Structure-based mutation analysis TSD

No citations, I don't read THAT many books :P

The journal of this task can be found here here.

Mutations

As the week before only disease causing SNPs were assigned to us some mutations had to be replaced. Additionally the reference pdb stricture limited the possibilities as only the second domain was retained fpr the following analzsis. Thus a almost new set of SNPs was chosen:

R178H, R178C, P183L, D207E, S293I, F434L, L451V, E482K, L484Q, E506D

Structure preparation

There are two structures resolved for the HEXA_HUMAN reference sequence used for the course of this practical. The struture of this Uniprot entry is found in the alpha-chains of the PDB-IDs and 2gjx and 2gk1 both form the same publication <ref name="hexa_pdb_ref">Lemieux, M., Mark, B., & Cherney, M. (2006). Crystallographic Structure of Human beta-Hexosaminidase A: Interpretation of Tay-Sachs Mutations and Loss of GM2 Ganglioside Hydrolysis. Journal of molecular biology, 359(4), 913-29. doi:10.1016/j.jmb.2006.04.004</ref>. Unfortunately a 14 residue stretch towards the N-terminus of the protein (residues 75 to 88) is unresolved in both structures. However as previously shown the alpha subunit of Hex A consists of two domains. The N-terminal domain, Glyco_hydro_20b, is not involved in catalysis. Therefore, to evade problems with the missing backbone in the course of this task, the structure was truncated to contain only the C-terminal, catalytic domain, Glyco_hydro_20. In concordance with previous tasks and based on the experimental data in for both structures, shown in <xr id="tbl:struct_comp"/>, 2gjx was chosen as the reference structure. Details on the alteration of the structure according to the measures described above can be found in the journal.

<figtable id="tbl:struct_comp">

Table 1: Comparison of experimental parameters for the two resolved structures of UniProt entry P06865. The parameters are important for choosing the structcture used for the structure based mutation analysis. Coverage is the sequence residues covered by the structure according to UniProtKB. This however is based on the SEQRES data. It should be noted that there is an unresolved region (residues 75 to 88) in both structures.

PDB-ID:Chain	Coverage	Resolution (Å)	R-value	R-free	pH
2gjx:A	23-529	2.8	0.270	0.288	5.5
2gk1:A	23-529	3.25	0.277	0.322	5.5

</figtable>