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| - | [[Image:2gqa.gif|left|200px]] | |
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| - | {{Structure
| + | ==Structure of NADH-reduced SYE1, an OYE homologue from S. oneidensis== |
| - | |PDB= 2gqa |SIZE=350|CAPTION= <scene name='initialview01'>2gqa</scene>, resolution 1.700Å
| + | <StructureSection load='2gqa' size='340' side='right'caption='[[2gqa]], [[Resolution|resolution]] 1.70Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> | + | <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> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> |
| - | |GENE=
| + | <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> |
| - | |DOMAIN=
| + | <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> |
| - | |RELATEDENTRY=[[2gou|2GOU]], [[2gq8|2GQ8]], [[2gq9|2GQ9]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gqa OCA], [http://www.ebi.ac.uk/pdbsum/2gqa PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2gqa RCSB]</span>
| + | == 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/2gqa_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=2gqa ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | '''Structure of NADH-reduced SYE1, an OYE homologue from S. oneidensis'''
| + | ==See Also== |
| - | | + | *[[NADPH dehydrogenase|NADPH dehydrogenase]] |
| - | | + | __TOC__ |
| - | ==Overview==
| + | </StructureSection> |
| - | 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.
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Shewanella oneidensis MR-1]] |
| - | ==About this Structure== | + | [[Category: Savvides SN]] |
| - | 2GQA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GQA OCA].
| + | [[Category: Van den Hemel D]] |
| - | | + | |
| - | ==Reference==
| + | |
| - | 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://www.ncbi.nlm.nih.gov/pubmed/16857682 16857682]
| + | |
| - | [[Category: Shewanella oneidensis]] | + | |
| - | [[Category: Single protein]] | + | |
| - | [[Category: Hemel, D van den.]]
| + | |
| - | [[Category: Savvides, S N.]] | + | |
| - | [[Category: flavoenzyme]] | + | |
| - | [[Category: fmn]]
| + | |
| - | [[Category: old yellow enzyme]]
| + | |
| - | [[Category: reduction by nadh]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:20:02 2008''
| + | |
