TABLE 3.
Comparison of crystal structures of GCase
The abbreviations used are as follows: GOL, glycerol; IFG, isofagomine; CBE, conduritol B epoxide; ND, not determined.
| PDB code | Protein source+molecule at active site | Space group | pH | Loop 1 conformation | Tyr-313 H-bond to catalytic residues | Trp-312 H-bond to helix 7a | Ref. |
|---|---|---|---|---|---|---|---|
| 1OGS | Imiglucerase | C2221 | 4.5 | Extended | Glu-235 | 1 | 25 |
| Extended | Glu-235 | ||||||
| 2NT0 | Imiglucerase | P21 | 4.5 | Extended | Glu-235 | 26 | |
| +GOL | Extended | Glu-235 | |||||
| 3GXM | Imiglucerase | P21 | 4.5 | α-Helical | 1 | 28 | |
| Extended | Glu-235 | ||||||
| 3GXD | Imiglucerase | P21 | 4.5b | α-Helical | 1 | 28 | |
| Extended | |||||||
| 3GXI | Imiglucerase | P21 | 5.5 | α-Helical | 1 | 28 | |
| Extended | Glu-235 | ||||||
| 2J25 | Imiglucerase | C2221 | 5.5 | α-Helical | 1 | 24 | |
| Extended | Glu-235 | ||||||
| 2F61 | Imiglucerase | C2221 | 6.0 | Extended | 1 | 11 | |
| Extended | Glu-235 | ||||||
| 2NT1 | Imiglucerase | P21 | 7.5c | α-Helical | 1 | 26 | |
| Extended | Glu-340 | ||||||
| 2NSX | Imiglucerase | P21 | 4.5 | α-Helical (IFG) | Glu-340 | 26 | |
| +IFG | Extended (GOL) | ||||||
| 3GXF | Imiglucerase | P21 | 7.5c | α-Helical (IFG) | Glu-340 | 28 | |
| +IFG | Extended (GOL) | ||||||
| 1Y7V | Imiglucerase | C2221 | 4.6 | Extended | Glu-235 | 27 | |
| +CBE | Extended | Glu-235 | |||||
| 2WKL | Velaglucerase alfa | C2221 | 7.0 | α-Helical | 1 | 30 | |
| Extended | Glu-235 | 1 | |||||
| 2V3F | Taliglucerase alfa | P21 | 6.5 | α-Helical | Glu-340 | 29 | |
| +BTB | α-Helical | Glu-340 | |||||
| 2V3D | Taliglucerase alfa | P21 | 6.5 | α-Helical | Glu-340 | 29 | |
| +NB-DNJ | α-Helical | Glu-340 | |||||
| 2V3E | Taliglucerase alfa | P21 | 6.5 | α-Helical | Glu-340 | 29 | |
| +NN-DNJ | α-Helical | Glu-340 | |||||
| 3KE0 | N370S GCase | C2221 | 5.4 | Extended | Glu-235 | 1 | This study |
| Extended | Glu-235 | 1 | |||||
| 3KEH | N370S GCase | C2221 | 7.1 | Extended | Glu-235 | 1 | This study |
| Extended | Glu-235 | NDd |
a Numbering of the helix is same as Ref. 25.
b This was crystallized at pH 5.5 and soaked to pH 4.5.
c A very similar condition as was used for N370S crystallization at neutral pH. The final pH is likely at pH 7.1.
d The side chain of Trp-312 in one of the confirmations has poorer density than the other one. Its density is at the same position, but the orientation is a little bit hard to define.