3xim - Revision history

OCA at 10:35, 1 March 2024

OCA — Fri, 01 Mar 2024 10:35:49 GMT

←Older revision		Revision as of 10:35, 1 March 2024
Line 1:		Line 1:

	==ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS==		==ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS==
-	<StructureSection load='3xim' size='340' side='right' caption='[[3xim]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3xim' size='340' side='right'caption='[[3xim]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3xim]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Actmi Actmi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3XIM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3XIM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3xim]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinoplanes_missouriensis Actinoplanes missouriensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3XIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3XIM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CO:COBALT+(II)+ION'>CO</scene~~>, ~~<scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.3Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http:~~/~~/en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase]~~, ~~with EC number [http~~:~~//www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene></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=3xim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3xim OCA], [~~http~~://pdbe.org/3xim PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3xim RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3xim PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3xim 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=3xim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3xim OCA], [https://pdbe.org/3xim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3xim RCSB], [https://www.ebi.ac.uk/pdbsum/3xim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3xim ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/XYLA_ACTM4 XYLA_ACTM4]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 20:
	</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=3xim 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=3xim ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Site-specific substitutions of arginine for lysine in the thermostable D-xylose isomerase (XI) from Actinoplanes missouriensis are shown to impart significant heat stability enhancement in the presence of sugar substrates most probably by interfering with nonenzymatic glycation. The same substitutions are also found to increase heat stability in the absence of any sugar derivatives, where a mechanism based on prevention of glycation can no longer be invoked. This rather conservative substitution is moreover shown to improve thermostability in two other structurally unrelated proteins, human copper, zinc-superoxide dismutase (CuZnSOD) and D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Bacillus subtilis. The stabilizing effect of Lys----Arg substitutions is rationalized on the basis of a detailed analysis of the crystal structures of wild-type XI and of engineered variants with Lys----Arg substitution at four distinct locations, residues 253, 309, 319, and 323. Molecular model building analysis of the structures of wild-type and mutant CuZnSOD (K9R) and GAPDH (G281K and G281R) is used to explain the observed stability enhancement in these proteins. In addition to demonstrating that even thermostable proteins can lend themselves to further stability improvement, our findings provide direct evidence that arginine residues are important stabilizing elements in proteins. Moreover, the stabilizing role of electrostatic interactions, particularly between subunits in oligomeric proteins, is documented.
-
-	Arginine residues as stabilizing elements in proteins.,Mrabet NT, Van den Broeck A, Van den brande I, Stanssens P, Laroche Y, Lambeir AM, Matthijssens G, Jenkins J, Chiadmi M, van Tilbeurgh H, et al. Biochemistry. 1992 Mar 3;31(8):2239-53. PMID:1540579<ref>PMID:1540579</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3xim" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[D-xylose isomerase\|D-xylose isomerase]]	+	*[[D-xylose isomerase 3D structures\|D-xylose isomerase 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Actmi~~]]	+	[[Category: Actinoplanes missouriensis]]
-	[[Category: ~~Xylose isomerase]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Brande, I Van Den~~]]	+	[[Category: Chiadmi M]]
-	[[Category: Chiadmi, M]]	+	[[Category: Demaeyer M]]
-	[[Category: Demaeyer, M]]	+	[[Category: Janin J]]
-	~~[[Category: Denbroek, A Van~~]]	+	[[Category: Jenkins J]]
-	[[Category: Janin, J]]	+	[[Category: Lambeir A-M]]
-	[[Category: Jenkins, J]]	+	[[Category: Laroche Y]]
-	[[Category: Lambeir, A M]]	+	[[Category: Lasters I]]
-	[[Category: Laroche, Y]]	+	[[Category: Matthyssens G]]
-	[[Category: Lasters, I]]	+	[[Category: Mrabet NT]]
-	[[Category: Matthyssens, G]]	+	[[Category: Quax WJ]]
-	[[Category: Mrabet~~, N T~~]]	+	[[Category: Rey F]]
-	[[Category: Quax~~, W J~~]]	+	[[Category: Stanssens P]]
-	[[Category: Rey, F]]	+	[[Category: Van Den Brande I]]
-	[[Category: Stanssens, P]]	+	[[Category: Van Denbroek A]]
-	[[Category: Vantilbeurgh, H]]	+	[[Category: Vantilbeurgh H]]
-	[[Category: Wodak~~, S J~~]]	+	[[Category: Wodak SJ]]

