3emy: Difference between revisions
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==Crystal structure of Trichoderma reesei aspartic proteinase complexed with pepstatin A== | |||
<StructureSection load='3emy' size='340' side='right'caption='[[3emy]], [[Resolution|resolution]] 1.85Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3emy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Hypocrea_jecorina Hypocrea jecorina]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3c9y 3c9y]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EMY FirstGlance]. <br> | |||
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=STA:STATINE'>STA</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3c9y|3c9y]], [[3c9x|3c9x]]</div></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=3emy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3emy OCA], [https://pdbe.org/3emy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3emy RCSB], [https://www.ebi.ac.uk/pdbsum/3emy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3emy ProSAT]</span></td></tr> | |||
</table> | |||
== 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/em/3emy_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3emy 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. | |||
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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3emy" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
== | __TOC__ | ||
< | </StructureSection> | ||
[[Category: | [[Category: Hypocrea jecorina]] | ||
[[Category: Golubev, A M | [[Category: Large Structures]] | ||
[[Category: Gustchina, A | [[Category: Golubev, A M]] | ||
[[Category: Krauchenco, S | [[Category: Gustchina, A]] | ||
[[Category: Nascimento, A S | [[Category: Krauchenco, S]] | ||
[[Category: Polikarpov, I | [[Category: Nascimento, A S]] | ||
[[Category: Wlodawer, A | [[Category: Polikarpov, I]] | ||
[[Category: Wlodawer, A]] | |||
[[Category: Aspartic proteinase]] | [[Category: Aspartic proteinase]] | ||
[[Category: Aspartyl protease]] | [[Category: Aspartyl protease]] | ||