1spw - Revision history

OCA at 09:09, 22 May 2024

2024-05-22T09:09:25Z

←Older revision		Revision as of 09:09, 22 May 2024
Line 19:		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=1spw 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=1spw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Despite their high sequence homology, rubredoxins from Desulfovibrio gigas and D. desulfuricans are stabilized to very different extents by compatible solutes such as diglycerol phosphate, the major osmolyte in the hyperthermophilic archaeon Archaeoglobus fulgidus[Lamosa P, Burke A, Peist R, Huber R, Liu M Y, Silva G, Rodrigues-Pousada C, LeGall J, Maycock C and Santos H (2000) Appl Environ Microbiol66, 1974-1979]. The principal structural difference between these two proteins is the absence of the hairpin loop in the rubredoxin from D. desulfuricans. Therefore, mutants of D. gigas rubredoxin bearing deletions in the loop region were constructed to investigate the importance of this structural feature on protein intrinsic stability, as well as on its capacity to undergo stabilization by compatible solutes. The three-dimensional structure of the mutant bearing the largest deletion, Delta17/29, was determined by 1H-NMR, demonstrating that, despite the drastic deletion, the main structural features were preserved. The dependence of the NH chemical shifts on temperature and solute concentration (diglycerol phosphate or mannosylglycerate) provide evidence of subtle conformational changes induced by the solute. The kinetic stability (as assessed from the absorption decay at 494 nm) of six mutant rubredoxins was determined at 90 degrees C and the stabilizing effect exerted by both solutes was assessed. The extent of protection conferred by each solute was highly dependent on the specific mutant examined: while the half-life for iron release in the wild-type D. gigas rubredoxin increased threefold in the presence of 0.1 M diglycerol phosphate, mutant Delta23/29 was destabilized. This study provides evidence for solute-induced compaction of the protein structure and occurrence of weak, specific interactions with the protein surface. The relevance of these findings to our understanding of the molecular basis for protein stabilization is discussed.
		+
		+	Structural determinants of protein stabilization by solutes. The important of the hairpin loop in rubredoxins.,Pais TM, Lamosa P, dos Santos W, Legall J, Turner DL, Santos H FEBS J. 2005 Feb;272(4):999-1011. PMID:15691333<ref>PMID:15691333</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1spw" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Rubredoxin 3D structures\|Rubredoxin 3D structures]]		*[[Rubredoxin 3D structures\|Rubredoxin 3D structures]]
	*[[Rubredoxin PDB structures\|Rubredoxin PDB structures]]		*[[Rubredoxin PDB structures\|Rubredoxin PDB structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:34, 1 May 2024

2024-05-01T08:34:02Z

←Older revision		Revision as of 08:34, 1 May 2024
Line 1:		Line 1:

	==Solution Structure of a Loop Truncated Mutant from D. gigas Rubredoxin, NMR==		==Solution Structure of a Loop Truncated Mutant from D. gigas Rubredoxin, NMR==
-	<StructureSection load='1spw' size='340' side='right'caption='[[1spw~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='1spw' size='340' side='right'caption='[[1spw]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1spw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_19364 Atcc 19364~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SPW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1spw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Megalodesulfovibrio_gigas Megalodesulfovibrio gigas]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SPW FirstGlance]. <br>
-	</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=1spw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1spw OCA], [https://pdbe.org/1spw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1spw RCSB], [https://www.ebi.ac.uk/pdbsum/1spw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1spw ProSAT]</span></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=1spw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1spw OCA], [https://pdbe.org/1spw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1spw RCSB], [https://www.ebi.ac.uk/pdbsum/1spw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1spw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~RUBR_DESGI RUBR_DESGI]~~] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. Electron acceptor for cytoplasmic lactate dehydrogenase.	+	[https://www.uniprot.org/uniprot/RUBR_MEGGA RUBR_MEGGA] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. Electron acceptor for cytoplasmic lactate dehydrogenase.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		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=1spw 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=1spw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Despite their high sequence homology, rubredoxins from Desulfovibrio gigas and D. desulfuricans are stabilized to very different extents by compatible solutes such as diglycerol phosphate, the major osmolyte in the hyperthermophilic archaeon Archaeoglobus fulgidus[Lamosa P, Burke A, Peist R, Huber R, Liu M Y, Silva G, Rodrigues-Pousada C, LeGall J, Maycock C and Santos H (2000) Appl Environ Microbiol66, 1974-1979]. The principal structural difference between these two proteins is the absence of the hairpin loop in the rubredoxin from D. desulfuricans. Therefore, mutants of D. gigas rubredoxin bearing deletions in the loop region were constructed to investigate the importance of this structural feature on protein intrinsic stability, as well as on its capacity to undergo stabilization by compatible solutes. The three-dimensional structure of the mutant bearing the largest deletion, Delta17/29, was determined by 1H-NMR, demonstrating that, despite the drastic deletion, the main structural features were preserved. The dependence of the NH chemical shifts on temperature and solute concentration (diglycerol phosphate or mannosylglycerate) provide evidence of subtle conformational changes induced by the solute. The kinetic stability (as assessed from the absorption decay at 494 nm) of six mutant rubredoxins was determined at 90 degrees C and the stabilizing effect exerted by both solutes was assessed. The extent of protection conferred by each solute was highly dependent on the specific mutant examined: while the half-life for iron release in the wild-type D. gigas rubredoxin increased threefold in the presence of 0.1 M diglycerol phosphate, mutant Delta23/29 was destabilized. This study provides evidence for solute-induced compaction of the protein structure and occurrence of weak, specific interactions with the protein surface. The relevance of these findings to our understanding of the molecular basis for protein stabilization is discussed.

