Entry M0181    phosphonoacetaldehyde hydrolase

Next Step

Step 01

Lys53 attacks the carbonyl carbon of the phosphonoacetaldehyde aldehyde in a nucleophilic addition.

GIF of Reaction Step M0181.stg01

Comment: There are two kinetically equivalent routes for the formation of the dipolar intermediate (first step) which give rise to two alternative mechanisms. One in which the native state includes protonated His56 and neutral Lys53 (shown here) and other in which Lys53 is protonated and His56 is neutral. However, the extensive hydrogen bond network that incorporates the proton on the His56 ring (comprising the ring N(1)H of the His56, the backbone carbonyl of Ala45, the N(3)H hydrogen bond to Wat-120, and the hydrogen bond between Wat-120 and the sulfur atom of Met49) may serve to increase the basicity of His56 to a value greater than that of Lys53 when the enzyme is in the closed conformation. Consequently, at neutral pH, which is both the pH optimum for catalysis and the prevailing pH in the cell, His56 is charged and Lys53 is not [1].


Bimolecular Nucleophilic Addition

Mechanism Components

Overall Reactant Used
Bond Formation
Enzyme-Substrate Bond Formation
Bond Order Change
Intermediate Formation

Amino acids involved in the reaction step.

Amino Acid Location of Function Activity Function
His56 Side Chain spectator Hydrogen Bond Donor
Ala45 Main Chain Carbonyl spectator Hydrogen Bond Acceptor
Electrostatic Stabiliser
Met49 Side Chain spectator Hydrogen Bond Acceptor
Electrostatic Stabiliser
Arg160 Side Chain spectator Hydrogen Bond Donor
Electrostatic Stabiliser
Asp12 Side Chain spectator Metal Ligand
Hydrogen Bond Acceptor
Lys53 Side Chain reactant Nucleophile
Polar Interaction

Metal Cofactors involved in Step 01

Metal Type Metal Identity Chain Activity Function
magnesium MG 502 x spectator Substrate Binding
Electrostatic Stabiliser

Reactive Centre

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

View similar reactions in MACiE.