OCA at 16:14, 27 February 2019

OCA — Wed, 27 Feb 2019 16:14:59 GMT

←Older revision		Revision as of 16:14, 27 February 2019
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xi/3xim_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xi/3xim_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 21:08, 4 August 2016

OCA — Thu, 04 Aug 2016 21:08:56 GMT

←Older revision		Revision as of 21:08, 4 August 2016
Line 1:		Line 1:
		+
	==ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS==		==ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS==
	<StructureSection load='3xim' size='340' side='right' caption='[[3xim]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3xim' size='340' side='right' caption='[[3xim]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3xim]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Actinoplanes_missouriensis Actinoplanes missouriensis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3XIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3XIM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3xim]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Actmi Actmi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3XIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3XIM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </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=3xim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3xim OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3xim RCSB], [http://www.ebi.ac.uk/pdbsum/3xim 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=3xim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3xim OCA], [http://pdbe.org/3xim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3xim RCSB], [http://www.ebi.ac.uk/pdbsum/3xim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3xim ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 16:
	<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=3xim ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 26:
	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 3xim" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Actinoplanes missouriensis~~]]	+	[[Category: Actmi]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
	[[Category: Brande, I Van Den]]		[[Category: Brande, I Van Den]]

OCA at 08:41, 21 December 2014

OCA — Sun, 21 Dec 2014 08:41:39 GMT

←Older revision		Revision as of 08:41, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3xim\| PDB=3xim \| SCENE= }}~~	+	==ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS==
-	===ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS===	+	<StructureSection load='3xim' size='340' side='right' caption='[[3xim]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_1540579}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3xim]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Actinoplanes_missouriensis Actinoplanes missouriensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3XIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3XIM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </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=3xim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3xim OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3xim RCSB], [http://www.ebi.ac.uk/pdbsum/3xim 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/xi/3xim_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 ==
		+	Site-specific substitutions of arginine for lysine in the thermostable D-xylose isomerase (XI) from Actinoplanes missouriensis are shown to impart significant heat stability enhancement in the presence of sugar substrates most probably by interfering with nonenzymatic glycation. The same substitutions are also found to increase heat stability in the absence of any sugar derivatives, where a mechanism based on prevention of glycation can no longer be invoked. This rather conservative substitution is moreover shown to improve thermostability in two other structurally unrelated proteins, human copper, zinc-superoxide dismutase (CuZnSOD) and D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Bacillus subtilis. The stabilizing effect of Lys----Arg substitutions is rationalized on the basis of a detailed analysis of the crystal structures of wild-type XI and of engineered variants with Lys----Arg substitution at four distinct locations, residues 253, 309, 319, and 323. Molecular model building analysis of the structures of wild-type and mutant CuZnSOD (K9R) and GAPDH (G281K and G281R) is used to explain the observed stability enhancement in these proteins. In addition to demonstrating that even thermostable proteins can lend themselves to further stability improvement, our findings provide direct evidence that arginine residues are important stabilizing elements in proteins. Moreover, the stabilizing role of electrostatic interactions, particularly between subunits in oligomeric proteins, is documented.

-	~~==About this Structure==~~	+	Arginine residues as stabilizing elements in proteins.,Mrabet NT, Van den Broeck A, Van den brande I, Stanssens P, Laroche Y, Lambeir AM, Matthijssens G, Jenkins J, Chiadmi M, van Tilbeurgh H, et al. Biochemistry. 1992 Mar 3;31(8):2239-53. PMID:1540579<ref>PMID:1540579</ref>
-	~~[[3xim]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Actinoplanes_missouriensis Actinoplanes missouriensis]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3XIM OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[D-xylose isomerase\|D-xylose isomerase]]		*[[D-xylose isomerase\|D-xylose isomerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:001540579</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Actinoplanes missouriensis]]		[[Category: Actinoplanes missouriensis]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
-	[[Category: Brande, I Van Den.]]	+	[[Category: Brande, I Van Den]]
-	[[Category: Chiadmi, M.]]	+	[[Category: Chiadmi, M]]
-	[[Category: Demaeyer, M.]]	+	[[Category: Demaeyer, M]]
-	[[Category: Denbroek, A Van.]]	+	[[Category: Denbroek, A Van]]
-	[[Category: Janin, J.]]	+	[[Category: Janin, J]]
-	[[Category: Jenkins, J.]]	+	[[Category: Jenkins, J]]
-	[[Category: Lambeir, A M.]]	+	[[Category: Lambeir, A M]]
-	[[Category: Laroche, Y.]]	+	[[Category: Laroche, Y]]
-	[[Category: Lasters, I.]]	+	[[Category: Lasters, I]]
-	[[Category: Matthyssens, G.]]	+	[[Category: Matthyssens, G]]
-	[[Category: Mrabet, N T.]]	+	[[Category: Mrabet, N T]]
-	[[Category: Quax, W J.]]	+	[[Category: Quax, W J]]
-	[[Category: Rey, F.]]	+	[[Category: Rey, F]]
-	[[Category: Stanssens, P.]]	+	[[Category: Stanssens, P]]
-	[[Category: Vantilbeurgh, H.]]	+	[[Category: Vantilbeurgh, H]]
-	[[Category: Wodak, S J.]]	+	[[Category: Wodak, S J]]

