Protein modeling with α-N-acetylgalactosaminase from E. meningoseptica

Our modelling aims to improve the activity of α-N-acetylgalactosaminidase from E. meningoseptica . There would be many practical advantages for a more efficient enzyme: For instance, conversion has to be completed as fast as possible for routine tasks in hospitals. An another example would be to compensate for a possible loss of activity, by being fixed onto a membrane. In order to achieve this we used the experimentally - determined structure of α-N-acetylgalactosaminidase from Liu et al. (2007).

As described in “Bacterial glycosidases for the production of universal red blood cells”, the active site consists of Tyr307, Tyr225, His228, Glu149, Tyr179 and Arg213. With this we tried to examine the interactions of the residues with the substrate. The precise distances, which would allow interactions, are listed in Table 1. The values refer to Schulz & Schirmer's „Principles of Protein Structure“.

Table 1: Different distances between residues which would allow interactions.

It was found that the substrate in the active site (Figure 1) is not stabilized at OH - 6 by residues (Substate Structure), as already mentioned in Liu et. al. (2007). It has been verified with the Protein Interactions Calculator that no interactions with OH - 6 were detected.

Figure 1: Active site of N-Agal with CASTp in PyMOL.

Figure 2: Mutation Asp186.

Figure 2: Mutation Asn186.