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The PBP6 is composed of 4 monomers which are almost identical to each other. The differences are found in some loops and in the amino acids of the active site.

Active site

The amino acids that compose the are: Ser40 and Lys43, which organised in a catalytic diad through a hydrogen bond, alongside with Ser106, Asp 108, Lys 209 and Thr 210. The oxygen from Ser40 binds to the carbon from the peptide bond between the two D-alanines, which causes the formation of the acylenzyme complex after the terminal D-alanine leaves. When a substrate is fixated, the enzyme undergoes a conformation change (see below), which causes Lys43 to be exposed to the solvent. Lys43 deprotonates a catalytic water molecule which then binds to the carbon from the acylenzyme complex in order to regenerate the enzyme and free the peptide which has been shortened by one amino acid.

Binding site

Other amino acids allow the selective fixation of the ligand to the enzyme. The residues 79 to 83, 212 to 218 and 242 to 248 are responsible for this. These residues undergo a conformation change during substrate fixation. Ser 83, specifically, is thought to be capable of stabilising the leaving group during the acylation reaction through hydrogen bonds. Another important part of the selective fixation process is the oxyanion hole, which is a hole in the enzyme structure created by the backbone nitrogens. These nitrogens stabilise the carbonyl oxygen from the D-Ala-D-Ala peptide bond. The Ser106, Thr210, Thr212 and Arg244 residues stabilise the C-terminal of the peptide through hydrogen bonds and bonds through water molecules (see structure 3itb). It can be seen that PBP6 presents both a binding site and an active site with a precise configuratio that makes it specific to its substrate.

Ampicillin mimicry

Ampicillin stop the synthesis of peptidoglycan by competitive inhibition of PBP6. 3ita shows the acylenzyme complex of PBP6 with ampicillin. Ampicillin presents structural characteristic which are similar to the enzyme substrate which allow it to bind to its active site. It however also possesses characteristics which allow it to stop the enzyme from functionning. It can use the same mechanisms as the enzyme substrate , and specifically the oxyanion hole. It can use the same mechanisms as the enzyme substrate thanks to its 03 carboxylate group for example. It also forms a hydrogen bond with the Thr212 residue. Similarly, Arg244 also binds to the C3 carboxylate group through a water molecule. However, PBP6 cannot hydrolise the amide bond from ampicillin. This is due to the bond in question being contained inside the beta-lactam cycle of the antibiotic. Additionally, the sulfur atom from the ampicillin molecule sterically hinders the interaction between Lys43 and the . As a result, no water molecule can be protonated in order to perform the hydrolisis. It can be seen that through its structure, ampicilline imitates the natural substrate of PBP6 and stops it from performing its catalysis.