Fabry:Structure-based mutation analysis

Fabry Disease » Structure-based mutation analysis

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The following analyses were performed on the basis of the α-Galactosidase A sequence. Please consult the journal for the commands used to generate the results.

Preparation

<figtable id="tab:Prep"> All available PDB structures assigned to the Uniprot entry P06280 along with the according Resolution,
Coverage and R-factor. The R-factor was obtained from the PDBsum page. The chosen structure 3S5Y is highlighted.

Entry	Method	Resolution (Å)	Chain	Positions (up to 429)	R-factor	R-free	pH	PDBsum	PDB
1R46	X-ray	3.25	A/B	32-422	0.262	0.301	8.0	[»]	[»]
1R47	X-ray	3.45	A/B	32-422	0.285	0.321	8.0	[»]	[»]
3GXN	X-ray	3.01	A/B	32-421	0.239	0.301	4.5	[»]	[»]
3GXP	X-ray	2.20	A/B	32-422	0.204	0.265	4.5	[»]	[»]
3GXT	X-ray	2.70	A/B	32-422	0.245	0.306	4.5	[»]	[»]
3HG2	X-ray	2.30	A/B	32-422	0.178	0.202	4.6	[»]	[»]
3HG3	X-ray	1.90	A/B	32-426	0.167	0.197	6.5	[»]	[»]
3HG4	X-ray	2.30	A/B	32-423	0.166	0.221	4.6	[»]	[»]
3HG5	X-ray	2.30	A/B	32-422	0.192	0.227	4.6	[»]	[»]
3LX9	X-ray	2.04	A/B	32-422	0.178	0.218	6.5	[»]	[»]
3LXA	X-ray	3.04	A/B	32-426	0.216	0.244	6.5	[»]	[»]
3LXB	X-ray	2.85	A/B	32-427	0.227	0.264	6.5	[»]	[»]
3LXC	X-ray	2.35	A/B	32-422	0.186	0.237	6.5	[»]	[»]
3S5Y	X-ray	2.10	A/B	32-422	0.195	0.230	5.1	[»]	[»]
3S5Z	X-ray	2.00	A/B	32-421	0.211	0.234	5.1	[»]	[»]
3TV8	X-ray	2.64	A/B	32-422	0.203	0.239	4.6	[»]	[»]

</figtable>

We did not choose the structure 3HG3, although it has the best resolution (1.90 Å) and the second best R-factor (see <xr id="tab:Prep"/>), which is a measure of the agreement between the crystallographic model and the experimental X-ray diffraction data <ref>R-factor (crystallography) (May 17, 2012‎) http://en.wikipedia.org/wiki/R-factor_%28crystallography%29, June 20, 2012</ref>, since it has an Alanin at position 170 (part of the active site) instead of an Aspartic acid. After excluding those structures, that had deviations in the sequence, we had to choose between ten sequences (1R46, 1R47, 3GXN, 3GXP, 3GXT, 3HG2, 3HG4, 3HG5, 3S5Y, 3S5Z) and decided to use 3S5Y. This structure has the advantage of a good pH, very good coverage and still reasonable resolution and R-factor.

Vizualisation

<figure id="fig:allSNPs">

All SNPs mapped onto the structure 3S5Y, chain A. Mutated sites are shown in red. The active site (residues 170 and 231) is shown in pink, substrate binding site (position 203-207) in cyan and the existing five disulfide bonds (52 ↔ 94, 56 ↔ 63, 142 ↔ 172, 202 ↔ 223, 378 ↔ 382) are highlighted in yellow. Ligands are depicted in lines representation in dark cyan.

</figure>

From the first glance, we would consider A143T as disease causing, because it is located right next to a Cysteine, that forms a disulfide bond (yellow) and might interfere with it. The same applies for S65T, which is in the structural neighborhood of this bond and also might cause atom clashes.
There is no mutation that can interfere with the active site(purple) or the substrate binding site (cyan).
The mutation N215S seems to play an important role in the binding of the ligand N-Acetyl-D-Glucosamine.
Both prolines Pro 323 and Pro 40 do not give the impression as if they would be very important. Also Arg 356 is on the surface of the protein and is not involved in any binding, although it might be influencing the nearby helix. This also is applicable for the SNP R118H.
It seems possible, that the mutation V316I does not have a big impact on the helix it is located in.
Neither Q279E nor I289V have an obvious reason to be considered as crucial in this structure.

Create mutation

SCWRL

Comparison energies

foldX

<figtable id="tab:energyStart"> ADD CAPTION HERE

Type	Energy
BackHbond	-528.41
SideHbond	-149.96
Energy_VdW	-1013.85
Electro	-25.51
Energy_SolvP	1310.89
Energy_SolvH	-1318.53
Energy_vdwclash	99.21
energy_torsion	26.73
backbone_vdwclash	478.11
Entropy_sidec	482.20
Entropy_mainc	1219.31
water bonds	-29.53
helix dipole	-12.51
loop_entropy	0.00
cis_bond	4.50
disulfide	-29.93
kn electrostatic	-0.98
partial covalent interactions	0.00
Energy_Ionisation	1.20
Entropy Complex	0.00
Total	34.82

</figtable>