3c9x: Difference between revisions

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-{{Seed}}
-[[Image:3c9x.png|left|200px]]
-<!--
+==Crystal structure of Trichoderma reesei aspartic proteinase==
-The line below this paragraph, containing "STRUCTURE_3c9x", creates the "Structure Box" on the page.
+<StructureSection load='3c9x' size='340' side='right'caption='[[3c9x]], [[Resolution|resolution]] 1.70&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'>[[3c9x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichoderma_reesei Trichoderma reesei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C9X 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]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-{{STRUCTURE_3c9x|  PDB=3c9x  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3c9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c9x OCA], [https://pdbe.org/3c9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c9x RCSB], [https://www.ebi.ac.uk/pdbsum/3c9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c9x ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q2WBH2_HYPJE Q2WBH2_HYPJE]
+== 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/c9/3c9x_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=3c9x ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structures of an aspartic proteinase from Trichoderma reesei (TrAsP) and of its complex with a competitive inhibitor, pepstatin A, were solved and refined to crystallographic R-factors of 17.9% (R(free)=21.2%) at 1.70 A resolution and 15.8% (R(free)=19.2%) at 1.85 A resolution, respectively. The three-dimensional structure of TrAsP is similar to structures of other members of the pepsin-like family of aspartic proteinases. Each molecule is folded in a predominantly beta-sheet bilobal structure with the N-terminal and C-terminal domains of about the same size. Structural comparison of the native structure and the TrAsP-pepstatin complex reveals that the enzyme undergoes an induced-fit, rigid-body movement upon inhibitor binding, with the N-terminal and C-terminal lobes tightly enclosing the inhibitor. Upon recognition and binding of pepstatin A, amino acid residues of the enzyme active site form a number of short hydrogen bonds to the inhibitor that may play an important role in the mechanism of catalysis and inhibition. The structures of TrAsP were used as a template for performing statistical coupling analysis of the aspartic protease family. This approach permitted, for the first time, the identification of a network of structurally linked residues putatively mediating conformational changes relevant to the function of this family of enzymes. Statistical coupling analysis reveals coevolved continuous clusters of amino acid residues that extend from the active site into the hydrophobic cores of each of the two domains and include amino acid residues from the flap regions, highlighting the importance of these parts of the protein for its enzymatic activity.
-===Crystal structure of Trichoderma reesei aspartic proteinase===
+Statistical coupling analysis of aspartic proteinases based on crystal structures of the Trichoderma reesei enzyme and its complex with pepstatin A.,Nascimento AS, Krauchenco S, Golubev AM, Gustchina A, Wlodawer A, Polikarpov I J Mol Biol. 2008 Oct 10;382(3):763-78. Epub 2008 Jul 22. PMID:18675276<ref>PMID:18675276</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3c9x" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18675276}}, adds the Publication Abstract to the page
+*[[Proteinase 3D structures|Proteinase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18675276 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18675276}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-C9X is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C9X OCA].
+[[Category: Trichoderma reesei]]
+[[Category: Golubev AM]]
-==Reference==
+[[Category: Gustchina A]]
-<ref group="xtra">PMID:18675276</ref><references group="xtra"/>
+[[Category: Krauchenco S]]
-[[Category: Aspergillopepsin I]]
+[[Category: Nascimento AS]]
-[[Category: Hypocrea jecorina]]
+[[Category: Polikarpov I]]
-[[Category: Golubev, A M.]]
+[[Category: Wlodawer A]]
-[[Category: Gustchina, A.]]
-[[Category: Krauchenco, S.]]
-[[Category: Nascimento, A S.]]
-[[Category: Polikarpov, I.]]
-[[Category: Wlodawer, A.]]
-[[Category: Aspartic proteinase]]
-[[Category: Aspartyl protease]]
-[[Category: Hydrolase]]
-[[Category: Protease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 19:11:55 2009''