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| | ==Crystal structure of autoprocessed form of Tk-subtilisin== | | ==Crystal structure of autoprocessed form of Tk-subtilisin== |
| - | <StructureSection load='2z2y' size='340' side='right' caption='[[2z2y]], [[Resolution|resolution]] 1.89Å' scene=''> | + | <StructureSection load='2z2y' size='340' side='right'caption='[[2z2y]], [[Resolution|resolution]] 1.89Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2z2y]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z2Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z2Y FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2z2y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z2Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z2Y FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.89Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2z2x|2z2x]], [[2z2z|2z2z]], [[2z30|2z30]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2z2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z2y OCA], [https://pdbe.org/2z2y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z2y RCSB], [https://www.ebi.ac.uk/pdbsum/2z2y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z2y ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z2y OCA], [http://pdbe.org/2z2y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z2y RCSB], [http://www.ebi.ac.uk/pdbsum/2z2y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z2y ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TKSU_THEKO TKSU_THEKO]] Has a broad substrate specificity with a slight preference to large hydrophobic amino acid residues at the P1 position. | + | [https://www.uniprot.org/uniprot/TKSU_THEKO TKSU_THEKO] Has a broad substrate specificity with a slight preference to large hydrophobic amino acid residues at the P1 position. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z2/2z2y_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z2/2z2y_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | ==See Also== | | ==See Also== |
| - | *[[Subtilisin|Subtilisin]] | + | *[[Subtilisin 3D structures|Subtilisin 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Subtilisin]] | + | [[Category: Large Structures]] |
| - | [[Category: Kanaya, S]] | + | [[Category: Thermococcus kodakarensis KOD1]] |
| - | [[Category: Koga, Y]] | + | [[Category: Kanaya S]] |
| - | [[Category: Matsumura, H]] | + | [[Category: Koga Y]] |
| - | [[Category: Takano, K]] | + | [[Category: Matsumura H]] |
| - | [[Category: Tanaka, S]] | + | [[Category: Takano K]] |
| - | [[Category: Autoprocessed]]
| + | [[Category: Tanaka S]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Thermococcus kodakaraensis]]
| + | |
| Structural highlights
Function
TKSU_THEKO Has a broad substrate specificity with a slight preference to large hydrophobic amino acid residues at the P1 position.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Subtilisin from the hyperthermophilic archaeon Thermococcus kodakaraensis (Tk-subtilisin) is matured from Pro-Tk-subtilisin upon autoprocessing and degradation of the propeptide. The crystal structures of the autoprocessed and mature forms of Tk-subtilisin were determined at 1.89 A and 1.70 A resolution, respectively. Comparison of these structures with that of unautoprocessed Pro-Tk-subtilisin indicates that the structure of Tk-subtilisin is not seriously changed during maturation. However, one unique Ca(2+)-binding site (Ca-7) is identified in these structures. In addition, the N-terminal region of the mature domain (Gly70-Pro82), which binds tightly to the main body in the unautoprocessed form, is disordered and mostly truncated in the autoprocessed and mature forms, respectively. Interestingly, this site is formed also in the unautoprocessed form when its crystals are soaked with 10 mM CaCl(2), as revealed by the 1.87 A structure. Along with the formation of this site, the N-terminal region (Leu75-Thr80) is disordered, with the scissile peptide bond contacting with the active site. These results indicate that the calcium ion binds weakly to the Ca-7 site in the unautoprocessed form, but is trapped upon autoprocessing. We propose that the Ca-7 site is required to promote the autoprocessing reaction by stabilizing the autoprocessed form, in which the new N terminus of the mature domain is structurally disordered. Furthermore, the crystal structure of the Tk-propeptide:S324A-subtilisin complex, which was formed by the addition of separately expressed proteins, was determined at 1.65 A resolution. This structure is virtually identical with that of the autoprocessed form, indicating that the interaction between the two domains is highly intensive and specific.
Four new crystal structures of Tk-subtilisin in unautoprocessed, autoprocessed and mature forms: insight into structural changes during maturation.,Tanaka S, Matsumura H, Koga Y, Takano K, Kanaya S J Mol Biol. 2007 Sep 28;372(4):1055-69. Epub 2007 Jul 26. PMID:17706669[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Tanaka S, Matsumura H, Koga Y, Takano K, Kanaya S. Four new crystal structures of Tk-subtilisin in unautoprocessed, autoprocessed and mature forms: insight into structural changes during maturation. J Mol Biol. 2007 Sep 28;372(4):1055-69. Epub 2007 Jul 26. PMID:17706669 doi:http://dx.doi.org/10.1016/j.jmb.2007.07.027
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