2gqa: Difference between revisions

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 <StructureSection load='2gqa' size='340' side='right'caption='[[2gqa]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2gqa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GQA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2gqa]] 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=2GQA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GQA FirstGlance]. <br>
-</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=SO4:SULFATE+ION'>SO4</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]] 1.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2gou|2gou]], [[2gq8|2gq8]], [[2gq9|2gq9]]</div></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=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=2gqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gqa OCA], [https://pdbe.org/2gqa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gqa RCSB], [https://www.ebi.ac.uk/pdbsum/2gqa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gqa ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8EEC8_SHEON Q8EEC8_SHEON]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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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=2gqa ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-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.
-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:16857682<ref>PMID:16857682</ref>
+==See Also==
+*[[NADPH dehydrogenase|NADPH dehydrogenase]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2gqa" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Sheon]]
+[[Category: Shewanella oneidensis MR-1]]
-[[Category: Hemel, D van den]]
+[[Category: Savvides SN]]
-[[Category: Savvides, S N]]
+[[Category: Van den Hemel D]]
-[[Category: Flavoenzyme]]
-[[Category: Fmn]]
-[[Category: Old Yellow Enzyme]]
-[[Category: Oxidoreductase]]
-[[Category: Reduction by nadh]]