5xck - Revision history

OCA at 07:59, 22 November 2023

OCA — Wed, 22 Nov 2023 07:59:37 GMT

←Older revision		Revision as of 07:59, 22 November 2023
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	==Crystal structure of Vps29 double mutant (D62A/H86A) from Entamoeba histolytica==		==Crystal structure of Vps29 double mutant (D62A/H86A) from Entamoeba histolytica==
-	<StructureSection load='5xck' size='340' side='right' caption='[[5xck]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5xck' size='340' side='right'caption='[[5xck]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xck]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Enthi Enthi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XCK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XCK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xck]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Entamoeba_histolytica Entamoeba histolytica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XCK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XCK FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5xce\|5xce]], [[5xch\|5xch]], [[5xcj\|5xcj]]</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]] 2.2Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">vsp, EhVPS29, CL6EHI_025270, EHI_025270 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=5759 ENTHI])~~</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=5xck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xck OCA], [https://pdbe.org/5xck PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xck RCSB], [https://www.ebi.ac.uk/pdbsum/5xck PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xck ProSAT]</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=5xck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xck OCA], [~~http~~://pdbe.org/5xck PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xck RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xck PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xck ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9BI08_ENTHI Q9BI08_ENTHI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5xck" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xck" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Vacuolar protein sorting-associated protein 3D structures\|Vacuolar protein sorting-associated protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Enthi]]
-	[[Category: Datta, S]]
-	[[Category: Gourinath, S]]
-	[[Category: Srivastava, V K]]
-	[[Category: Tomar, P]]
-	[[Category: Yadav, R]]
-	[[Category: Calcineurin-like phosphoesterase superfamily domain]]
	[[Category: Entamoeba histolytica]]		[[Category: Entamoeba histolytica]]
-	[[Category: ~~Metallophosphatase fold~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Protein transport~~]]	+	[[Category: Datta S]]
-	[[Category: ~~Vacuolar protein sorting 29~~]]	+	[[Category: Gourinath S]]
		+	[[Category: Srivastava VK]]
		+	[[Category: Tomar P]]
		+	[[Category: Yadav R]]

OCA at 07:54, 6 December 2017

OCA — Wed, 06 Dec 2017 07:54:07 GMT

←Older revision		Revision as of 07:54, 6 December 2017
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	<StructureSection load='5xck' size='340' side='right' caption='[[5xck]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5xck' size='340' side='right' caption='[[5xck]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xck]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XCK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XCK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xck]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enthi Enthi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XCK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XCK FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xce\|5xce]], [[5xch\|5xch]], [[5xcj\|5xcj]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xce\|5xce]], [[5xch\|5xch]], [[5xcj\|5xcj]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vsp, EhVPS29, CL6EHI_025270, EHI_025270 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5759 ENTHI])</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=5xck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xck OCA], [http://pdbe.org/5xck PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xck RCSB], [http://www.ebi.ac.uk/pdbsum/5xck PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xck ProSAT]</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=5xck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xck OCA], [http://pdbe.org/5xck PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xck RCSB], [http://www.ebi.ac.uk/pdbsum/5xck PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xck ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Enthi]]
	[[Category: Datta, S]]		[[Category: Datta, S]]
	[[Category: Gourinath, S]]		[[Category: Gourinath, S]]

OCA at 07:08, 18 October 2017

OCA — Wed, 18 Oct 2017 07:08:40 GMT

←Older revision		Revision as of 07:08, 18 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xck is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Vps29 double mutant (D62A/H86A) from Entamoeba histolytica==
		+	<StructureSection load='5xck' size='340' side='right' caption='[[5xck]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xck]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XCK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XCK FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xce\|5xce]], [[5xch\|5xch]], [[5xcj\|5xcj]]</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=5xck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xck OCA], [http://pdbe.org/5xck PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xck RCSB], [http://www.ebi.ac.uk/pdbsum/5xck PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xck ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Vps29 is the smallest subunit of retromer complex with metallo-phosphatase fold. Although the role of metal in Vps29 is in quest, its metal binding mutants has been reported to affect the localization of the retromer complex in human cells. In this study, we report the structural and thermodynamic consequences of these mutations in Vps29 from the protozoan parasite, Entamoeba histolytica (EhVps29). EhVps29 is a zinc binding protein as revealed by X-ray crystallography and isothermal titration calorimetry. The metal binding pocket of EhVps29 exhibits marked differences in its 3-dimensional architecture and metal coordination in comparison to its human homologs and other metallo-phosphatases. Alanine substitutions of the metal-coordinating residues showed significant alteration in the binding affinity of EhVps29 for zinc. We also determined the crystal structures of metal binding defective mutants (D62A and D62A/H86A) of EhVps29. Based on our results, we propose that the metal atoms or the bound water molecules in the metal binding site are important for maintaining the structural integrity of the protein. Further cellular studies in the amoebic trophozoites showed that the overexpression of wild type EhVps29 leads to reduction in intracellular cysteine protease activity suggesting its crucial role in secretion of the proteases. This article is protected by copyright. All rights reserved.

