4ge0 - Revision history

OCA at 15:44, 14 March 2024

OCA — Thu, 14 Mar 2024 15:44:21 GMT

←Older revision		Revision as of 15:44, 14 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ge0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GE0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GE0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ge0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GE0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GE0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.45Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=4ge0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ge0 OCA], [https://pdbe.org/4ge0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ge0 RCSB], [https://www.ebi.ac.uk/pdbsum/4ge0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ge0 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=4ge0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ge0 OCA], [https://pdbe.org/4ge0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ge0 RCSB], [https://www.ebi.ac.uk/pdbsum/4ge0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ge0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/DJ1_SCHPO DJ1_SCHPO]		[https://www.uniprot.org/uniprot/DJ1_SCHPO DJ1_SCHPO]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Cysteine residues with depressed pK(a) values are critical for the functions of many proteins. Several types of interactions can stabilize cysteine thiolate anions, including hydrogen bonds between thiol(ate)s and nearby residues as well as electrostatic interactions involving charged residues or dipoles. Dipolar stabilization of thiolates by peptide groups has been suggested to play a particularly important role near the N-termini of alpha-helices. Using a combination of X-ray crystallography, site-directed mutagenesis, and spectroscopic methods, we show that the reactive cysteine residue (Cys111) in Schizosaccharomyces pombe DJ-1 experiences a 0.6 unit depression of its thiol pK(a) as a consequence of a hydrogen bond donated by a threonine sidechain (Thr114) to a nearby peptide carbonyl oxygen at the N-terminus of an alpha-helix. This extended hydrogen bonded interaction is consistent with a sum of dipoles model whereby the distal hydrogen bond polarizes and strengthens the direct hydrogen bond between the proximal amide hydrogen and the cysteine thiol(ate). Therefore, our results suggest that the local dipolar enhancement of hydrogen bonds can appreciably stabilize cysteine thiolate formation. However, the substitution of a valine residue with a proline at the i+3 position has only a minor effect (0.3 units) on the pK(a) of Cys111. As proline has a reduced peptide dipole moment, this small effect suggests that a more extended helix macrodipolar effect does not play a major role in this system. (c) 2012 The Authors Journal compilation (c) 2012 FEBS.
-
-	Influence of Peptide Dipoles and Hydrogen Bonds on Reactive Cysteine pK(a) Values in Fission Yeast DJ-1.,Madzelan P, Labunksa T, Wilson MA FEBS J. 2012 Sep 12. doi: 10.1111/febs.12004. PMID:22971103<ref>PMID:22971103</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4ge0" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:52, 26 October 2022

OCA — Wed, 26 Oct 2022 06:52:51 GMT

←Older revision		Revision as of 06:52, 26 October 2022
Line 1:		Line 1:

	==Schizosaccharomyces pombe DJ-1 T114P mutant==		==Schizosaccharomyces pombe DJ-1 T114P mutant==
-	<StructureSection load='4ge0' size='340' side='right' caption='[[4ge0]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='4ge0' size='340' side='right'caption='[[4ge0]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ge0]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cbs_356 Cbs 356~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GE0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4GE0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ge0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GE0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GE0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~EDO~~:~~1,2~~-~~ETHANEDIOL~~'>~~EDO~~</scene>, <scene name='pdbligand=MG:~~MAGNESIUM+ION~~'>MG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~CSD~~:~~3-SULFINOALANINE~~'>~~CSD~~</scene>~~</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=4ge0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ge0 OCA], [https://pdbe.org/4ge0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ge0 RCSB], [https://www.ebi.ac.uk/pdbsum/4ge0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ge0 ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gdh\|4gdh]], [[4ge3\|4ge3]]</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPAC22E12.03c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])~~</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=4ge0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ge0 OCA], [~~http~~://pdbe.org/4ge0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ge0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ge0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ge0 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DJ1_SCHPO DJ1_SCHPO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cbs 356~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Labunska, T~~]]	+	[[Category: Schizosaccharomyces pombe]]
-	[[Category: ~~Madzelan, P~~]]	+	[[Category: Labunska T]]
-	[[Category: ~~Wilson, M A~~]]	+	[[Category: Madzelan P]]
-	[[Category: ~~Cysteine-sulfinic acid]]~~	+	[[Category: Wilson MA]]
-	~~[[Category: Dj-1/pfpi family]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 18:58, 4 August 2016

OCA — Thu, 04 Aug 2016 18:58:54 GMT

←Older revision		Revision as of 18:58, 4 August 2016
Line 1:		Line 1:
		+
	==Schizosaccharomyces pombe DJ-1 T114P mutant==		==Schizosaccharomyces pombe DJ-1 T114P mutant==
	<StructureSection load='4ge0' size='340' side='right' caption='[[4ge0]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='4ge0' size='340' side='right' caption='[[4ge0]], [[Resolution\|resolution]] 1.45Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gdh\|4gdh]], [[4ge3\|4ge3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gdh\|4gdh]], [[4ge3\|4ge3]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPAC22E12.03c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPAC22E12.03c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</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=4ge0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ge0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ge0 RCSB], [http://www.ebi.ac.uk/pdbsum/4ge0 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=4ge0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ge0 OCA], [http://pdbe.org/4ge0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ge0 RCSB], [http://www.ebi.ac.uk/pdbsum/4ge0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ge0 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 4ge0" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:51, 19 November 2014