OCA: Protected "3xim" [edit=sysop:move=sysop]

OCA — Thu, 16 May 2013 07:41:02 GMT

Protected "3xim" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:41, 16 May 2013

OCA at 07:40, 16 May 2013

OCA — Thu, 16 May 2013 07:40:58 GMT

←Older revision		Revision as of 07:40, 16 May 2013
Line 1:		Line 1:
-	{{Seed}}
-	[[Image:3xim.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3xim", 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_3xim\| PDB=3xim \| SCENE= }}		{{STRUCTURE_3xim\| PDB=3xim \| SCENE= }}
-
	===ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS===		===ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_1540579}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 1540579 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_1540579}}		{{ABSTRACT_PUBMED_1540579}}

	==About this Structure==		==About this Structure==
-	~~3XIM~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Actinoplanes_missouriensis Actinoplanes missouriensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3XIM OCA].	+	[[3xim]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Actinoplanes_missouriensis Actinoplanes missouriensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3XIM OCA].
		+
		+	==See Also==
		+	*[[D-xylose isomerase\|D-xylose isomerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~1540579~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:001540579</ref><references group="xtra"/><references/>
	[[Category: Actinoplanes missouriensis]]		[[Category: Actinoplanes missouriensis]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
Line 42:		Line 29:
	[[Category: Vantilbeurgh, H.]]		[[Category: Vantilbeurgh, H.]]
	[[Category: Wodak, S J.]]		[[Category: Wodak, S J.]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:04:08 2009''

OCA at 15:04, 17 February 2009

OCA — Tue, 17 Feb 2009 15:04:09 GMT

←Older revision		Revision as of 15:04, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3XIM is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Actinoplanes_missouriensis Actinoplanes missouriensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3XIM OCA].	+	3XIM is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Actinoplanes_missouriensis Actinoplanes missouriensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3XIM OCA].

	==Reference==		==Reference==
-	Arginine residues as stabilizing elements in proteins., Mrabet NT, Van den Broeck A, Van den brande I, Stanssens P, Laroche Y, Lambeir AM, Matthijssens G, Jenkins J, Chiadmi M, van Tilbeurgh H, et al., Biochemistry. 1992 Mar 3;31(8):2239-53. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/1540579 1540579]~~	+	<ref group="xtra">PMID:1540579</ref><references group="xtra"/>
	[[Category: Actinoplanes missouriensis]]		[[Category: Actinoplanes missouriensis]]
-	[[Category: Single protein]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
	[[Category: Brande, I Van Den.]]		[[Category: Brande, I Van Den.]]
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	[[Category: Wodak, S J.]]		[[Category: Wodak, S J.]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 13~~:12:~~47 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:04:08 2009''

OCA at 10:12, 3 July 2008

OCA — Thu, 03 Jul 2008 10:12:47 GMT

←Older revision		Revision as of 10:12, 3 July 2008
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-	[[Image:3xim.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3xim.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_3xim\| PDB=3xim \| SCENE= }}		{{STRUCTURE_3xim\| PDB=3xim \| SCENE= }}

-	~~'''~~ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS~~'''~~	+	===ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS===


