2exd: Difference between revisions

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OCA

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 ==The solution structure of the C-terminal domain of a nfeD homolog from Pyrococcus horikoshii==
-<StructureSection load='2exd' size='340' side='right' caption='[[2exd]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2exd' size='340' side='right'caption='[[2exd]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2exd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrho Pyrho]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EXD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2exd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXD FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH0471 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 PYRHO])</td></tr>
+</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2exd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exd OCA], [http://pdbe.org/2exd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2exd RCSB], [http://www.ebi.ac.uk/pdbsum/2exd PDBsum]</span></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=2exd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exd OCA], [https://pdbe.org/2exd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2exd RCSB], [https://www.ebi.ac.uk/pdbsum/2exd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2exd ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/O58204_PYRHO O58204_PYRHO]
 == 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/ex/2exd_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ex/2exd_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 16: / Line 19: @@
 </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=2exd ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Nodulation formation efficiency D (NfeD) is a member of a class of membrane-anchored ClpP-class proteases. There is a second class of NfeD homologs that lack the ClpP domain. The genes of both NfeD classes usually are part of an operon that also contains a gene for a prokaryotic homolog of stomatin. (Stomatin is a major integral-membrane protein of mammalian erythrocytes.) Such NfeD/stomatin homolog gene pairs are present in more than 290 bacterial and archaeal genomes, and their protein products may be part of the machinery used for quality control of membrane proteins. Herein, we report the structure of the isolated C-terminal domain of PH0471, a Pyrococcus horikoshii NfeD homolog, which lacks the ClpP domain. This C-terminal domain (termed NfeDC) contains a five-strand beta-barrel, which is structurally very similar to the OB-fold (oligosaccharide/oligonucleotide-binding fold) domain. However, there is little sequence similarity between it and previously characterized OB-fold domains. The NfeDC domain lacks the conserved surface residues that are necessary for the binding of an OB-fold domain to DNA/RNA, an ion. Instead, its surface is composed of residues that are uniquely conserved in NfeD homologs and that form the structurally conserved surface turns and beta-bulges. There is also a conserved tryptophan present on the surface. We propose that, in general, NfeDC domains may interact with other spatially proximal membrane proteins and thereby regulate their activities.
-The solution structure of the C-terminal domain of NfeD reveals a novel membrane-anchored OB-fold.,Kuwahara Y, Ohno A, Morii T, Yokoyama H, Matsui I, Tochio H, Shirakawa M, Hiroaki H Protein Sci. 2008 Nov;17(11):1915-24. Epub 2008 Aug 7. PMID:18687870<ref>PMID:18687870</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2exd" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Pyrho]]
+[[Category: Large Structures]]
-[[Category: Hiroaki, H]]
+[[Category: Pyrococcus horikoshii OT3]]
-[[Category: Kuwahara, Y]]
+[[Category: Hiroaki H]]
-[[Category: Morii, T]]
+[[Category: Kuwahara Y]]
-[[Category: Ohno, A]]
+[[Category: Morii T]]
-[[Category: Shirakawa, M]]
+[[Category: Ohno A]]
-[[Category: Tochio, H]]
+[[Category: Shirakawa M]]
-[[Category: Membrane protein]]
+[[Category: Tochio H]]
-[[Category: Nfed]]