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New page: left|200px<br /><applet load="1rwu" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rwu" /> '''Solution structure of conserved protein YbeD...
 
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[[Image:1rwu.gif|left|200px]]<br /><applet load="1rwu" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1rwu" />
'''Solution structure of conserved protein YbeD from E. coli'''<br />


==Overview==
==Solution structure of conserved protein YbeD from E. coli==
Lipoic acid is an essential prosthetic group in several metabolic, pathways. The biosynthetic pathway of protein lipoylation in Escherichia, coli involves gene products of the lip operon. YbeD is a conserved, bacterial protein located in the dacA-lipB intergenic region. Here, we, report the nuclear magnetic resonance structure of YbeD from E. coli. The, structure includes a beta alpha beta beta alpha beta fold with two, alpha-helices on one side of a four-strand antiparallel beta-sheet. The, beta 2-beta 3 loop shows the highest sequence conservation and is likely, functionally important. The beta-sheet surface contains a patch of, conserved hydrophobic residues, suggesting a role in protein-protein, interactions. YbeD shows striking structural homology to the regulatory, domain from d-3-phosphoglycerate dehydrogenase, hinting at a role in the, allosteric regulation of lipoic acid biosynthesis or the glycine cleavage, system.
<StructureSection load='1rwu' size='340' side='right'caption='[[1rwu]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1rwu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RWU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RWU FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1rwu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rwu OCA], [https://pdbe.org/1rwu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rwu RCSB], [https://www.ebi.ac.uk/pdbsum/1rwu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rwu ProSAT], [https://www.topsan.org/Proteins/NESGC/1rwu TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/YBED_ECOLI YBED_ECOLI]
== 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/rw/1rwu_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=1rwu ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Lipoic acid is an essential prosthetic group in several metabolic pathways. The biosynthetic pathway of protein lipoylation in Escherichia coli involves gene products of the lip operon. YbeD is a conserved bacterial protein located in the dacA-lipB intergenic region. Here, we report the nuclear magnetic resonance structure of YbeD from E. coli. The structure includes a beta alpha beta beta alpha beta fold with two alpha-helices on one side of a four-strand antiparallel beta-sheet. The beta 2-beta 3 loop shows the highest sequence conservation and is likely functionally important. The beta-sheet surface contains a patch of conserved hydrophobic residues, suggesting a role in protein-protein interactions. YbeD shows striking structural homology to the regulatory domain from d-3-phosphoglycerate dehydrogenase, hinting at a role in the allosteric regulation of lipoic acid biosynthesis or the glycine cleavage system.


==About this Structure==
Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains.,Kozlov G, Elias D, Semesi A, Yee A, Cygler M, Gehring K J Bacteriol. 2004 Dec;186(23):8083-8. PMID:15547281<ref>PMID:15547281</ref>
1RWU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RWU OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains., Kozlov G, Elias D, Semesi A, Yee A, Cygler M, Gehring K, J Bacteriol. 2004 Dec;186(23):8083-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15547281 15547281]
</div>
<div class="pdbe-citations 1rwu" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Arrowsmith, C.H.]]
[[Category: Arrowsmith CH]]
[[Category: Gehring, K.]]
[[Category: Gehring K]]
[[Category: Kozlov, G.]]
[[Category: Kozlov G]]
[[Category: NESG, Northeast.Structural.Genomics.Consortium.]]
[[Category: mixed alpha-beta fold]]
[[Category: nesg]]
[[Category: northeast structural genomics consortium]]
[[Category: protein structure initiative]]
[[Category: psi]]
[[Category: structural genomics]]
 
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