-	~~Authors~~: ~~Srivastava, V.K~~., ~~Yadav~~, R., ~~Tomar~~, P., ~~Gourinath~~, S., ~~Datta~~, S.	+	Structural and thermodynamic characterization of metal binding in Vps29 from Entamoeba histolytica: Implication in retromer function.,Srivastava VK, Yadav R, Natsuki W, Tomar P, Mukherjee M, Gourinath S, Nakada-Tsukui K, Nozaki T, Datta S Mol Microbiol. 2017 Sep 12. doi: 10.1111/mmi.13836. PMID:28898487<ref>PMID:28898487</ref>

-	~~Description: Crystal structure~~ of ~~Vps29 double mutant (D62A~~/~~H86A) from Entamoeba histolytica~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Tomar, P]]~~	+	<div class="pdbe-citations 5xck" style="background-color:#fffaf0;"></div>
-	~~[[Category: Srivastava, V.K]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Datta, S]]		[[Category: Datta, S]]
-	[[Category: Yadav, R]]
	[[Category: Gourinath, S]]		[[Category: Gourinath, S]]
		+	[[Category: Srivastava, V K]]
		+	[[Category: Tomar, P]]
		+	[[Category: Yadav, R]]
		+	[[Category: Calcineurin-like phosphoesterase superfamily domain]]
		+	[[Category: Entamoeba histolytica]]
		+	[[Category: Metallophosphatase fold]]
		+	[[Category: Protein transport]]
		+	[[Category: Vacuolar protein sorting 29]]

OCA at 15:24, 27 September 2017

OCA — Wed, 27 Sep 2017 15:24:00 GMT

←Older revision		Revision as of 15:24, 27 September 2017
Line 7:		Line 7:
	Description: Crystal structure of Vps29 double mutant (D62A/H86A) from Entamoeba histolytica		Description: Crystal structure of Vps29 double mutant (D62A/H86A) from Entamoeba histolytica
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Datta, S]]
	[[Category: Tomar, P]]		[[Category: Tomar, P]]
-	[[Category: Yadav, R]]
	[[Category: Srivastava, V.K]]		[[Category: Srivastava, V.K]]
		+	[[Category: Datta, S]]
		+	[[Category: Yadav, R]]
	[[Category: Gourinath, S]]		[[Category: Gourinath, S]]

OCA: Protected "5xck" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 12:29:31 GMT

Protected "5xck" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:29, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xck is ON HOLD until Paper Publication Authors: Srivastava, V.K., Yadav, R., Tomar, P., Gourinath, S., Datta, S. Description: Crystal structure of...

OCA — Wed, 05 Apr 2017 12:29:30 GMT

New page: '''Unreleased structure''' The entry 5xck is ON HOLD until Paper Publication Authors: Srivastava, V.K., Yadav, R., Tomar, P., Gourinath, S., Datta, S. Description: Crystal structure of...

New page

'''Unreleased structure'''

The entry 5xck is ON HOLD until Paper Publication

Authors: Srivastava, V.K., Yadav, R., Tomar, P., Gourinath, S., Datta, S.

Description: Crystal structure of Vps29 double mutant (D62A/H86A) from Entamoeba histolytica
[[Category: Unreleased Structures]]
[[Category: Datta, S]]
[[Category: Tomar, P]]
[[Category: Yadav, R]]
[[Category: Srivastava, V.K]]
[[Category: Gourinath, S]]