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Entry M0163    3.1.26.4    calf thymus ribonuclease H

Next Step

Step 01

His124 deprotonates water, which attacks the phosphate of RNA in a nucleophilic substitution that results in the cleavage of the phosphate bond, the 5' end of the RNA molecule reprotonates from magnesium activated water.

Rate Determining Step

GIF of Reaction Step M0163.stg01


Comment: Reaction proceeds through a pentavalent transition state. The pro-RP-oxygen of the phosphate group 3' to the scissile phosphodiester bond contributes to orient His124 to the best position for catalytic function through the formation of a hydrogen bond [1].



Mechanisms

Proton Transfer
Bimolecular Nucleophilic Substitution

Mechanism Components

Overall Reactant Used
Bond Formation
Bond Cleavage
Overall Product Formed
Hydrolysis

Amino acids involved in the reaction step.

Amino Acid Location of Function Activity Function
His124 Side Chain reactant Hydrogen Bond Donor
Hydrogen Bond Acceptor
Proton Acceptor

Metal Cofactors involved in Step 01

Metal Type Metal Identity Chain Activity Function
magnesium MG 300 x spectator Substrate Binding
Electrostatic Stabiliser
Increase Electrophilicity
Activator

Reactive Centre

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

View similar reactions in MACiE.


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