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PDBsum entry 1gxw

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Hydrolase PDB id
1gxw
Jmol
Contents
Protein chain
316 a.a. *
Ligands
VAL-LYS
SCN
Metals
_CA ×4
_ZN
Waters ×170
* Residue conservation analysis

References listed in PDB file
Key reference
Title The 2.2 a resolution structure of thermolysin (tln) crystallized in the presence of potassium thiocyanate.
Authors J.F.Gaucher, M.Selkti, T.Prangé, A.Tomas.
Ref. Acta Crystallogr D Biol Crystallogr, 2002, 58, 2198-2200. [DOI no: 10.1107/S0907444902015457]
PubMed id 12454500
Abstract
A new crystallization protocol for thermolysin (EC 3.4.24.27) from Bacillus thermoproteolyticus is presented. After dissolving the protein in the presence of KSCN, which avoids the use of DMSO and CsCl, crystals were obtained following the salting-in method. Crystal cell parameters are isomorphous with those previously reported from DMSO/CsCl mixtures. The new SCN(-) crystal structure has been analyzed. It shows the presence of one thiocyanate ion in the catalytic site and several rearrangements in the S(1) and S(2) subsites. These results are in agreement with the measurements of Inouye et al. [(1998), J. Biochem. (Tokyo), 123, 847-852], who observed in solution that the solubility of TLN, which is particularly poor in low ionic strength solutions, increases dramatically in the presence of several neutral salts. The results reported here suggest possible explanations for the solubility increase and for the inhibitory effects of high SCN(-) concentrations on thermolysin activity.
Figure 1.
Figure 1 Stereoimages illustrating the mode of binding of the SCN ion to TLN and the rearrangement of the subsite S1-S2. (a) Partial structure of the active site of TLN crystallized in the presence of DMSO/CsCl. (b) Partial structure of the same active site of TLN crystallized in the presence of KSCN. Tyr157 rotates about the [1] angle toward Asp150. The SCN ion tightly binds His231, Glu166 and a water molecule (VMD; Humphrey et al., 1996[Humphrey, W., Dalke, A. & Schulten, K. (1996). J. Mol. Graph. 14, 33-38, 27-28.]).
The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 2198-2200) copyright 2002.
Secondary reference #1
Title Effect of salts on the solubility of thermolysin: a remarkable increase in the solubility as well as the activity by the addition of salts without aggregation or dispersion of thermolysin.
Authors K.Inouye, K.Kuzuya, B.Tonomura.
Ref. J Biochem, 1998, 123, 847-852.
PubMed id 9562615
Abstract
Secondary reference #2
Title Structure of thermolysin refined at 1.6 a resolution.
Authors M.A.Holmes, B.W.Matthews.
Ref. J Mol Biol, 1982, 160, 623-639. [DOI no: 10.1016/0022-2836(82)90319-9]
PubMed id 7175940
Full text Abstract
Figure 3.
FIG. 3. Conformational diagram for the backbone of thermolysin. Residues that are outside the ``allowed'' regions for a hard-sphere model are numbered.
Figure 4.
FIG. 4. Stereo diagram illustrating the apparent thermal motion of t,he thermolysin molecule. Larger circles correspond to residues with greater apparen motion. The radius of each c~wlr l\as obtained 1)~ taking the verage R value for all atoms in that residue, subtracting a constant value of 4.0 AZ (in order to make differences in apparent motion more obvious) and drawing the circle at t,hr SO'?; probabilit? level (Johson, 196.5).
The above figures are reproduced from the cited reference with permission from Elsevier
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