2z2y: Difference between revisions

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-{{Seed}}
-[[Image:2z2y.png|left|200px]]
-<!--
+==Crystal structure of autoprocessed form of Tk-subtilisin==
-The line below this paragraph, containing "STRUCTURE_2z2y", creates the "Structure Box" on the page.
+<StructureSection load='2z2y' size='340' side='right'caption='[[2z2y]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.89&#8491;</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>
-{{STRUCTURE_2z2y|  PDB=2z2y  |  SCENE=  }}
+<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>
+</table>
+== Function ==
+[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 ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <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/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z2y ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== 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.
-===Crystal structure of autoprocessed form of Tk-subtilisin===
+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<ref>PMID:17706669</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2z2y" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17706669}}, adds the Publication Abstract to the page
+*[[Subtilisin 3D structures|Subtilisin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17706669 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17706669}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Z2Y is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z2Y OCA].
+[[Category: Thermococcus kodakarensis KOD1]]
+[[Category: Kanaya S]]
-==Reference==
+[[Category: Koga Y]]
-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:[http://www.ncbi.nlm.nih.gov/pubmed/17706669 17706669]
+[[Category: Matsumura H]]
-[[Category: Protein complex]]
+[[Category: Takano K]]
-[[Category: Subtilisin]]
+[[Category: Tanaka S]]
-[[Category: Thermococcus kodakarensis]]
-[[Category: Kanaya, S.]]
-[[Category: Koga, Y.]]
-[[Category: Matsumura, H.]]
-[[Category: Takano, K.]]
-[[Category: Tanaka, S.]]
-[[Category: Autoprocessed]]
-[[Category: Crystal structure]]
-[[Category: Hydrolase]]
-[[Category: Subtilisin]]
-[[Category: Thermococcus kodakaraensis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 18:04:53 2008''