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Entry M0182    4.1.3.30    methylisocitrate lyase

Next Step

Step 01

Asp58 deprotonates water which depotonates the alcohol group of the (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate substrate. This initiates an elimination that produces the pyruvate poduct and an intermediate.

GIF of Reaction Step M0182.stg01


Comment: The identity of the catalytic base in this step is not clear. Four possible alternatives for this mechanism have been suggested. There are two possible water molecule candidates, one hydrogen bonded to Asp58 and the other to Glu115. Both water molecules are anchored to the magnesium cofactor. Another alternative is that the Arg158 guanidinium group may serve as a proton shuttle, however the Arg158 is already positively charged. Finally, the Tyr43 hydroxyl group which is hydrogen bonded to His113 (which is in turn hydrogen bonded to an internal water and Glu115) may also act as the base. However, a protein with similar function in the same family lacks this tyrosine histidine pair and instead has two phenylalanine residues, We show here the Asp58 alternative due to mutational studies showing the Asp58 is essential for catalytic turnover [1].



Mechanisms

Proton Transfer
Bimolecular Elimination

Mechanism Components

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

Amino acids involved in the reaction step.

Amino Acid Location of Function Activity Function
Asn210 Side Chain spectator Hydrogen Bond Donor
Electrostatic Stabiliser
Glu188 Side Chain spectator Hydrogen Bond Acceptor
Hydrogen Bond Donor
Electrostatic Stabiliser
Cys123 Side Chain spectator Not Active
Arg158 Side Chain spectator Hydrogen Bond Donor
Electrostatic Stabiliser
Asp58 Side Chain reactant Hydrogen Bond Acceptor
Proton Acceptor

Metal Cofactors involved in Step 01

Metal Type Metal Identity Chain Activity Function
magnesium MG 1001 A spectator Increase Acidity
Substrate Binding
Activator
Electrostatic Stabiliser

Reactive Centre

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

View similar reactions in MACiE.


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