2gq9: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2gq9.gif|left|200px]]<br /><applet load="2gq9" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2gq9, resolution 1.700&Aring;" />
-'''Structure of SYE1, an OYE homologue from S. oneidensis, in complex with p-hydroxybenzaldehyde'''<br />
-==Overview==
+==Structure of SYE1, an OYE homologue from S. oneidensis, in complex with p-hydroxybenzaldehyde==
-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.
+<StructureSection load='2gq9' size='340' side='right'caption='[[2gq9]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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>
+<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>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8EEC8_SHEON Q8EEC8_SHEON]
+== 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/gq/2gq9_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=2gq9 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-GQ9 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].
+*[[NADPH dehydrogenase|NADPH dehydrogenase]]
+__TOC__
-==Reference==
+</StructureSection>
-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]
+[[Category: Large Structures]]
-[[Category: Shewanella oneidensis]]
+[[Category: Shewanella oneidensis MR-1]]
-[[Category: Single protein]]
+[[Category: Savvides SN]]
-[[Category: Hemel, D.van.den.]]
+[[Category: Van den Hemel D]]
-[[Category: Savvides, S.N.]]
-[[Category: FMN]]
-[[Category: HBA]]
-[[Category: SO4]]
-[[Category: flavoenzyme]]
-[[Category: fmn]]
-[[Category: old yellow enzyme]]
-[[Category: phenolic ligands]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 20:05:44 2008''