1mgo: Difference between revisions

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~~[[Image:1mgo.gif|left|200px]]~~

~~{{Structure~~

==Horse Liver Alcohol Dehydrogenase Phe93Ala Mutant==

~~|PDB~~= 1mgo |~~SIZE~~=~~350|CAPTION~~= <~~scene name~~='~~initialview01~~'>1mgo</~~scene~~>, ~~resolution~~ 1.20&~~Aring~~;

|~~SITE~~=

== Structural highlights ==

~~|LIGAND~~= <scene name='pdbligand=ZN:~~ZINC+ION~~'>ZN</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PFB:2,3,4,5,6-PENTAFLUOROBENZYL+ALCOHOL'>PFB</scene> ~~and~~ <scene name='pdbligand=~~MPD~~:~~(4S)-2-METHYL-2,4-PENTANEDIOL~~'>~~MPD~~</scene>

<table><tr><td colspan='2'>[[1mgo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MGO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MGO FirstGlance]. <br>

~~|ACTIVITY~~= [http://en.~~wikipedia~~.org/~~wiki/Alcohol_dehydrogenase Alcohol dehydrogenase~~], ~~with EC number~~ [~~http~~://www.~~brenda-enzymes~~.~~info~~/~~php~~/~~result_flat~~.~~php4~~?~~ecno~~=1.1.1.~~1 1~~.1.1.1]

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2Å</td></tr>

|~~GENE~~= ~~M64864 (~~[http://~~www~~.~~ncbi~~.~~nlm~~.~~nih~~.~~gov~~/~~Taxonomy~~/~~Browser~~/~~wwwtax~~.~~cgi~~?~~mode~~=~~Info&srchmode=5&id=9796 Equus caballus~~])

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PFB:2,3,4,5,6-PENTAFLUOROBENZYL+ALCOHOL'>PFB</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1mgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mgo OCA], [https://pdbe.org/1mgo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mgo RCSB], [https://www.ebi.ac.uk/pdbsum/1mgo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mgo ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/ADH1E_HORSE ADH1E_HORSE]

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

Check<jmol>

<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mg/1mgo_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=1mgo ConSurf].

~~'''Horse Liver Alcohol Dehydrogenase Phe93Ala Mutant'''~~

==See Also==

*[[Alcohol dehydrogenase 3D structures|Alcohol dehydrogenase 3D structures]]

__TOC__

~~==Overview==~~

</StructureSection>

The relationship between substrate mobility and catalysis was studied with wild-type and Phe93Ala (F93A) horse liver alcohol dehydrogenase (ADH). Wild-type ADH binds 2,3,4,5,6-pentafluorobenzyl alcohol in one position as shown by X-ray results, and (19)F NMR shows five resonances for the fluorines of the bound alcohol. The two meta-fluorines exchange positions with a rate constant of about 4 s(-1), indicating that mobility (ring flipping) of the benzyl alcohol is relatively restricted. The wild-type enzyme binds 2,3-difluorobenzyl alcohol in two alternative conformations that are related by a ring flip and a small translation of the fluorinated benzene ring, and the (19)F NMR spectrum shows three resonances for the two bound fluorines, consistent with the two orientations. Phe-93 interacts with the bound benzyl alcohols, and the F93A substitution decreases the rate constants for hydride transfer for benzyl alcohol oxidation and benzaldehyde reduction by 7.4- and 130-fold, respectively. The structure of F93A ADH crystallized with NAD(+) and 2,3,4,5,6-pentafluorobenzyl alcohol is similar to the structure of the wild-type enzyme complex except that the pentafluorobenzyl alcohol is not found in one position. The (19)F NMR spectrum of the F93A ADH-NAD(+)-pentafluorobenzyl alcohol complex shows three resonances for the bound fluorines. Line shape analysis of the spectrum suggests the bound pentafluorobenzyl ring undergoes rapid ring-flipping at about 20 000 s(-1). The F93A substitution greatly increases the mobility of the benzyl alcohol but modestly and differentially decreases the probability that the substrate is preorganized for hydride transfer.

==~~About this Structure~~==

~~1MGO is a~~ [[~~Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus~~]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MGO OCA~~].

