5z5a - Revision history

OCA at 08:45, 22 November 2023

OCA — Wed, 22 Nov 2023 08:45:39 GMT

←Older revision		Revision as of 08:45, 22 November 2023
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	<StructureSection load='5z5a' size='340' side='right'caption='[[5z5a]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5z5a' size='340' side='right'caption='[[5z5a]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z5a]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Z5A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z5a]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z5A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VN3:VANADATE+ION'>VN3</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]] 1.8Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5z5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5a OCA], [~~http~~://pdbe.org/5z5a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z5a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z5a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5a ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VN3:VANADATE+ION'>VN3</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=5z5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5a OCA], [https://pdbe.org/5z5a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z5a RCSB], [https://www.ebi.ac.uk/pdbsum/5z5a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5a ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8X270_THEKO Q8X270_THEKO]
	<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: ~~Kim, S J~~]]	+	[[Category: Thermococcus kodakarensis KOD1]]
-	[[Category: ~~Ku, B~~]]	+	[[Category: Kim SJ]]
-	[[Category: ~~Yun, H Y~~]]	+	[[Category: Ku B]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Yun HY]]
-	~~[[Category: Tyrosine phosphatase~~]]	+

OCA at 21:14, 28 October 2020

OCA — Wed, 28 Oct 2020 21:14:26 GMT

←Older revision		Revision as of 21:14, 28 October 2020
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	==Crystal structure of Tk-PTP in the active form==		==Crystal structure of Tk-PTP in the active form==
-	<StructureSection load='5z5a' size='340' side='right' caption='[[5z5a]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5z5a' size='340' side='right'caption='[[5z5a]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z5a]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5A OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z5A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z5a]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Z5A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VN3:VANADATE+ION'>VN3</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VN3:VANADATE+ION'>VN3</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=5z5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5a OCA], [http://pdbe.org/5z5a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z5a RCSB], [http://www.ebi.ac.uk/pdbsum/5z5a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5a ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5z5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5a OCA], [http://pdbe.org/5z5a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z5a RCSB], [http://www.ebi.ac.uk/pdbsum/5z5a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5a ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5z5a" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5z5a" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tyrosine phosphatase 3D structures\|Tyrosine phosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Kim, S J]]		[[Category: Kim, S J]]
	[[Category: Ku, B]]		[[Category: Ku, B]]

OCA at 07:09, 4 July 2018

OCA — Wed, 04 Jul 2018 07:09:52 GMT

←Older revision		Revision as of 07:09, 4 July 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5z5a is ~~ON HOLD~~	+	==Crystal structure of Tk-PTP in the active form==
		+	<StructureSection load='5z5a' size='340' side='right' caption='[[5z5a]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5z5a]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z5A FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=VN3:VANADATE+ION'>VN3</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=5z5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5a OCA], [http://pdbe.org/5z5a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z5a RCSB], [http://www.ebi.ac.uk/pdbsum/5z5a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5a ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein tyrosine phosphatases (PTPs) originating from eukaryotes or bacteria have been under intensive structural and biochemical investigation, whereas archaeal PTP proteins have not been investigated extensively; therefore, they are poorly understood. Here, we present the crystal structures of Tk-PTP derived from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1, in both the active and inactive forms. Tk-PTP adopts a common dual-specificity phosphatase (DUSP) fold, but it undergoes an atypical temperature-dependent conformational change in its P-loop and alpha4-alpha5 loop regions, switching between the inactive and active forms. Through comprehensive analyses of Tk-PTP, including additional structural determination of the G95A mutant form, enzymatic activity assays, and structural comparison with the other archaeal PTP, it was revealed that the presence of the GG motif in the P-loop is necessary but not sufficient for the structural flexibility of Tk-PTP. It was also proven that Tk-PTP contains dual general acid/base residues unlike most of the other DUSP proteins, and that both the residues are critical in its phosphatase activity. This work provides the basis for expanding our understanding of the previously uncharacterized PTP proteins from archaea, the third domain of living organisms.

-	~~Authors~~:	+	Structural study reveals the temperature-dependent conformational flexibility of Tk-PTP, a protein tyrosine phosphatase from Thermococcus kodakaraensis KOD1.,Yun HY, Lee J, Kim H, Ryu H, Shin HC, Oh BH, Ku B, Kim SJ PLoS One. 2018 May 23;13(5):e0197635. doi: 10.1371/journal.pone.0197635., eCollection 2018. PMID:29791483<ref>PMID:29791483</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5z5a" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kim, S J]]
		+	[[Category: Ku, B]]
		+	[[Category: Yun, H Y]]
		+	[[Category: Hydrolase]]
		+	[[Category: Tyrosine phosphatase]]

OCA: Protected "5z5a" [edit=sysop:move=sysop]

OCA — Wed, 24 Jan 2018 17:12:13 GMT

Protected "5z5a" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:12, 24 January 2018

OCA: New page: '''Unreleased structure''' The entry 5z5a is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 24 Jan 2018 17:12:12 GMT

New page: '''Unreleased structure''' The entry 5z5a is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5z5a is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]