3fpl: Difference between revisions

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-[[Image:3fpl.png|left|200px]]
-<!--
+==Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of C. beijerinckii ADH by T. brockii ADH==
-The line below this paragraph, containing "STRUCTURE_3fpl", creates the "Structure Box" on the page.
+<StructureSection load='3fpl' size='340' side='right'caption='[[3fpl]], [[Resolution|resolution]] 1.90&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'>[[3fpl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_beijerinckii Clostridium beijerinckii] and [https://en.wikipedia.org/wiki/Thermoanaerobacter_brockii Thermoanaerobacter brockii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FPL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FPL 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3fpl|  PDB=3fpl  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3fpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fpl OCA], [https://pdbe.org/3fpl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fpl RCSB], [https://www.ebi.ac.uk/pdbsum/3fpl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fpl ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ADH_THEBR ADH_THEBR] Alcohol dehydrogenase with a preference for medium chain secondary alcohols, such as 2-butanol and isopropanol. Has very low activity with primary alcohols, such as ethanol. Under physiological conditions, the enzyme reduces aldehydes and 2-ketones to produce secondary alcohols. Is also active with acetaldehyde and propionaldehyde.[https://www.uniprot.org/uniprot/ADH_CLOBE ADH_CLOBE] Alcohol dehydrogenase with a preference for medium chain secondary alcohols, such as 2-butanol and isopropanol. Has very low activity with primary alcohols, such as ethanol. Under physiological conditions, the enzyme reduces aldehydes and 2-ketones to produce secondary alcohols. Is active with acetaldehyde and propionaldehyde.<ref>PMID:8349550</ref> <ref>PMID:20102159</ref>
+== 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/fp/3fpl_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=3fpl ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The cofactor-binding domains (residues 153-295) of the alcohol dehydrogenases from the thermophile Thermoanaerobacter brockii (TbADH), the mesophilic bacterium Clostridium beijerinckii (CbADH), and the protozoan parasite Entamoeba histolytica (EhADH1) have been exchanged. Three chimeras have been constructed. In the first chimera, the cofactor-binding domain of thermophilic TbADH was replaced with the cofactor-binding domain of its mesophilic counterpart CbADH [chimera Chi21((TCT))]. This domain exchange significantly destabilized the parent thermophilic enzyme (DeltaT(1/2) = -18 degrees C). The reverse exchange in CbADH [chimera Chi22((CTC))], however, had little effect on the thermal stability of the parent mesophilic protein. Furthermore, substituting the cofactor-binding domain of TbADH with the homologous domain of EhADH1 [chimera Chi23((TET))] substantially reduced the thermal stability of the thermophilic ADH (DeltaT(1/2) = -51 degrees C) and impeded the oligomerization of the enzyme. All three chimeric proteins and one of their site-directed mutants were crystallized, and their three-dimensional (3D) structures were determined. Comparison of the 3D structures of the chimeras and the chimeric mutant with the structures of their parent ADHs showed no significant changes to their Calpha chains, suggesting that the difference in the thermal stability of the three parent ADHs and their chimeric mutants could be due to a limited number of substitutions located at strategic positions, mainly at the oligomerization interfaces. Indeed, stabilization of the chimeras was achieved, to a significant extent, either by introduction of a proline residue at a strategic position in the major horse liver ADH-type dimerization interface (DeltaT(1/2) = 35 degrees C) or by introduction of intersubunit electrostatic interactions (DeltaT(1/2) = 6 degrees C).
-===Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of C. beijerinckii ADH by T. brockii ADH===
+Biochemical and Structural Properties of Chimeras Constructed by Exchange of Cofactor-Binding Domains in Alcohol Dehydrogenases from Thermophilic and Mesophilic Microorganisms.,Goihberg E, Peretz M, Tel-Or S, Dym O, Shimon L, Frolow F, Burstein Y Biochemistry. 2010 Feb 9. PMID:20102159<ref>PMID:20102159</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_20102159}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3fpl" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 20102159 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_20102159}}
-==About this Structure==
-[[3fpl]] is a 1 chain structure of [[Alcohol dehydrogenase]] with sequence from [http://en.wikipedia.org/wiki/Clostridium_beijerinckii,_thermoanaerobacter_brockii Clostridium beijerinckii, thermoanaerobacter brockii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FPL OCA].
 ==See Also==
 *[[Alcohol dehydrogenase|Alcohol dehydrogenase]]
-*[[Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of C. beijerinckii ADH by T. brockii ADH|Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of C. beijerinckii ADH by T. brockii ADH]]
+*[[Alcohol dehydrogenase 3D structures|Alcohol dehydrogenase 3D structures]]
-*[[Chimeres of alcohol dehydrogenases|Chimeres of alcohol dehydrogenases]]
+== References ==
-*[[Q165E/S254K Double Mutant Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of T. brockii ADH by C. beijerinckii ADH|Q165E/S254K Double Mutant Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of T. brockii ADH by C. beijerinckii ADH]]
+<references/>
-*[[Tetrameric alcohol dehydrogenases|Tetrameric alcohol dehydrogenases]]
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Clostridium beijerinckii]]
-<ref group="xtra">PMID:020102159</ref><references group="xtra"/>
+[[Category: Large Structures]]
-[[Category: Clostridium beijerinckii, thermoanaerobacter brockii]]
+[[Category: Thermoanaerobacter brockii]]
-[[Category: Burstein, Y.]]
+[[Category: Burstein Y]]
-[[Category: Felix, F.]]
+[[Category: Felix F]]
-[[Category: Goihberg, E.]]
+[[Category: Goihberg E]]
-[[Category: Shimon, L.]]
+[[Category: Shimon L]]
-[[Category: Bacterial alcohol dehydrogenase]]
-[[Category: Chimera]]
-[[Category: Domain exchange]]
-[[Category: Metal-binding]]
-[[Category: Nadp]]
-[[Category: Oxidoreductase]]
-[[Category: Oxydoreductase]]