~~==Reference==~~

Mobility of fluorobenzyl alcohols bound to liver alcohol dehydrogenases as determined by NMR and X-ray crystallographic studies., Rubach JK, Plapp BV, Biochemistry. 2002 Dec 31;41(52):15770-9. PMID:[http:/~~/www.ncbi.nlm.nih.gov/pubmed/12501206 12501206]~~

~~[[Category: Alcohol dehydrogenase]]~~

[[Category: Equus caballus]]

[[Category: ~~Single protein~~]]

[[Category: Large Structures]]

[[Category: Plapp~~, B V.~~]]

[[Category: Plapp BV]]

[[Category: Rubach~~, J K.~~]]

[[Category: Rubach JK]]

~~[[Category: MPD]]~~

~~[[Category: NAD]]~~

~~[[Category: PFB]]~~

~~[[Category: ZN]]~~

~~[[Category: alcohol]]~~

~~[[Category: dehydrogenase]]~~

~~[[Category: mutant]]~~

~~[[Category: nicotinamide coenzyme]]~~

~~[[Category: substrate binding site]]~~

~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:43:11 2008''~~

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@@ Line 1: / Line 1: @@
-[[Image:1mgo.gif|left|200px]]
- {{Structure
+==Horse Liver Alcohol Dehydrogenase Phe93Ala Mutant==
-|PDB= 1mgo |SIZE=350|CAPTION= <scene name='initialview01'>1mgo</scene>, resolution 1.20&Aring;
+<StructureSection load='1mgo' size='340' side='right'caption='[[1mgo]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PFB:2,3,4,5,6-PENTAFLUOROBENZYL+ALCOHOL'>PFB</scene> and <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>
+<table><tr><td colspan='2'>[[1mgo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MGO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MGO FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Alcohol_dehydrogenase Alcohol dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.1 1.1.1.1]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2&#8491;</td></tr>
-|GENE= M64864 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9796 Equus caballus])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PFB:2,3,4,5,6-PENTAFLUOROBENZYL+ALCOHOL'>PFB</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1mgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mgo OCA], [https://pdbe.org/1mgo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mgo RCSB], [https://www.ebi.ac.uk/pdbsum/1mgo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mgo ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ADH1E_HORSE ADH1E_HORSE]
+== 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/mg/1mgo_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=1mgo ConSurf].
+<div style="clear:both"></div>
-'''Horse Liver Alcohol Dehydrogenase Phe93Ala Mutant'''
+==See Also==
+*[[Alcohol dehydrogenase 3D structures|Alcohol dehydrogenase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The relationship between substrate mobility and catalysis was studied with wild-type and Phe93Ala (F93A) horse liver alcohol dehydrogenase (ADH). Wild-type ADH binds 2,3,4,5,6-pentafluorobenzyl alcohol in one position as shown by X-ray results, and (19)F NMR shows five resonances for the fluorines of the bound alcohol. The two meta-fluorines exchange positions with a rate constant of about 4 s(-1), indicating that mobility (ring flipping) of the benzyl alcohol is relatively restricted. The wild-type enzyme binds 2,3-difluorobenzyl alcohol in two alternative conformations that are related by a ring flip and a small translation of the fluorinated benzene ring, and the (19)F NMR spectrum shows three resonances for the two bound fluorines, consistent with the two orientations. Phe-93 interacts with the bound benzyl alcohols, and the F93A substitution decreases the rate constants for hydride transfer for benzyl alcohol oxidation and benzaldehyde reduction by 7.4- and 130-fold, respectively. The structure of F93A ADH crystallized with NAD(+) and 2,3,4,5,6-pentafluorobenzyl alcohol is similar to the structure of the wild-type enzyme complex except that the pentafluorobenzyl alcohol is not found in one position. The (19)F NMR spectrum of the F93A ADH-NAD(+)-pentafluorobenzyl alcohol complex shows three resonances for the bound fluorines. Line shape analysis of the spectrum suggests the bound pentafluorobenzyl ring undergoes rapid ring-flipping at about 20 000 s(-1). The F93A substitution greatly increases the mobility of the benzyl alcohol but modestly and differentially decreases the probability that the substrate is preorganized for hydride transfer.
-==About this Structure==
-MGO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MGO OCA].
-==Reference==
-Mobility of fluorobenzyl alcohols bound to liver alcohol dehydrogenases as determined by NMR and X-ray crystallographic studies., Rubach JK, Plapp BV, Biochemistry. 2002 Dec 31;41(52):15770-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12501206 12501206]
-[[Category: Alcohol dehydrogenase]]
 [[Category: Equus caballus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Plapp, B V.]]
+[[Category: Plapp BV]]
-[[Category: Rubach, J K.]]
+[[Category: Rubach JK]]
-[[Category: MPD]]
-[[Category: NAD]]
-[[Category: PFB]]
-[[Category: ZN]]
-[[Category: alcohol]]
-[[Category: dehydrogenase]]
-[[Category: mutant]]
-[[Category: nicotinamide coenzyme]]
-[[Category: substrate binding site]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:43:11 2008''