2asy: Difference between revisions

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{{Seed}}
[[Image:2asy.png|left|200px]]


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==Solution Structure of ydhR protein from Escherichia coli==
The line below this paragraph, containing "STRUCTURE_2asy", creates the "Structure Box" on the page.
<StructureSection load='2asy' size='340' side='right'caption='[[2asy]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2asy]] is a 2 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=2ASY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ASY FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2asy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2asy OCA], [https://pdbe.org/2asy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2asy RCSB], [https://www.ebi.ac.uk/pdbsum/2asy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2asy ProSAT]</span></td></tr>
{{STRUCTURE_2asy|  PDB=2asy  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/YDHR_ECOLI YDHR_ECOLI] May function as monoxygenase and play a role in the metabolism of aromatic compounds (Potential).
== 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/as/2asy_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=2asy ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
YdhR is a 101-residue conserved protein from Escherichia coli. Sequence searches reveal that the protein has &gt;50% identity to proteins found in a variety of other bacterial genomes. Using size exclusion chromatography and fluorescence spectroscopy, we determined that ydhR exists in a dimeric state with a dissociation constant of approximately 40 nM. The three-dimensional structure of dimeric ydhR was determined using NMR spectroscopy. A total of 3400 unambiguous NOEs, both manually and automatically assigned, were used for the structure calculation that was refined using an explicit hydration shell. A family of 20 structures was obtained with a backbone RMSD of 0.48 A for elements of secondary structure. The structure reveals a dimeric alpha,beta fold characteristic of the alpha+beta barrel superfamily of proteins. Bioinformatic approaches were used to show that ydhR likely belongs to a recently identified group of mono-oxygenase proteins that includes ActVA-Orf6 and YgiN and are involved in the oxygenation of polyaromatic ring compounds.


===Solution Structure of ydhR protein from Escherichia coli===
Solution structure of the Escherichia coli protein ydhR: a putative mono-oxygenase.,Revington M, Semesi A, Yee A, Shaw GS Protein Sci. 2005 Dec;14(12):3115-20. Epub 2005 Oct 31. PMID:16260765<ref>PMID:16260765</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2asy" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 16260765 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_16260765}}
__TOC__
 
</StructureSection>
==About this Structure==
2ASY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ASY OCA].
 
==Reference==
Solution structure of the Escherichia coli protein ydhR: a putative mono-oxygenase., Revington M, Semesi A, Yee A, Shaw GS, Protein Sci. 2005 Dec;14(12):3115-20. Epub 2005 Oct 31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16260765 16260765]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: OCSP, Ontario Centre for Structural Proteomics.]]
[[Category: Revington M]]
[[Category: Revington, M.]]
[[Category: Semesi A]]
[[Category: Semesi, A.]]
[[Category: Shaw GS]]
[[Category: Shaw, G S.]]
[[Category: Yee A]]
[[Category: Yee, A.]]
[[Category: Dimeric apha+beta barrel]]
[[Category: Homodimer]]
[[Category: Ocsp]]
[[Category: Ontario centre for structural proteomic]]
[[Category: Structural genomic]]
 
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Latest revision as of 09:23, 22 May 2024

Solution Structure of ydhR protein from Escherichia coli

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