1ilb - Revision history

OCA at 11:01, 4 August 2021

OCA — Wed, 04 Aug 2021 11:01:55 GMT

←Older revision		Revision as of 11:01, 4 August 2021
Line 4:		Line 4:
	<StructureSection load='1ilb' size='340' side='right'caption='[[1ilb]]' scene=''>		<StructureSection load='1ilb' size='340' side='right'caption='[[1ilb]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ILB FirstGlance]. <br>	+	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ILB 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=1ilb FirstGlance], [~~http~~://www.ebi.ac.uk/pdbsum/1ilb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ilb 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=1ilb FirstGlance], [https://www.ebi.ac.uk/pdbsum/1ilb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ilb ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:56, 30 October 2019

OCA — Wed, 30 Oct 2019 09:56:55 GMT

←Older revision		Revision as of 09:56, 30 October 2019
Line 2:		Line 2:

	==THEORETICAL MODEL OF REDUCED E. COLI GLUTAREDOXIN 3==		==THEORETICAL MODEL OF REDUCED E. COLI GLUTAREDOXIN 3==
-	<StructureSection load='1ilb' size='340' side='right' caption='[[1ilb]]' scene=''>	+	<StructureSection load='1ilb' size='340' side='right'caption='[[1ilb]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ILB FirstGlance]. <br>		<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ILB FirstGlance]. <br>
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Theoretical Model]]		[[Category: Theoretical Model]]
		+	[[Category: Large Structures]]
	[[Category: Berndt, K D]]		[[Category: Berndt, K D]]
	[[Category: Foloppe, N]]		[[Category: Foloppe, N]]

OCA at 08:56, 10 January 2018

OCA — Wed, 10 Jan 2018 08:56:52 GMT

←Older revision		Revision as of 08:56, 10 January 2018
Line 5:		Line 5:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ILB FirstGlance]. <br>		<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ILB 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=1ilb FirstGlance], [http://www.ebi.ac.uk/pdbsum/1ilb 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=1ilb FirstGlance], [http://www.ebi.ac.uk/pdbsum/1ilb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ilb ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:03, 11 February 2016

OCA — Thu, 11 Feb 2016 09:03:18 GMT

←Older revision		Revision as of 09:03, 11 February 2016
Line 1:		Line 1:
		+	{{Theoretical_model}}
		+
	==THEORETICAL MODEL OF REDUCED E. COLI GLUTAREDOXIN 3==		==THEORETICAL MODEL OF REDUCED E. COLI GLUTAREDOXIN 3==
	<StructureSection load='1ilb' size='340' side='right' caption='[[1ilb]]' scene=''>		<StructureSection load='1ilb' size='340' side='right' caption='[[1ilb]]' scene=''>
Line 18:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Theoretical Model]]
	[[Category: Berndt, K D]]		[[Category: Berndt, K D]]
	[[Category: Foloppe, N]]		[[Category: Foloppe, N]]

OCA at 12:44, 11 September 2015

OCA — Fri, 11 Sep 2015 12:44:58 GMT

←Older revision		Revision as of 12:44, 11 September 2015
Line 13:		Line 13:
	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 1ilb" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:34, 2 January 2015

OCA — Fri, 02 Jan 2015 09:34:13 GMT

←Older revision		Revision as of 09:34, 2 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ILB FirstGlance]. <br>		<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ILB 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=1ilb FirstGlance], [http://www.ebi.ac.uk/pdbsum/1ilb 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=1ilb FirstGlance], [http://www.ebi.ac.uk/pdbsum/1ilb PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:51, 28 September 2014

OCA — Sun, 28 Sep 2014 10:51:59 GMT

←Older revision		Revision as of 10:51, 28 September 2014
Line 1:		Line 1:
-	~~{{Theoretical_model}}~~	+	==THEORETICAL MODEL OF REDUCED E. COLI GLUTAREDOXIN 3==
		+	<StructureSection load='1ilb' size='340' side='right' caption='[[1ilb]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ILB 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=1ilb FirstGlance], [http://www.ebi.ac.uk/pdbsum/1ilb PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The chemistry of active-site cysteine residues is central to the activity of thiol-disulfide oxidoreductases of the thioredoxin superfamily. In these reactions, a nucleophilic thiolate is required, but the associated pK(a) values differ vastly in the superfamily, from less than 4 in DsbA to greater than 7 in Trx. The factors that stabilize this thiolate are, however, not clearly established. The glutaredoxins (Grxs), which are members of this superfamily, contain a Cys-Pro-Tyr-Cys motif in their active site. In reduced Grxs, the pK(a) of the N-terminal active-site nucleophilic cysteine residue is lowered significantly, and the stabilization of the corresponding thiolate is expected to influence the redox potential of these enzymes. Here, we use a combination of long molecular dynamics (MD) simulations, pK(a) calculations, and experimental investigations to derive the structure and dynamics of the reduced active site from Escherichia coli Grx3, and investigate the factors that stabilize the thiolate. Several different MD simulations converged toward a consensus conformation for the active-site cysteine residues (Cys11 and Cys14), after a number of local conformational changes. Key features of the model were tested experimentally by measurement of NMR scalar coupling constants, and determination of pK(a) values of selected residues. The pK(a) values of the Grx3 active-site residues were calculated during the MD simulations, and support the underlying structural model. The structure of Grx3, in combination with the pK(a) calculations, indicate that the pK(a) of the N-terminal active-site cysteine residue in Grx3 is intermediate between that of its counterpart in DsbA and Trx. The pK(a) values in best agreement with experiment are obtained with a low (<4) protein dielectric constant. The calculated pK(a) values fluctuate significantly in response to protein dynamics, which underscores the importance of the details of the underlying structures when calculating pK(a) values. The thiolate of Cys11 is stabilized primarily by direct hydrogen bonding with the amide protons of Tyr13 and Cys14 and the thiol proton of Cys14, rather than by long-range interactions from charged groups or from a helix macrodipole. From the comparison of reduced Grx3 with other members of the thioredoxin superfamily, a unifying theme for the structural basis of thiol pK(a) differences in this superfamily begins to emerge.

