A QM/MM study of the catalytic mechanism of aspartate ammonia lyase

• The catalytic mechanism of aspartate ammonia lyase has been studied by using QM/MM method.
• Ser318 functions as the catalytic base to abstract the Cβ proton of substrate l-aspartate.
• The abstraction of Cβ proton of l-aspartate by Ser318 is the rate-limiting step.
• His188 is a dispensable residue, but its protonation state can influence the active site structure.

Aspartate ammonia lyase (Asp) is one of three types of ammonia lyases specific for aspartate or its derivatives as substrates, which catalyzes the reversible reaction of l-aspartate to yield fumarate and ammonia. In this paper, the catalytic mechanism of Asp has been studied by using combined quantum-mechanical/molecular-mechanical (QM/MM) approach. The calculation results indicate that the overall reaction only contains two elementary steps. The first step is the abstraction of Cβ proton of l-aspartate by Ser318, which is calculated to be rate limiting. The second step is the cleavage of CαN bond of l-aspartate to form fumarate and ammonia. Ser318 functions as the catalytic base, whereas His188 is a dispensable residue, but its protonation state can influence the active site structure and the existing form of leaving amino group, thereby influences the activity of the enzyme, which can well explain the pH dependence of enzymatic activity. Mutation of His188 to Ala only changes the active site structure and slightly elongates the distance of Cβ proton of substrate with Ser318, causing the enzyme to remain significant but reduced activity.

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