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Entry M0203    3.2.1.17    lysozyme

Next Step

Step 01

Asp52 attacks the C1 of the peptidoglycan in a nucleophilic substitution that results in the NAG portion of the peptidoglycan being covalently attached to the enzyme and the NAM being released. NAM deprotonates Glu35.

Rate Determining Step

GIF of Reaction Step M0203.stg01


Comment: During this step, the C1 migrates (in an electrophilic manner) from above the ring plane to below the ring plane to approach the catalytic nucleophile (Asp52), which hardly changes its position during the course of the reaction. In order to observe the intermediate formed in this step of the reaction, it is necessary to have a situation in which the rate of formation of the intermediate is significantly greater than the rate of its breakdown. The fact that it has proven difficult to engineer this situation is indicative of the fact that the rate of the hydrolysis of the intermediate is significantly greater than the rate of its formation. The PDB structure 1H6M represents the covalently bound intermediate, which is the product of this reaction step [1].



Mechanisms

Bimolecular Nucleophilic Substitution
Proton Transfer

Mechanism Components

Bond Cleavage
Bond Formation
Enzyme-Substrate Bond Formation
Intermediate Formation
Overall Product Formed
Overall Reactant Used

Amino acids involved in the reaction step.

Amino Acid Location of Function Activity Function
Glu35 Side Chain reactant Hydrogen Bond Donor
Proton Donor
Asp52 Side Chain reactant Polar Non-polar interaction
Nucleophile

Reactive Centre

Bonds Formed Bonds Cleaved Bonds Changed in Order Atom Types Involved
C-O
O-H
C-O
O-H
None
C
H
O

View similar reactions in MACiE.


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