1w1k: Difference between revisions

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-[[Image:1w1k.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1w1k", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1w1k|  PDB=1w1k  |  SCENE=  }}
-'''STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: ILE238THR MUTANT'''
+==STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: Ile238Thr Mutant==
+<StructureSection load='1w1k' size='340' side='right'caption='[[1w1k]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1w1k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W1K 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]] 2.55&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EUG:2-METHOXY-4-[(1E)-PROP-1-EN-1-YL]PHENOL'>EUG</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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=1w1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w1k OCA], [https://pdbe.org/1w1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w1k RCSB], [https://www.ebi.ac.uk/pdbsum/1w1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w1k ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VAOX_PENSI VAOX_PENSI] Catalyzes the conversion of vanillin alcohol to vanillin, and also the conversion of a wide range of phenolic compounds bearing side chains of variable size at the para position of the aromatic ring. Crucial for the degradation of the secondary metabolites derived from the degradation of the lignin. Catalyzes besides the oxidation of 4-hydroxybenzyl alcohols, the oxidative deamination of 4-hydroxybenzylamines, the oxidative demethylation of 4-(methoxy-methyl)phenols and the oxidative hydration of 4-allylphenols. Most active with 4-allylphenols.
+== 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/w1/1w1k_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1w1k ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The flavoenzyme vanillyl-alcohol oxidase was subjected to random mutagenesis to generate mutants with enhanced reactivity to creosol (2-methoxy-4-methylphenol). The vanillyl-alcohol oxidase-mediated conversion of creosol proceeds via a two-step process in which the initially formed vanillyl alcohol (4-hydroxy-3-methoxybenzyl alcohol) is oxidized to the widely used flavor compound vanillin (4-hydroxy-3-methoxybenzaldehyde). The first step of this reaction is extremely slow due to the formation of a covalent FAD N-5-creosol adduct. After a single round of error-prone PCR, seven mutants were generated with increased reactivity to creosol. The single-point mutants I238T, F454Y, E502G, and T505S showed an up to 40-fold increase in catalytic efficiency (kcat/Km) with creosol compared with the wild-type enzyme. This enhanced reactivity was due to a lower stability of the covalent flavin-substrate adduct, thereby promoting vanillin formation. The catalytic efficiencies of the mutants were also enhanced for other ortho-substituted 4-methylphenols, but not for p-cresol (4-methylphenol). The replaced amino acid residues are not located within a distance of direct interaction with the substrate, and the determined three-dimensional structures of the mutant enzymes are highly similar to that of the wild-type enzyme. These results clearly show the importance of remote residues, not readily predicted by rational design, for the substrate specificity of enzymes.
-==Overview==
+Laboratory-evolved vanillyl-alcohol oxidase produces natural vanillin.,van den Heuvel RH, van den Berg WA, Rovida S, van Berkel WJ J Biol Chem. 2004 Aug 6;279(32):33492-500. Epub 2004 May 28. PMID:15169773<ref>PMID:15169773</ref>
-The flavoenzyme vanillyl-alcohol oxidase was subjected to random mutagenesis to generate mutants with enhanced reactivity to creosol (2-methoxy-4-methylphenol). The vanillyl-alcohol oxidase-mediated conversion of creosol proceeds via a two-step process in which the initially formed vanillyl alcohol (4-hydroxy-3-methoxybenzyl alcohol) is oxidized to the widely used flavor compound vanillin (4-hydroxy-3-methoxybenzaldehyde). The first step of this reaction is extremely slow due to the formation of a covalent FAD N-5-creosol adduct. After a single round of error-prone PCR, seven mutants were generated with increased reactivity to creosol. The single-point mutants I238T, F454Y, E502G, and T505S showed an up to 40-fold increase in catalytic efficiency (kcat/Km) with creosol compared with the wild-type enzyme. This enhanced reactivity was due to a lower stability of the covalent flavin-substrate adduct, thereby promoting vanillin formation. The catalytic efficiencies of the mutants were also enhanced for other ortho-substituted 4-methylphenols, but not for p-cresol (4-methylphenol). The replaced amino acid residues are not located within a distance of direct interaction with the substrate, and the determined three-dimensional structures of the mutant enzymes are highly similar to that of the wild-type enzyme. These results clearly show the importance of remote residues, not readily predicted by rational design, for the substrate specificity of enzymes.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-W1K is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium simplicissimum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W1K OCA].
+</div>
+<div class="pdbe-citations 1w1k" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Laboratory-evolved vanillyl-alcohol oxidase produces natural vanillin., van den Heuvel RH, van den Berg WA, Rovida S, van Berkel WJ, J Biol Chem. 2004 Aug 6;279(32):33492-500. Epub 2004 May 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15169773 15169773]
+*[[Vanillyl-alcohol oxidase|Vanillyl-alcohol oxidase]]
-[[Category: Alcohol oxidase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Penicillium simplicissimum]]
-[[Category: Single protein]]
+[[Category: Van Den Heuvel RH]]
-[[Category: Heuvel, R H.Van Den.]]
-[[Category: Catalysis]]
-[[Category: Fad]]
-[[Category: Flavoenzyme]]
-[[Category: Oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 13:01:37 2008''