6dr7 - Revision history

OCA at 06:12, 11 October 2023

2023-10-11T06:12:59Z

←Older revision		Revision as of 06:12, 11 October 2023
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	<StructureSection load='6dr7' size='340' side='right'caption='[[6dr7]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6dr7' size='340' side='right'caption='[[6dr7]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dr7]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus~~ pestis~~" (lehmann and neumann 1896) migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DR7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DR7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dr7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DR7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DR7 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ACT:ACETATE+ION'>ACT</scene~~>, ~~<scene name='pdbligand=VO4:VANADATE+ION'>VO4</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]] 1.849Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6dr1\|6dr1]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">yopH, YPCD1.67c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])~~</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=6dr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dr7 OCA], [https://pdbe.org/6dr7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dr7 RCSB], [https://www.ebi.ac.uk/pdbsum/6dr7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dr7 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=6dr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dr7 OCA], [~~http~~://pdbe.org/6dr7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dr7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dr7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dr7 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O68720_YERPE O68720_YERPE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Hengge, A C~~]]	+	[[Category: Yersinia pestis]]
-	[[Category: ~~Johnson, S J~~]]	+	[[Category: Hengge AC]]
-	[[Category: ~~Moise, G~~]]	+	[[Category: Johnson SJ]]
-	[[Category: ~~Morales, Y~~]]	+	[[Category: Moise G]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Morales Y]]
-	~~[[Category: Phosphatase]]~~	+
-	~~[[Category: Ptp]]~~	+
-	~~[[Category: Ptpase]]~~	+
-	~~[[Category: Yoph~~]]	+

OCA at 08:34, 27 November 2019

2019-11-27T08:34:07Z

←Older revision		Revision as of 08:34, 27 November 2019
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	==YopH PTP1B WPD loop Chimera 2 PTPase bound to vanadate==		==YopH PTP1B WPD loop Chimera 2 PTPase bound to vanadate==
-	<StructureSection load='6dr7' size='340' side='right' caption='[[6dr7]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='6dr7' size='340' side='right'caption='[[6dr7]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dr7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DR7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DR7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dr7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DR7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DR7 FirstGlance]. <br>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Hengge, A C]]		[[Category: Hengge, A C]]
	[[Category: Johnson, S J]]		[[Category: Johnson, S J]]

OCA at 10:29, 5 September 2018

2018-09-05T10:29:26Z

←Older revision		Revision as of 10:29, 5 September 2018
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	<StructureSection load='6dr7' size='340' side='right' caption='[[6dr7]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6dr7' size='340' side='right' caption='[[6dr7]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dr7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DR7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DR7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dr7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pestis"_(lehmann_and_neumann_1896)_migula_1900 "bacillus pestis" (lehmann and neumann 1896) migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DR7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DR7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dr1\|6dr1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dr1\|6dr1]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yopH, YPCD1.67c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632 "Bacillus pestis" (Lehmann and Neumann 1896) Migula 1900])</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=6dr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dr7 OCA], [http://pdbe.org/6dr7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dr7 RCSB], [http://www.ebi.ac.uk/pdbsum/6dr7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dr7 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=6dr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dr7 OCA], [http://pdbe.org/6dr7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dr7 RCSB], [http://www.ebi.ac.uk/pdbsum/6dr7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dr7 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:28, 29 August 2018

2018-08-29T07:28:01Z

←Older revision		Revision as of 07:28, 29 August 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6dr7 is ~~ON HOLD until Paper~~ Publication	+	==YopH PTP1B WPD loop Chimera 2 PTPase bound to vanadate==
		+	<StructureSection load='6dr7' size='340' side='right' caption='[[6dr7]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dr7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DR7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DR7 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6dr1\|6dr1]]</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=6dr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dr7 OCA], [http://pdbe.org/6dr7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dr7 RCSB], [http://www.ebi.ac.uk/pdbsum/6dr7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dr7 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	To study factors that affect WPD-loop motion in protein tyrosine phosphatases (PTPs), a chimera of PTP1B and YopH was created by transposing the WPD loop from PTP1B to YopH. Several subsequent mutations proved to be necessary to obtain a soluble, active enzyme. That chimera, termed chimera 3, retains productive WPD-loop motions and general acid catalysis with a pH dependency similar to that of the native enzymes. Kinetic isotope effects show the mechanism and transition state for phosphoryl transfer are unaltered. Catalysis of the chimera is slower than that of either of its parent enzymes, although its rate is comparable to those of most native PTPs. X-ray crystallography and nuclear magnetic resonance were used to probe the structure and dynamics of chimera 3. The chimera's structure was found to sample an unproductive hyper-open conformation of its WPD loop, a geometry that has not been observed in either of the parents or in other native PTPs. The reduced catalytic rate is attributed to the protein's sampling of this conformation in solution, reducing the fraction in the catalytically productive loop-closed conformation.

-	~~Authors: Moise~~, G., ~~Morales~~, Y., Johnson, S.J.~~, Hengge, A~~.C.	+	A YopH PTP1B Chimera Shows the Importance of the WPD-Loop Sequence to the Activity, Structure, and Dynamics of Protein Tyrosine Phosphatases.,Moise G, Morales Y, Beaumont V, Caradonna T, Loria JP, Johnson SJ, Hengge AC Biochemistry. 2018 Aug 28. doi: 10.1021/acs.biochem.8b00663. PMID:30110154<ref>PMID:30110154</ref>

-	~~Description: YopH PTP1B WPD loop Chimera 2 PTPase bound to vanadate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Morales~~, Y]]	+	<div class="pdbe-citations 6dr7" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Hengge~~, ~~A.C~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hengge, A C]]
		+	[[Category: Johnson, S J]]
	[[Category: Moise, G]]		[[Category: Moise, G]]
-	[[Category: ~~Johnson~~, ~~S.J~~]]	+	[[Category: Morales, Y]]
		+	[[Category: Hydrolase]]
		+	[[Category: Phosphatase]]
		+	[[Category: Ptp]]
		+	[[Category: Ptpase]]
		+	[[Category: Yoph]]

OCA at 04:01, 27 June 2018

2018-06-27T04:01:04Z

←Older revision		Revision as of 04:01, 27 June 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6dr7 is ON HOLD	+	The entry 6dr7 is ON HOLD until Paper Publication

	Authors: Moise, G., Morales, Y., Johnson, S.J., Hengge, A.C.		Authors: Moise, G., Morales, Y., Johnson, S.J., Hengge, A.C.

OCA: Protected "6dr7" [edit=sysop:move=sysop]

2018-06-20T04:11:24Z

Protected "6dr7" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:11, 20 June 2018

OCA: New page: '''Unreleased structure''' The entry 6dr7 is ON HOLD Authors: Moise, G., Morales, Y., Johnson, S.J., Hengge, A.C. Description: YopH PTP1B WPD loop Chimera 2 PTPase bound to vanadate [[...

2018-06-20T04:11:23Z

New page: '''Unreleased structure''' The entry 6dr7 is ON HOLD Authors: Moise, G., Morales, Y., Johnson, S.J., Hengge, A.C. Description: YopH PTP1B WPD loop Chimera 2 PTPase bound to vanadate [[...

New page

'''Unreleased structure'''

The entry 6dr7 is ON HOLD

Authors: Moise, G., Morales, Y., Johnson, S.J., Hengge, A.C.

Description: YopH PTP1B WPD loop Chimera 2 PTPase bound to vanadate
[[Category: Unreleased Structures]]
[[Category: Morales, Y]]
[[Category: Hengge, A.C]]
[[Category: Moise, G]]
[[Category: Johnson, S.J]]