2gou: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="2gou" size="350" color="white" frame="true" align="right" spinBox="true" caption="2gou, resolution 1.400Å" /> '''Structure of wild t...
 
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2gou.gif|left|200px]]<br /><applet load="2gou" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2gou, resolution 1.400&Aring;" />
'''Structure of wild type, oxidized SYE1, an OYE homologue from S. oneidensis'''<br />


==Overview==
==Structure of wild type, oxidized SYE1, an OYE homologue from S. oneidensis==
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='2gou' size='340' side='right'caption='[[2gou]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2gou]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GOU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GOU 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]] 1.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=2gou FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gou OCA], [https://pdbe.org/2gou PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gou RCSB], [https://www.ebi.ac.uk/pdbsum/2gou PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gou 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/go/2gou_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=2gou ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2GOU 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=BOG:'>BOG</scene>, <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=FMN:'>FMN</scene>, <scene name='pdbligand=PE4:'>PE4</scene> and <scene name='pdbligand=TRS:'>TRS</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GOU 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]]
[[Category: Single protein]]
[[Category: Savvides SN]]
[[Category: Hemel, D.van.den.]]
[[Category: Van den Hemel D]]
[[Category: Savvides, S.N.]]
[[Category: BOG]]
[[Category: FMN]]
[[Category: PE4]]
[[Category: SO4]]
[[Category: TRS]]
[[Category: flavoenzyme]]
[[Category: fmn]]
[[Category: old yeallow enzyme]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 20:04:44 2008''

Latest revision as of 12:28, 14 February 2024

Structure of wild type, oxidized SYE1, an OYE homologue from S. oneidensisStructure of wild type, oxidized SYE1, an OYE homologue from S. oneidensis

Structural highlights

2gou is a 1 chain structure with sequence from Shewanella oneidensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.4Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q8EEC8_SHEON

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2gou, resolution 1.40Å

Drag the structure with the mouse to rotate

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

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2gou&oldid=4058769"