-	Structural determinants of protein stabilization by solutes. The important of the hairpin loop in rubredoxins.,Pais TM, Lamosa P, dos Santos W, Legall J, Turner DL, Santos H FEBS J. 2005 Feb;272(4):999-1011. PMID:15691333<ref>PMID:15691333</ref>	+	==See Also==
-		+	*[[Rubredoxin 3D structures\|Rubredoxin 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+	*[[Rubredoxin PDB structures\|Rubredoxin PDB structures]]
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 1spw" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 19364]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lamosa, P~~]]	+	[[Category: Megalodesulfovibrio gigas]]
-	[[Category: ~~LeGall, J~~]]	+	[[Category: Lamosa P]]
-	[[Category: ~~Pais, T M~~]]	+	[[Category: LeGall J]]
-	[[Category: ~~Santos, H~~]]	+	[[Category: Pais TM]]
-	[[Category: Santos~~, W dos~~]]	+	[[Category: Santos H]]
-	[[Category: Turner~~, D L~~]]	+	[[Category: Turner DL]]
-	[[Category: ~~Electron transport]]~~	+	[[Category: Dos Santos W]]
-	~~[[Category: Truncated loop~~]]	+

OCA at 07:35, 22 September 2021

2021-09-22T07:35:37Z

←Older revision		Revision as of 07:35, 22 September 2021
Line 3:		Line 3:
	<StructureSection load='1spw' size='340' side='right'caption='[[1spw]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1spw' size='340' side='right'caption='[[1spw]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1spw]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_19364 Atcc 19364]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SPW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1spw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_19364 Atcc 19364]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SPW FirstGlance]. <br>
-	</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=1spw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1spw OCA], [~~http~~://pdbe.org/1spw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1spw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1spw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1spw ProSAT]</span></td></tr>	+	</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=1spw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1spw OCA], [https://pdbe.org/1spw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1spw RCSB], [https://www.ebi.ac.uk/pdbsum/1spw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1spw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RUBR_DESGI RUBR_DESGI]] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. Electron acceptor for cytoplasmic lactate dehydrogenase.	+	[[https://www.uniprot.org/uniprot/RUBR_DESGI RUBR_DESGI]] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. Electron acceptor for cytoplasmic lactate dehydrogenase.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 14:01, 18 December 2019

2019-12-18T14:01:07Z

←Older revision		Revision as of 14:01, 18 December 2019
Line 1:		Line 1:

