2exd - Revision history

OCA at 06:40, 1 May 2024

2024-05-01T06:40:00Z

← Older revision		Revision as of 06:40, 1 May 2024
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	==The solution structure of the C-terminal domain of a nfeD homolog from Pyrococcus horikoshii==		==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 ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2exd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii~~ Pyrococcus horikoshii]. 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>		<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 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~70601 Pyrococcus horikoshii])~~</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'>[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>		<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>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/O58204_PYRHO O58204_PYRHO]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 17:		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].		</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="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®/PubMed®, 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__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii OT3]]
	[[Category: Hiroaki, H]]		[[Category: Hiroaki H]]
	[[Category: Kuwahara, Y]]		[[Category: Kuwahara Y]]
	[[Category: Morii, T]]		[[Category: Morii T]]
	[[Category: Ohno, A]]		[[Category: Ohno A]]
	[[Category: Shirakawa, M]]		[[Category: Shirakawa M]]
	[[Category: Tochio, H]]		[[Category: Tochio H]]
	~~[[Category: Membrane protein]]~~
	~~[[Category: Nfed~~]]

OCA at 12:33, 10 February 2021

2021-02-10T12:33:44Z

← Older revision		Revision as of 12:33, 10 February 2021
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	==The solution structure of the C-terminal domain of a nfeD homolog from Pyrococcus horikoshii==		==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]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2exd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. 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 Pyrococcus horikoshii]. 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 Pyrococcus horikoshii])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0471 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2exd ProSAT]</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>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Hiroaki, H]]		[[Category: Hiroaki, H]]

OCA at 08:08, 25 July 2018

2018-07-25T08:08:05Z

← Older revision		Revision as of 08:08, 25 July 2018
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<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>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 07:29, 18 October 2016

2016-10-18T07:29:30Z

← Older revision		Revision as of 07:29, 18 October 2016
Line 1:		Line 1:

	==The solution structure of the C-terminal domain of a nfeD homolog from Pyrococcus horikoshii==		==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]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== 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 [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. 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>
	</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='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 Pyrococcus horikoshii])</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'>[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], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2exd ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Pyrho~~]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Hiroaki, H]]		[[Category: Hiroaki, H]]
	[[Category: Kuwahara, Y]]		[[Category: Kuwahara, Y]]

OCA at 02:47, 9 February 2016

2016-02-09T02:47:45Z

← Older revision		Revision as of 02:47, 9 February 2016
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</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="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:51, 10 September 2015

2015-09-10T17:51:48Z

← Older revision		Revision as of 17:51, 10 September 2015
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	<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]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2exd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii Pyrococcus horikoshii~~]. 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 [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>
	</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=~~53953 Pyrococcus horikoshii~~])</td></tr>		</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>
	<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://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'>[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>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2exd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Pyrococcus horikoshii~~]]		[[Category: Pyrho]]
	[[Category: Hiroaki, H]]		[[Category: Hiroaki, H]]
	[[Category: Kuwahara, Y]]		[[Category: Kuwahara, Y]]

OCA at 16:35, 15 January 2015

2015-01-15T16:35:41Z

← Older revision		Revision as of 16:35, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2exd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. 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 [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. 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>
	</td></tr><tr><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=53953 Pyrococcus horikoshii])</td></tr>		</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=53953 Pyrococcus horikoshii])</td></tr>
	<tr><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://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'>[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://www.rcsb.org/pdb/explore.do?structureId=2exd RCSB], [http://www.ebi.ac.uk/pdbsum/2exd PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Hiroaki, H.]]		[[Category: Hiroaki, H]]
	[[Category: Kuwahara, Y.]]		[[Category: Kuwahara, Y]]
	[[Category: Morii, T.]]		[[Category: Morii, T]]
	[[Category: Ohno, A.]]		[[Category: Ohno, A]]
	[[Category: Shirakawa, M.]]		[[Category: Shirakawa, M]]
	[[Category: Tochio, H.]]		[[Category: Tochio, H]]
	[[Category: Membrane protein]]		[[Category: Membrane protein]]
	[[Category: Nfed]]		[[Category: Nfed]]

OCA at 01:49, 30 September 2014

2014-09-30T01:49:31Z

← Older revision		Revision as of 01:49, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2exd~~.~~png~~\|~~left~~\|~~200px~~]]		==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=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2exd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. 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>
			</td></tr><tr><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=53953 Pyrococcus horikoshii])</td></tr>
			<tr><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://www.rcsb.org/pdb/explore.do?structureId=2exd RCSB], [http://www.ebi.ac.uk/pdbsum/2exd PDBsum]</span></td></tr>
			<table>
			== 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>
			<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/chain_selection.php?pdb_ID=2ata 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.

	~~{{STRUCTURE_2exd\| PDB=2exd \| SCENE= }}~~		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>

	~~===The solution structure~~ of the ~~C-terminal domain of a nfeD homolog from Pyrococcus horikoshii===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18687870}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2exd]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2EXD OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:018687870<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Hiroaki, H.]]		[[Category: Hiroaki, H.]]

OCA: Protected "2exd" [edit=sysop:move=sysop]

2013-01-07T11:44:32Z

Protected "2exd" [edit=sysop:move=sysop]

← Older revision	Revision as of 11:44, 7 January 2013
(No difference)

OCA at 11:44, 7 January 2013

2013-01-07T11:44:29Z

← Older revision		Revision as of 11:44, 7 January 2013
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	~~{{Seed}}~~
	[[Image:2exd.png\|left\|200px]]		[[Image:2exd.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2exd", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2exd\| PDB=2exd \| SCENE= }}		{{STRUCTURE_2exd\| PDB=2exd \| SCENE= }}

	===The solution structure of the C-terminal domain of a nfeD homolog from Pyrococcus horikoshii===		===The solution structure of the C-terminal domain of a nfeD homolog from Pyrococcus horikoshii===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18687870}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18687870 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18687870}}		{{ABSTRACT_PUBMED_18687870}}

	==About this Structure==		==About this Structure==
	~~2EXD~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii_ot3~~ Pyrococcus horikoshii ~~ot3~~]. Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXD OCA].		[[2exd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXD OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18687870~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018687870</ref><references group="xtra"/>
	[[Category: Pyrococcus horikoshii ~~ot3~~]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Hiroaki, H.]]		[[Category: Hiroaki, H.]]
	[[Category: Kuwahara, Y.]]		[[Category: Kuwahara, Y.]]
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	[[Category: Membrane protein]]		[[Category: Membrane protein]]
	[[Category: Nfed]]		[[Category: Nfed]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 20 15:51:05 2009''~~