1i2e: Difference between revisions

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-[[Image:1i2e.jpg|left|200px]]<br /><applet load="1i2e" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1i2e, resolution 1.8&Aring;" />
-'''Ribonuclease T1 V16A mutant, form I'''<br />
-==Overview==
+==Ribonuclease T1 V16A mutant, form I==
-Differential scanning calorimetry, urea denaturation, and X-ray crystallography were combined to study the structural and energetic consequences of refilling an engineered cavity in the hydrophobic core of RNase T1 with CH(3), SH, and OH groups. Three valines that cluster together in the major hydrophobic core of T1 were each replaced with Ala, Ser, Thr, and Cys. Compared to the wild-type protein, all these mutants reduce the thermodynamic stability of the enzyme considerably. The relative order of stability at all three positions is as follows: Val &gt; Ala approximately equal to Thr &gt; Ser. The effect of introducing a sulfhydryl group is more variable. Surprisingly, a Val --&gt; Cys mutation in a hydrophobic environment can be as or even more destabilizing than a Val --&gt; Ser mutation. Furthermore, our results reveal that the penalty for introducing an OH group into a hydrophobic cavity is roughly the same as the gain obtained from filling the cavity with a CH(3) group. The inverse equivalence of the behavior of hydroxyl and methyl groups seems to be crucial for the unique three-dimensional structure of the proteins. The importance of negative design elements in this context is highlighted.
+<StructureSection load='1i2e' size='340' side='right'caption='[[1i2e]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1i2e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I2E FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2GP:GUANOSINE-2-MONOPHOSPHATE'>2GP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1i2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i2e OCA], [https://pdbe.org/1i2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i2e RCSB], [https://www.ebi.ac.uk/pdbsum/1i2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i2e ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNT1_ASPOR RNT1_ASPOR]
+== 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/i2/1i2e_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=1i2e ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-I2E is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=2GP:'>2GP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I2E OCA].
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Hydrophobic core manipulations in ribonuclease T1., De Vos S, Backmann J, Prevost M, Steyaert J, Loris R, Biochemistry. 2001 Aug 28;40(34):10140-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11513591 11513591]
 [[Category: Aspergillus oryzae]]
-[[Category: Ribonuclease T(1)]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Backmann J]]
-[[Category: Backmann, J.]]
+[[Category: De Vos S]]
-[[Category: Loris, R.]]
+[[Category: Loris R]]
-[[Category: Steyaert, J.]]
+[[Category: Steyaert J]]
-[[Category: Vos, S De.]]
-[[Category: 2GP]]
-[[Category: CA]]
-[[Category: cavity creation]]
-[[Category: hydrophobic core packing]]
-[[Category: ribonuclease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:07:14 2008''