	==Solution Structure of a Loop Truncated Mutant from D. gigas Rubredoxin, NMR==		==Solution Structure of a Loop Truncated Mutant from D. gigas Rubredoxin, NMR==
-	<StructureSection load='1spw' size='340' side='right' caption='[[1spw]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='1spw' size='340' side='right'caption='[[1spw]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1spw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19364 Atcc 19364]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SPW FirstGlance]. <br>		<table><tr><td colspan='2'>[[1spw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19364 Atcc 19364]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SPW FirstGlance]. <br>
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 19364]]		[[Category: Atcc 19364]]
		+	[[Category: Large Structures]]
	[[Category: Lamosa, P]]		[[Category: Lamosa, P]]
	[[Category: LeGall, J]]		[[Category: LeGall, J]]

OCA at 07:43, 14 March 2018

2018-03-14T07:43:35Z

←Older revision		Revision as of 07:43, 14 March 2018
Line 1:		Line 1:
		+
	==Solution Structure of a Loop Truncated Mutant from D. gigas Rubredoxin, NMR==		==Solution Structure of a Loop Truncated Mutant from D. gigas Rubredoxin, NMR==
	<StructureSection load='1spw' size='340' side='right' caption='[[1spw]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1spw' size='340' side='right' caption='[[1spw]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1spw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19364 Atcc 19364]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SPW FirstGlance]. <br>		<table><tr><td colspan='2'>[[1spw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19364 Atcc 19364]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SPW FirstGlance]. <br>
-	</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=1spw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1spw OCA], [http://pdbe.org/1spw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1spw RCSB], [http://www.ebi.ac.uk/pdbsum/1spw PDBsum]</span></td></tr>	+	</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=1spw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1spw OCA], [http://pdbe.org/1spw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1spw RCSB], [http://www.ebi.ac.uk/pdbsum/1spw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1spw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sp/1spw_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sp/1spw_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>
	</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=1spw ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:41, 11 September 2015

2015-09-11T10:41:47Z

←Older revision		Revision as of 10:41, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1spw' size='340' side='right' caption='[[1spw]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1spw' size='340' side='right' caption='[[1spw]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1spw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Desulfovibrio_gigas Desulfovibrio gigas~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SPW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1spw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19364 Atcc 19364]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SPW FirstGlance]. <br>
-	</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=1spw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1spw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1spw RCSB], [http://www.ebi.ac.uk/pdbsum/1spw PDBsum]</span></td></tr>	+	</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=1spw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1spw OCA], [http://pdbe.org/1spw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1spw RCSB], [http://www.ebi.ac.uk/pdbsum/1spw PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 25:
	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 1spw" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desulfovibrio gigas~~]]	+	[[Category: Atcc 19364]]
	[[Category: Lamosa, P]]		[[Category: Lamosa, P]]
	[[Category: LeGall, J]]		[[Category: LeGall, J]]

OCA at 15:22, 25 December 2014

2014-12-25T15:22:07Z

←Older revision		Revision as of 15:22, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1spw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SPW FirstGlance]. <br>		<table><tr><td colspan='2'>[[1spw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SPW FirstGlance]. <br>
-	</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=1spw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1spw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1spw RCSB], [http://www.ebi.ac.uk/pdbsum/1spw PDBsum]</span></td></tr>	+	</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=1spw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1spw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1spw RCSB], [http://www.ebi.ac.uk/pdbsum/1spw PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RUBR_DESGI RUBR_DESGI]] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. Electron acceptor for cytoplasmic lactate dehydrogenase.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Desulfovibrio gigas]]		[[Category: Desulfovibrio gigas]]
-	[[Category: Lamosa, P.]]	+	[[Category: Lamosa, P]]
-	[[Category: LeGall, J.]]	+	[[Category: LeGall, J]]
-	[[Category: Pais, T M.]]	+	[[Category: Pais, T M]]
-	[[Category: Santos, H.]]	+	[[Category: Santos, H]]
-	[[Category: Santos, W dos.]]	+	[[Category: Santos, W dos]]
-	[[Category: Turner, D L.]]	+	[[Category: Turner, D L]]
	[[Category: Electron transport]]		[[Category: Electron transport]]
	[[Category: Truncated loop]]		[[Category: Truncated loop]]

