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Entry M0232    5.99.1.2    DNA topoisomerase (type IB)

Previous Step

Step 02

The DNA-enzyme complex rotates around the uncleaved DNA strand, relaxing the supercoiled DNA. Water deprotonates Arg130, which in turn deprotonates Lys167, which deprotonates the rotated 5'-OH initiating a nucleophilic in-line substitution at the DNA phosphate with a trigonal bipyramidal transition state/ The eliminated Tyr274 deprotonates the initial acidic water molecule.

GIF of Reaction Step M0232.stg02


Comment: Before this catalytic step occurs the DNA-enzyme intermediate rotates around the uncleaved DNA strand, relaxing the supercoiled DNA. It is assumed that the proton shuttling events are simply a reverse of those seen in the first step of this reaction.



Mechanisms

Proton Transfer
Bimolecular Nucleophilic Substitution

Mechanism Components

Bond Cleavage
Bond Formation
Enzyme-Substrate Bond Cleavage
Enzyme Regenerated
Intermediate Terminated
Bond Order Change
Proton Relay

Amino acids involved in the reaction step.

Amino Acid Location of Function Activity Function
Tyr274 Side Chain reactant Proton Acceptor
Hydrogen Bond Acceptor
Nucleofuge
Lys167 Side Chain reactant Proton Donor
Proton Acceptor
Proton Relay
Hydrogen Bond Donor
Electrostatic Stabiliser
Attractive Charge Charge Interaction
Arg130 Side Chain reactant Hydrogen Bond Donor
Proton Donor
Proton Acceptor
Proton Relay
Electrostatic Stabiliser
Attractive Charge Charge Interaction
His265 Side Chain spectator Hydrogen Bond Donor
Electrostatic Stabiliser
Arg223 Side Chain spectator Hydrogen Bond Donor
Electrostatic Stabiliser
Attractive Charge Charge Interaction

Reactive Centre

Bonds Formed Bonds Cleaved Bonds Changed in Order Atom Types Involved
N-H
N-H
O-H
O-H
P-O
N-H
N-H
O-H
O-H
P-O
The C-N bond changes from a single to double bond
The C-N bond changes from a double to single bond
C
H
N
O
P

View similar reactions in MACiE.


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