc activated water initiates a nucleophilic attack on the DNA phosphate, concomitantly eliminating the 5'-ribose in a substitution reaction which proceeds through a pentavalent transition state.

Rate Determining Step

GIF of Reaction Step M0011.stg01


Comment: This reaction proceeds via a pentavalent transition state. Water is activated to hydroxide by two of the Zn(II) ions (ZN301 and ZN303) and the Glu261.



Mechanisms

Bimolecular Nucleophilic Substitution

Mechanism Components

Bond Cleavage
Bond Formation
Overall Reactant Used
Overall Product Formed

Amino acids involved in the reaction step.

Amino Acid Location of Function Activity Function
Glu261 Side Chain spectator Hydrogen Bond Acceptor
Metal Ligand
Electrostatic Stabiliser

Metal Cofactors involved in Step 01

Metal Type Metal Identity Chain Activity Function
zinc ZN 301 x spectator Electrostatic Stabiliser
Increase Nucleophilicity
Activator
Substrate Binding
Activator
Increase Electrophilicity
zinc ZN 302 x spectator Electrostatic Stabiliser
Substrate Binding
Activator
Increase Electrophilicity
zinc ZN 303 x spectator Electrostatic Stabiliser
Increase Nucleophilicity
Activator
Substrate Binding
Activator
Increase Electrophilicity

Reactive Centre

Bonds Formed Bonds Cleaved Bonds Changed in Order Atom Types Involved
P-O
P-O
None
O
P

View similar reactions in MACiE.


spacer
spacer