OCA at 14:04, 29 September 2014

2014-09-29T14:04:07Z

←Older revision		Revision as of 14:04, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1spw.~~png\|left~~\|200px]]	+	==Solution Structure of a Loop Truncated Mutant from D. gigas Rubredoxin, NMR==
		+	<StructureSection load='1spw' size='340' side='right' caption='[[1spw]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1spw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SPW FirstGlance]. <br>
		+	</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=1spw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1spw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1spw RCSB], [http://www.ebi.ac.uk/pdbsum/1spw 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/sp/1spw_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 ==
		+	Despite their high sequence homology, rubredoxins from Desulfovibrio gigas and D. desulfuricans are stabilized to very different extents by compatible solutes such as diglycerol phosphate, the major osmolyte in the hyperthermophilic archaeon Archaeoglobus fulgidus[Lamosa P, Burke A, Peist R, Huber R, Liu M Y, Silva G, Rodrigues-Pousada C, LeGall J, Maycock C and Santos H (2000) Appl Environ Microbiol66, 1974-1979]. The principal structural difference between these two proteins is the absence of the hairpin loop in the rubredoxin from D. desulfuricans. Therefore, mutants of D. gigas rubredoxin bearing deletions in the loop region were constructed to investigate the importance of this structural feature on protein intrinsic stability, as well as on its capacity to undergo stabilization by compatible solutes. The three-dimensional structure of the mutant bearing the largest deletion, Delta17/29, was determined by 1H-NMR, demonstrating that, despite the drastic deletion, the main structural features were preserved. The dependence of the NH chemical shifts on temperature and solute concentration (diglycerol phosphate or mannosylglycerate) provide evidence of subtle conformational changes induced by the solute. The kinetic stability (as assessed from the absorption decay at 494 nm) of six mutant rubredoxins was determined at 90 degrees C and the stabilizing effect exerted by both solutes was assessed. The extent of protection conferred by each solute was highly dependent on the specific mutant examined: while the half-life for iron release in the wild-type D. gigas rubredoxin increased threefold in the presence of 0.1 M diglycerol phosphate, mutant Delta23/29 was destabilized. This study provides evidence for solute-induced compaction of the protein structure and occurrence of weak, specific interactions with the protein surface. The relevance of these findings to our understanding of the molecular basis for protein stabilization is discussed.

-	~~{{STRUCTURE_1spw\| PDB=1spw \| SCENE= }}~~	+	Structural determinants of protein stabilization by solutes. The important of the hairpin loop in rubredoxins.,Pais TM, Lamosa P, dos Santos W, Legall J, Turner DL, Santos H FEBS J. 2005 Feb;272(4):999-1011. PMID:15691333<ref>PMID:15691333</ref>

-	~~===Solution Structure of a Loop Truncated Mutant from D. gigas Rubredoxin~~, ~~NMR===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15691333}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1spw]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015691333<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Desulfovibrio gigas]]		[[Category: Desulfovibrio gigas]]
	[[Category: Lamosa, P.]]		[[Category: Lamosa, P.]]

OCA: Protected "1spw" [edit=sysop:move=sysop]

2013-01-04T10:23:05Z

Protected "1spw" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:23, 4 January 2013

OCA at 10:23, 4 January 2013

2013-01-04T10:23:03Z

←Older revision		Revision as of 10:23, 4 January 2013
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-	{{Seed}}
	[[Image:1spw.png\|left\|200px]]		[[Image:1spw.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1spw", 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_1spw\| PDB=1spw \| SCENE= }}		{{STRUCTURE_1spw\| PDB=1spw \| SCENE= }}

	===Solution Structure of a Loop Truncated Mutant from D. gigas Rubredoxin, NMR===		===Solution Structure of a Loop Truncated Mutant from D. gigas Rubredoxin, NMR===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15691333}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15691333 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15691333}}		{{ABSTRACT_PUBMED_15691333}}

	==About this Structure==		==About this Structure==
-	~~1SPW~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA].	+	[[1spw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_gigas Desulfovibrio gigas]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SPW OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15691333~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015691333</ref><references group="xtra"/>
	[[Category: Desulfovibrio gigas]]		[[Category: Desulfovibrio gigas]]
	[[Category: Lamosa, P.]]		[[Category: Lamosa, P.]]
Line 31:		Line 19:
	[[Category: Santos, W dos.]]		[[Category: Santos, W dos.]]
	[[Category: Turner, D L.]]		[[Category: Turner, D L.]]
		+	[[Category: Electron transport]]
	[[Category: Truncated loop]]		[[Category: Truncated loop]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 20:10:55 2009''