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2gq9

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(New page: 200px<br /><applet load="2gq9" size="350" color="white" frame="true" align="right" spinBox="true" caption="2gq9, resolution 1.700&Aring;" /> '''Structure of SYE1, ...)
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[[Image:2gq9.gif|left|200px]]<br /><applet load="2gq9" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2gq9, resolution 1.700&Aring;" />
 
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'''Structure of SYE1, an OYE homologue from S. oneidensis, in complex with p-hydroxybenzaldehyde'''<br />
 
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==Overview==
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==Structure of SYE1, an OYE homologue from S. oneidensis, in complex with p-hydroxybenzaldehyde==
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We have recently reported that Shewanella oneidensis, a Gram-negative, gamma-proteobacterium with a rich arsenal of redox proteins, possesses, four old yellow enzyme (OYE) homologues. Here, we report a series of high, resolution crystal structures for one of these OYEs, Shewanella yellow, enzyme 1 (SYE1), in its oxidized form at 1.4A resolution, which binds a, molecule of PEG 400 in the active site, and in its NADH-reduced and, p-hydroxybenzaldehyde- and p-hydroxyacetophenone-bound forms at 1.7A, resolution. Although the overall structure of SYE1 reveals a monomeric, enzyme based on the alpha(8)beta(8) barrel scaffold observed for other, OYEs, the active site exhibits a unique combination of features: a, strongly butterfly-bent FMN cofactor both in the oxidized and NADH-reduced, forms, a collapsed and narrow active site tunnel, and a novel combination, of conserved residues involved in the binding of phenolic ligands., Furthermore, we identify a second p-hydroxybenzaldehyde-binding site in a, hydrophobic cleft next to the entry of the active site tunnel in the, capping subdomain, formed by a restructuring of Loop 3 to an "open", conformation. This constitutes the first evidence to date for the entire, family of OYEs that Loop 3 may indeed play a dynamic role in ligand, binding and thus provides insights into the elusive NADH complex and into, substrate binding in general. Structure-based sequence alignments indicate, that the novelties we observe in SYE1 are supported by conserved residues, in a number of structurally uncharacterized OYEs from the beta- and, gamma-proteobacteria, suggesting that SYE1 represents a new subfamily of, bacterial OYEs.
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<StructureSection load='2gq9' size='340' side='right'caption='[[2gq9]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2gq9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis_MR-1 Shewanella oneidensis MR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GQ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GQ9 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gq9 OCA], [https://pdbe.org/2gq9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gq9 RCSB], [https://www.ebi.ac.uk/pdbsum/2gq9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gq9 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q8EEC8_SHEON Q8EEC8_SHEON]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gq/2gq9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2gq9 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2GQ9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis] with <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=FMN:'>FMN</scene> and <scene name='pdbligand=HBA:'>HBA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GQ9 OCA].
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*[[NADPH dehydrogenase|NADPH dehydrogenase]]
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__TOC__
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==Reference==
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</StructureSection>
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Ligand-induced conformational changes in the capping subdomain of a bacterial old yellow enzyme homologue and conserved sequence fingerprints provide new insights into substrate binding., van den Hemel D, Brige A, Savvides SN, Van Beeumen J, J Biol Chem. 2006 Sep 22;281(38):28152-61. Epub 2006 Jul 20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16857682 16857682]
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[[Category: Large Structures]]
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[[Category: Shewanella oneidensis]]
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[[Category: Shewanella oneidensis MR-1]]
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[[Category: Single protein]]
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[[Category: Savvides SN]]
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[[Category: Hemel, D.van.den.]]
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[[Category: Van den Hemel D]]
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[[Category: Savvides, S.N.]]
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[[Category: FMN]]
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[[Category: HBA]]
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[[Category: SO4]]
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[[Category: flavoenzyme]]
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[[Category: fmn]]
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[[Category: old yellow enzyme]]
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[[Category: phenolic ligands]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 20:05:44 2008''
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Current revision

Structure of SYE1, an OYE homologue from S. oneidensis, in complex with p-hydroxybenzaldehyde

PDB ID 2gq9

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