3fpc

From Proteopedia

(Difference between revisions)

Current revision

Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-294 of T. brockii ADH by E. histolytica ADH

Structural highlights

3fpc is a 4 chain structure with sequence from Entamoeba histolytica and Thermoanaerobacter brockii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.4Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.ADH1_ENTHI 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.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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).

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Goihberg E, Peretz M, Tel-Or S, Dym O, Shimon L, Frolow F, Burstein Y. Biochemical and Structural Properties of Chimeras Constructed by Exchange of Cofactor-Binding Domains in Alcohol Dehydrogenases from Thermophilic and Mesophilic Microorganisms. Biochemistry. 2010 Feb 9. PMID:20102159 doi:10.1021/bi901730x
↑ Goihberg E, Peretz M, Tel-Or S, Dym O, Shimon L, Frolow F, Burstein Y. Biochemical and Structural Properties of Chimeras Constructed by Exchange of Cofactor-Binding Domains in Alcohol Dehydrogenases from Thermophilic and Mesophilic Microorganisms. Biochemistry. 2010 Feb 9. PMID:20102159 doi:10.1021/bi901730x

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3fpc"

@@ Line 1: / Line 1: @@
 ==Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-294 of T. brockii ADH by E. histolytica ADH==
-<StructureSection load='3fpc' size='340' side='right' caption='[[3fpc]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
+<StructureSection load='3fpc' size='340' side='right'caption='[[3fpc]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3fpc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enthi Enthi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FPC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3fpc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Entamoeba_histolytica Entamoeba histolytica] 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=3FPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FPC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3fpl|3fpl]]</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ADH1, ADH1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5759 ENTHI])</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=3fpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fpc OCA], [https://pdbe.org/3fpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fpc RCSB], [https://www.ebi.ac.uk/pdbsum/3fpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fpc ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alcohol_dehydrogenase_(NADP(+)) Alcohol dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.2 1.1.1.2] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fpc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fpc RCSB], [http://www.ebi.ac.uk/pdbsum/3fpc PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://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_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/ADH1_ENTHI ADH1_ENTHI] 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.<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/3fpc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fp/3fpc_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3fpc ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3fpc" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Alcohol dehydrogenase|Alcohol dehydrogenase]]
-*[[Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-294 of T. brockii ADH by E. histolytica ADH|Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-294 of T. brockii ADH by E. histolytica ADH]]
+*[[Alcohol dehydrogenase 3D structures|Alcohol dehydrogenase 3D structures]]
-*[[Chimeras of alcohol dehydrogenases|Chimeras of alcohol dehydrogenases]]
-*[[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]]
-*[[Tetrameric alcohol dehydrogenases|Tetrameric alcohol dehydrogenases]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Enthi]]
+[[Category: Entamoeba histolytica]]
-[[Category: Burstein, Y]]
+[[Category: Large Structures]]
-[[Category: Felix, F]]
+[[Category: Thermoanaerobacter brockii]]
-[[Category: Goihberg, E]]
+[[Category: Burstein Y]]
-[[Category: Shimon, L]]
+[[Category: Felix F]]
-[[Category: Bacterial alcohol dehydrogenase]]
+[[Category: Goihberg E]]
-[[Category: Chimera]]
+[[Category: Shimon L]]
-[[Category: Domain exchange]]
-[[Category: Metal-binding]]
-[[Category: Nadp]]
-[[Category: Oxidoreductase]]
-[[Category: Oxydoreductase]]

3fpc

From Proteopedia

Current revision

Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-294 of T. brockii ADH by E. histolytica ADH

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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