OCA — Wed, 19 Nov 2014 10:51:10 GMT

←Older revision		Revision as of 10:51, 19 November 2014
Line 1:		Line 1:
-	[[~~Image:~~4ge0.~~png~~\|~~left~~\|~~200px~~]]	+	==Schizosaccharomyces pombe DJ-1 T114P mutant==
		+	<StructureSection load='4ge0' size='340' side='right' caption='[[4ge0]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ge0]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GE0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GE0 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gdh\|4gdh]], [[4ge3\|4ge3]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPAC22E12.03c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</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=4ge0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ge0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ge0 RCSB], [http://www.ebi.ac.uk/pdbsum/4ge0 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cysteine residues with depressed pK(a) values are critical for the functions of many proteins. Several types of interactions can stabilize cysteine thiolate anions, including hydrogen bonds between thiol(ate)s and nearby residues as well as electrostatic interactions involving charged residues or dipoles. Dipolar stabilization of thiolates by peptide groups has been suggested to play a particularly important role near the N-termini of alpha-helices. Using a combination of X-ray crystallography, site-directed mutagenesis, and spectroscopic methods, we show that the reactive cysteine residue (Cys111) in Schizosaccharomyces pombe DJ-1 experiences a 0.6 unit depression of its thiol pK(a) as a consequence of a hydrogen bond donated by a threonine sidechain (Thr114) to a nearby peptide carbonyl oxygen at the N-terminus of an alpha-helix. This extended hydrogen bonded interaction is consistent with a sum of dipoles model whereby the distal hydrogen bond polarizes and strengthens the direct hydrogen bond between the proximal amide hydrogen and the cysteine thiol(ate). Therefore, our results suggest that the local dipolar enhancement of hydrogen bonds can appreciably stabilize cysteine thiolate formation. However, the substitution of a valine residue with a proline at the i+3 position has only a minor effect (0.3 units) on the pK(a) of Cys111. As proline has a reduced peptide dipole moment, this small effect suggests that a more extended helix macrodipolar effect does not play a major role in this system. (c) 2012 The Authors Journal compilation (c) 2012 FEBS.

-	~~{{STRUCTURE_4ge0\| PDB=4ge0 \| SCENE= }}~~	+	Influence of Peptide Dipoles and Hydrogen Bonds on Reactive Cysteine pK(a) Values in Fission Yeast DJ-1.,Madzelan P, Labunksa T, Wilson MA FEBS J. 2012 Sep 12. doi: 10.1111/febs.12004. PMID:22971103<ref>PMID:22971103</ref>

-	~~===Schizosaccharomyces pombe DJ-1 T114P mutant===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22971103}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[4ge0]] is a 4 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GE0 OCA].~~	+	</StructureSection>
-	[[Category: ~~Schizosaccharomyces pombe~~]]	+	[[Category: Cbs 356]]
-	[[Category: Labunska, T.]]	+	[[Category: Labunska, T]]
-	[[Category: Madzelan, P.]]	+	[[Category: Madzelan, P]]
-	[[Category: Wilson, M A.]]	+	[[Category: Wilson, M A]]
	[[Category: Cysteine-sulfinic acid]]		[[Category: Cysteine-sulfinic acid]]
	[[Category: Dj-1/pfpi family]]		[[Category: Dj-1/pfpi family]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 20:41, 26 September 2012

OCA — Wed, 26 Sep 2012 20:41:05 GMT

←Older revision		Revision as of 20:41, 26 September 2012
Line 1:		Line 1:
-	[[Image:4ge0.~~jpg~~\|left\|200px]]	+	[[Image:4ge0.png\|left\|200px]]

	{{STRUCTURE_4ge0\| PDB=4ge0 \| SCENE= }}		{{STRUCTURE_4ge0\| PDB=4ge0 \| SCENE= }}
Line 5:		Line 5:
	===Schizosaccharomyces pombe DJ-1 T114P mutant===		===Schizosaccharomyces pombe DJ-1 T114P mutant===

		+	{{ABSTRACT_PUBMED_22971103}}

	==About this Structure==		==About this Structure==

OCA at 05:55, 15 August 2012

OCA — Wed, 15 Aug 2012 05:55:57 GMT

←Older revision		Revision as of 05:55, 15 August 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4ge0.jpg\|left\|200px]]

-	~~The entry~~ 4ge0 ~~is ON HOLD~~	+	{{STRUCTURE_4ge0\| PDB=4ge0 \| SCENE= }}

-	~~Authors: Madzelan, P., Labunska, T., Wilson, M.A.~~	+	===Schizosaccharomyces pombe DJ-1 T114P mutant===

-	~~Description~~: Schizosaccharomyces pombe DJ-1 ~~T114P mutant~~	+
		+	==About this Structure==
		+	[[4ge0]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GE0 OCA].
		+	[[Category: Schizosaccharomyces pombe]]
		+	[[Category: Labunska, T.]]
		+	[[Category: Madzelan, P.]]
		+	[[Category: Wilson, M A.]]
		+	[[Category: Cysteine-sulfinic acid]]
		+	[[Category: Dj-1/pfpi family]]
		+	[[Category: Unknown function]]

OCA: Protected "4ge0" [edit=sysop:move=sysop]

OCA — Wed, 08 Aug 2012 05:01:55 GMT

Protected "4ge0" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:01, 8 August 2012

OCA: New page: '''Unreleased structure''' The entry 4ge0 is ON HOLD Authors: Madzelan, P., Labunska, T., Wilson, M.A. Description: Schizosaccharomyces pombe DJ-1 T114P mutant

OCA — Wed, 08 Aug 2012 05:01:54 GMT

New page: '''Unreleased structure''' The entry 4ge0 is ON HOLD Authors: Madzelan, P., Labunska, T., Wilson, M.A. Description: Schizosaccharomyces pombe DJ-1 T114P mutant

New page

'''Unreleased structure'''

The entry 4ge0 is ON HOLD

Authors: Madzelan, P., Labunska, T., Wilson, M.A.

Description: Schizosaccharomyces pombe DJ-1 T114P mutant