-	~~[[Image~~:~~1ilb~~.~~png\|left\|200px]]~~	+	Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli: comparison with functionally related proteins.,Foloppe N, Sagemark J, Nordstrand K, Berndt KD, Nilsson L J Mol Biol. 2001 Jul 6;310(2):449-70. PMID:11428900<ref>PMID:11428900</ref>

-	~~{{STRUCTURE_1ilb\| PDB=1ilb \| SCENE= }}~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~===THEORETICAL MODEL OF REDUCED E~~. ~~COLI GLUTAREDOXIN 3===~~	+	== References ==
-		+	<references/>
-	~~{{ABSTRACT_PUBMED_11428900}}~~	+	__TOC__
-		+	</StructureSection>
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011428900<~~/~~ref~~><~~ref group="xtra">PMID:014636602</ref><references group="xtra"~~/>	+
	[[Category: Berndt, K D]]		[[Category: Berndt, K D]]
	[[Category: Foloppe, N]]		[[Category: Foloppe, N]]

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

OCA — Sun, 21 Oct 2012 09:30:29 GMT

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

←Older revision

Revision as of 09:30, 21 October 2012

OCA at 09:30, 21 October 2012

OCA — Sun, 21 Oct 2012 09:30:26 GMT

←Older revision		Revision as of 09:30, 21 October 2012
Line 1:		Line 1:
	{{Theoretical_model}}		{{Theoretical_model}}
-	~~{{Seed}}~~	+
	[[Image:1ilb.png\|left\|200px]]		[[Image:1ilb.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1ilb", 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_1ilb\| PDB=1ilb \| SCENE= }}		{{STRUCTURE_1ilb\| PDB=1ilb \| SCENE= }}

	===THEORETICAL MODEL OF REDUCED E. COLI GLUTAREDOXIN 3===		===THEORETICAL MODEL OF REDUCED E. COLI GLUTAREDOXIN 3===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11428900}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11428900 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11428900}}		{{ABSTRACT_PUBMED_11428900}}
-
-	==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ILB OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11428900~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011428900</ref><ref group="xtra">PMID:014636602</ref><references group="xtra"/>
	[[Category: Berndt, K D]]		[[Category: Berndt, K D]]
	[[Category: Foloppe, N]]		[[Category: Foloppe, N]]
Line 30:		Line 16:
	[[Category: Nordstrand, K]]		[[Category: Nordstrand, K]]
	[[Category: Sagemark, J]]		[[Category: Sagemark, J]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 8 08:26:57 2010''

OCA at 05:26, 8 April 2010

OCA — Thu, 08 Apr 2010 05:26:58 GMT

←Older revision		Revision as of 05:26, 8 April 2010
Line 1:		Line 1:
-	~~'''Theoretical Model'''~~	+	{{Theoretical_model}}
		+	{{Seed}}
		+	[[Image:1ilb.png\|left\|200px]]

-	The ~~entry 1ILB is a Theoretical Model titled 'Theoretical Model of Reduced E~~. ~~Coli Glutaredoxin 3'~~.	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_1ilb", 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_1ilb\| PDB=1ilb \| SCENE= }}

-	~~[[Category:Theoretical Model]]~~	+	===THEORETICAL MODEL OF REDUCED E. COLI GLUTAREDOXIN 3===


-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 30 09~~:50:~~09 2008~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_11428900}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 11428900 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_11428900}}
		+
		+	==About this Structure==
		+	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ILB OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:11428900</ref><references group="xtra"/>
		+	[[Category: Berndt, K D]]
		+	[[Category: Foloppe, N]]
		+	[[Category: Nilsson, L]]
		+	[[Category: Nordstrand, K]]
		+	[[Category: Sagemark, J]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 8 08:26:57 2010''