Structure based mutation analysis of GBA

Introduction

Structure Selection

To carry out a structure-based analysis of the mutations chosen in Task 7 a crystal structure had to be chosen. According to Uniprot 19 different crystal structures of glucocerebrosidase exist. The table below shows the six different structures with a resolution of or better than 2 Angstrom. 2NT0 is chosen as template for the analysis carried out in this section, as no residues are missing, the R-value is quite low, and it has the best resolution among the structures without missing residues. Only incomplete structures have been resolved near the physiological pH (7.4), therefore a structure resolved at a more acid pH had to be chosen.

PDB ID	Resolution [Å]	R-factor	Coverage	pH	Missing Residues (A/B)
1OGS	2.00	0.195		4.6	0
2NT0	1.79	0.181	.	4.5	0
2V3D	1.96	0.157		6.5	9/8
2V3E	2.00	0.163		7.5	7/7
2V3F	1.95	0.154		6.5	8/14
3GXI	1.84	0.193		NULL	0

Mutation Mapping

Figure 1: 2NT0 with hilighted mutations (red) and active site residues (blue).

Figure 2: Close-up of active site of 2NT0 with hilighted mutations (red) and active site residues (blue).

SCWRL

Figure 1: Wildtype amino acids (red) and mutations created with SCWRL (green) and pymol mutagenesis (orange) hilighted on the structure of 2NT0.

Figure 2: Cartoon representation of 2NT0, chain A (gray) superimposed with the resulting structures of SCWRL (green).