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Entry M0190    5.3.3.2    isopentenyl-diphosphate delta-isomerase

Next Step

Step 01

The double bond of the isopentenyl diphosphate substrate deprotonates Tyr104.

GIF of Reaction Step M0190.stg01


Comment: The origin of the protonating H has not been conclusively stabilised. Glu116 is probably un-protonated given its location in the inner coordination sphere of the metal, there are also no order molecules observed that could serve as proton donors during this step. Thus it seems likely that the phenolic hydroxyl group in Tyr104 might be the source of the proton transferred to the double bond via Glu116 [2].



Mechanisms

Proton Transfer

Mechanism Components

Overall Reactant Used
Bond Formation
Bond Cleavage
Bond Order Change
Intermediate Formation
Proton Relay

Amino acids involved in the reaction step.

Amino Acid Location of Function Activity Function
Tyr104 Side Chain reactant Hydrogen Bond Donor
Proton Donor
Glu116 Side Chain reactant Hydrogen Bond Acceptor
Proton Acceptor
Proton Donor
Proton Relay
Metal Ligand
Trp161 Side Chain spectator Polar Non-polar interaction
Cys67 Side Chain spectator Hydrogen Bond Acceptor

Metal Cofactors involved in Step 01

Metal Type Metal Identity Chain Activity Function
manganese MN 201 A spectator Activator
magnesium MG 401 A spectator Substrate Binding
Electrostatic Stabiliser

Reactive Centre

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

View similar reactions in MACiE.


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