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Entry M0064    5.99.1.2    DNA topoisomerase (type IA)

Next Step

Step 01

Tyr328 acts as a nucleophilic, attacking the phosphorous of the DNA molecule, which proceeds through a pentavalent transition state, before eliminating the 5' DNA, with concomitant deprotonation of Glu7.

GIF of Reaction Step M0064.stg01


Comment: Phosphate group goes though a pentavalent transition state. There is no side-chain is close enough to the nucleophilic oxygen to act as a general base to promote the nucleophilic attack, but an electrostatic effect of the nearby positively charged Arg330 could lower the pKa of the tyrosine and stabilise the phenolate anion as the nucleophile [2].



Mechanisms

Proton Transfer
Bimolecular Nucleophilic Substitution

Mechanism Components

Overall Reactant Used
Bond Cleavage
Bond Formation
Enzyme-Substrate Bond Formation
Intermediate Formation

Amino acids involved in the reaction step.

Amino Acid Location of Function Activity Function
Lys8 Side Chain spectator Hydrogen Bond Donor
Electrostatic Stabiliser
Glu7 Side Chain reactant Proton Donor
Hydrogen Bond Donor
Tyr328 Side Chain reactant Nucleophile
Hydrogen Bond Acceptor
Arg330 Side Chain spectator Hydrogen Bond Donor
Electrostatic Stabiliser

Reactive Centre

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

View similar reactions in MACiE.


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