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Entry M0215    4.1.1.1    pyruvate decarboxylase

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Step 02

The carbanion of thiamine diphosphate attacks the carbonyl carbon of pyruvate in a nucleophilic addition that results in the cofactor undergoing double bond rearrangement that results in the deprotonation of Glu51B.

GIF of Reaction Step M0215.stg02


Comment: In Zymomonas mobilis it has been suggested that the pyruvate oxygen is protonated through a proton relay involving Tyr290. However, this residue is not present in the yeast enzyme. Therefore, this represents the most likely mechanism. [3]



Mechanisms

Bimolecular Nucleophilic Addition
Aldol Addition

Mechanism Components

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

Amino acids involved in the reaction step.

Amino Acid Location of Function Activity Function
Gly417A Main Chain Carbonyl spectator Hydrogen Bond Acceptor
Activator
Electrostatic Stabiliser
His114B Side Chain spectator Hydrogen Bond Donor
Polar Interaction
His115B Side Chain spectator Polar Interaction
Electrostatic Stabiliser
Asp28B Side Chain spectator Hydrogen Bond Acceptor
Glu477A Side Chain spectator Electrostatic Stabiliser
Glu51B Side Chain reactant Hydrogen Bond Donor
Proton Donor

Organic Cofactors involved in the reaction step

Cofactor Type Cofactor Activity Function
Thiamine diphosphate TPP557A reactant Hydrogen Bond Acceptor
Hydrogen Bond Donor
Proton Acceptor
Proton Donor
Nucleophile

Metal Cofactors involved in Step 02

Metal Type Metal Identity Chain Activity Function
magnesium MG 558 A spectator Cofactor Binding

Reactive Centre

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

View similar reactions in MACiE.


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