-	~~==Overview==~~	+	<!--
-	~~Site~~-~~specific substitutions of arginine for lysine in the thermostable D~~-~~xylose isomerase (XI) from Actinoplanes missouriensis are shown to impart significant heat stability enhancement in~~ the ~~presence of sugar substrates most probably by interfering with nonenzymatic glycation. The same substitutions are also found~~ to ~~increase heat stability in~~ the absence of any sugar derivatives, where a mechanism based on prevention of glycation can no longer be invoked. This rather conservative substitution is moreover shown to improve thermostability in two other structurally unrelated proteins, human copper, zinc-superoxide dismutase (~~CuZnSOD) and D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Bacillus subtilis. The stabilizing effect of Lys----Arg substitutions is rationalized~~ on ~~the basis of a detailed analysis of the crystal structures of wild-type XI and of engineered variants with Lys----Arg substitution~~ at ~~four distinct locations, residues 253, 309, 319, and 323~~. ~~Molecular model building analysis of the structures of wild-type and mutant CuZnSOD (K9R) and GAPDH (G281K and G281R~~) is ~~used to explain~~ the observed stability enhancement in these proteins. In addition to demonstrating that even thermostable proteins can lend themselves to further stability improvement, our findings provide direct evidence that arginine residues are important stabilizing elements in proteins. Moreover, the stabilizing role of electrostatic interactions, particularly between subunits in oligomeric proteins, is documented.	+	The line below this paragraph, {{ABSTRACT_PUBMED_1540579}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 1540579 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_1540579}}

	==About this Structure==		==About this Structure==
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	[[Category: Vantilbeurgh, H.]]		[[Category: Vantilbeurgh, H.]]
	[[Category: Wodak, S J.]]		[[Category: Wodak, S J.]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:15:31 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 13:12:47 2008''

OCA at 19:15, 4 May 2008

OCA — Sun, 04 May 2008 19:15:32 GMT

←Older revision		Revision as of 19:15, 4 May 2008
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	[[Image:3xim.jpg\|left\|200px]]		[[Image:3xim.jpg\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 3xim \|SIZE=350\|CAPTION= <scene name='initialview01'>3xim</scene>~~, ~~resolution 2~~.~~3Å~~	+	The line below this paragraph, containing "STRUCTURE_3xim", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <~~scene ~~name='pdbligand=CO:COBALT+(II~~)~~+ION'>CO</scene>~~, ~~<scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene>~~	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	~~\|ACTIVITY= <span class='plainlinks'>[http://en~~.~~wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span~~>	+	or leave the SCENE parameter empty for the default display.
-	\|~~GENE~~=	+	-->
-	\|~~DOMAIN~~=	+	{{STRUCTURE_3xim\| PDB=3xim \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3xim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3xim OCA], [http://www.ebi.ac.uk/pdbsum/3xim PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3xim RCSB]</span>	+
-	}}	+

	'''ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS'''		'''ARGININE RESIDUES AS STABILIZING ELEMENTS IN PROTEINS'''
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	[[Category: Vantilbeurgh, H.]]		[[Category: Vantilbeurgh, H.]]
	[[Category: Wodak, S J.]]		[[Category: Wodak, S J.]]
-	~~[[Category: isomerase(intramolecular oxidoreductse)]]~~	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:15:31 2008''
-		+
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:36:40 2008''	+

OCA at 02:36, 31 March 2008

OCA — Mon, 31 Mar 2008 02:36:48 GMT

←Older revision		Revision as of 02:36, 31 March 2008
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	\|PDB= 3xim \|SIZE=350\|CAPTION= <scene name='initialview01'>3xim</scene>, resolution 2.3Å		\|PDB= 3xim \|SIZE=350\|CAPTION= <scene name='initialview01'>3xim</scene>, resolution 2.3Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=~~SOR~~:~~D-SORBITOL~~'>~~SOR~~</scene> ~~and~~ <scene name='pdbligand=CO:~~COBALT (II) ION~~'>CO</scene>	+	\|LIGAND= <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SOR:D-SORBITOL'>SOR</scene>
-	\|ACTIVITY= [http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5]	+	\|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span>
	\|GENE=		\|GENE=
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3xim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3xim OCA], [http://www.ebi.ac.uk/pdbsum/3xim PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3xim RCSB]</span>
	}}		}}

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	[[Category: Vantilbeurgh, H.]]		[[Category: Vantilbeurgh, H.]]
	[[Category: Wodak, S J.]]		[[Category: Wodak, S J.]]
-	[[Category: CO]]
-	[[Category: SOR]]
	[[Category: isomerase(intramolecular oxidoreductse)]]		[[Category: isomerase(intramolecular oxidoreductse)]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 19~~:07:48 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:36:40 2008''