2rkx: Difference between revisions

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-[[Image:2rkx.png|left|200px]]
-<!--
+==The 3D structure of chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase==
-The line below this paragraph, containing "STRUCTURE_2rkx", creates the "Structure Box" on the page.
+<StructureSection load='2rkx' size='340' side='right'caption='[[2rkx]], [[Resolution|resolution]] 2.25&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'>[[2rkx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RKX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RKX 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]] 2.25&#8491;</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=2rkx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rkx OCA], [https://pdbe.org/2rkx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rkx RCSB], [https://www.ebi.ac.uk/pdbsum/2rkx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rkx ProSAT]</span></td></tr>
-{{STRUCTURE_2rkx|  PDB=2rkx  |  SCENE=  }}
+</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/rk/2rkx_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=2rkx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The design of new enzymes for reactions not catalysed by naturally occurring biocatalysts is a challenge for protein engineering and is a critical test of our understanding of enzyme catalysis. Here we describe the computational design of eight enzymes that use two different catalytic motifs to catalyse the Kemp elimination-a model reaction for proton transfer from carbon-with measured rate enhancements of up to 10(5) and multiple turnovers. Mutational analysis confirms that catalysis depends on the computationally designed active sites, and a high-resolution crystal structure suggests that the designs have close to atomic accuracy. Application of in vitro evolution to enhance the computational designs produced a &gt;200-fold increase in k(cat)/K(m) (k(cat)/K(m) of 2,600 M(-1)s(-1) and k(cat)/k(uncat) of &gt;10(6)). These results demonstrate the power of combining computational protein design with directed evolution for creating new enzymes, and we anticipate the creation of a wide range of useful new catalysts in the future.
-===The 3D structure of chain D, cyclase subunit of imidazoleglycerol_evolvedcerolphosphate synthase===
+Kemp elimination catalysts by computational enzyme design.,Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D Nature. 2008 May 8;453(7192):190-5. Epub 2008 Mar 19. PMID:18354394<ref>PMID:18354394</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18354394}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2rkx" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18354394 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_18354394}}
-==About this Structure==
-[[2rkx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RKX OCA].
 ==See Also==
-*[[Directed evolution|Directed evolution]]
+*[[Kemp eliminase|Kemp eliminase]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018354394</ref><references group="xtra"/>
+__TOC__
-[[Category: Albeck, S.]]
+</StructureSection>
-[[Category: Dym, O.]]
+[[Category: Large Structures]]
-[[Category: ISPC, Israel Structural Proteomics Center.]]
+[[Category: Albeck S]]
-[[Category: Khersonsky, O.]]
+[[Category: Dym O]]
-[[Category: Tawfik, D.]]
+[[Category: Khersonsky O]]
-[[Category: Alpha-beta barrel]]
+[[Category: Tawfik D]]
-[[Category: Amino-acid biosynthesis]]
-[[Category: Histidine biosynthesis]]
-[[Category: ISPC]]
-[[Category: Israel Structural Proteomics Center]]
-[[Category: Lyase]]
-[[Category: Structural genomic]]