7mov - Revision history

OCA at 16:17, 18 October 2023

OCA — Wed, 18 Oct 2023 16:17:26 GMT

←Older revision		Revision as of 16:17, 18 October 2023
Line 1:		Line 1:

	==PTP1B 1-301 F225Y-R199N mutations==		==PTP1B 1-301 F225Y-R199N mutations==
-	<StructureSection load='7mov' size='340' side='right'caption='[[7mov]]' scene=''>	+	<StructureSection load='7mov' size='340' side='right'caption='[[7mov]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7mov]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOV FirstGlance]. <br>
-	</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=7mov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mov OCA], [https://pdbe.org/7mov PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mov RCSB], [https://www.ebi.ac.uk/pdbsum/7mov PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mov ProSAT]</span></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]] 1.65Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=7mov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mov OCA], [https://pdbe.org/7mov PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mov RCSB], [https://www.ebi.ac.uk/pdbsum/7mov PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mov ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PTN1_HUMAN PTN1_HUMAN] Tyrosine-protein phosphatase which acts as a regulator of endoplasmic reticulum unfolded protein response. Mediates dephosphorylation of EIF2AK3/PERK; inactivating the protein kinase activity of EIF2AK3/PERK. May play an important role in CKII- and p60c-src-induced signal transduction cascades. May regulate the EFNA5-EPHA3 signaling pathway which modulates cell reorganization and cell-cell repulsion.<ref>PMID:21135139</ref> <ref>PMID:22169477</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Homologous enzymes often exhibit different catalytic rates despite a fully conserved active site. The canonical view is that an enzyme sequence defines its structure and function and, more recently, that intrinsic protein dynamics at different time scales enable and/or promote catalytic activity. Here, we show that, using the protein tyrosine phosphatase PTP1B, residues surrounding the PTP1B active site promote dynamically coordinated chemistry necessary for PTP1B function. However, residues distant to the active site also undergo distinct intermediate time scale dynamics and these dynamics are correlated with its catalytic activity and thus allow for different catalytic rates in this enzyme family. We identify these previously undetected motions using coevolutionary coupling analysis and nuclear magnetic resonance spectroscopy. Our findings strongly indicate that conserved dynamics drives the enzymatic activity of the PTP family. Characterization of these conserved dynamics allows for the identification of novel regulatory elements (therapeutic binding pockets) that can be leveraged for the control of enzymes.
		+
		+	Conserved conformational dynamics determine enzyme activity.,Torgeson KR, Clarkson MW, Granata D, Lindorff-Larsen K, Page R, Peti W Sci Adv. 2022 Aug 5;8(31):eabo5546. doi: 10.1126/sciadv.abo5546. Epub 2022 Aug 3. PMID:35921420<ref>PMID:35921420</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7mov" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Page R]]		[[Category: Page R]]
	[[Category: Peti W]]		[[Category: Peti W]]
	[[Category: Torgeson KR]]		[[Category: Torgeson KR]]

OCA at 11:02, 31 August 2022

OCA — Wed, 31 Aug 2022 11:02:46 GMT

←Older revision		Revision as of 11:02, 31 August 2022
Line 1:		Line 1:

	==PTP1B 1-301 F225Y-R199N mutations==		==PTP1B 1-301 F225Y-R199N mutations==
-	<StructureSection load='7mov' size='340' side='right'caption='[[7mov]]~~, [[Resolution\|resolution]] 1.65Å~~' scene=''>	+	<StructureSection load='7mov' size='340' side='right'caption='[[7mov]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[7mov]] is a 2 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOV FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=7mov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mov OCA], [https://pdbe.org/7mov PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mov RCSB], [https://www.ebi.ac.uk/pdbsum/7mov PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mov ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </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=7mov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mov OCA], [https://pdbe.org/7mov PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mov RCSB], [https://www.ebi.ac.uk/pdbsum/7mov PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mov ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[https://www.uniprot.org/uniprot/PTN1_HUMAN PTN1_HUMAN]] Tyrosine-protein phosphatase which acts as a regulator of endoplasmic reticulum unfolded protein response. Mediates dephosphorylation of EIF2AK3/PERK; inactivating the protein kinase activity of EIF2AK3/PERK. May play an important role in CKII- and p60c-src-induced signal transduction cascades. May regulate the EFNA5-EPHA3 signaling pathway which modulates cell reorganization and cell-cell repulsion.<ref>PMID:21135139</ref> <ref>PMID:22169477</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Homologous enzymes often exhibit different catalytic rates despite a fully conserved active site. The canonical view is that an enzyme sequence defines its structure and function and, more recently, that intrinsic protein dynamics at different time scales enable and/or promote catalytic activity. Here, we show that, using the protein tyrosine phosphatase PTP1B, residues surrounding the PTP1B active site promote dynamically coordinated chemistry necessary for PTP1B function. However, residues distant to the active site also undergo distinct intermediate time scale dynamics and these dynamics are correlated with its catalytic activity and thus allow for different catalytic rates in this enzyme family. We identify these previously undetected motions using coevolutionary coupling analysis and nuclear magnetic resonance spectroscopy. Our findings strongly indicate that conserved dynamics drives the enzymatic activity of the PTP family. Characterization of these conserved dynamics allows for the identification of novel regulatory elements (therapeutic binding pockets) that can be leveraged for the control of enzymes.
-
-	Conserved conformational dynamics determine enzyme activity.,Torgeson KR, Clarkson MW, Granata D, Lindorff-Larsen K, Page R, Peti W Sci Adv. 2022 Aug 5;8(31):eabo5546. doi: 10.1126/sciadv.abo5546. Epub 2022 Aug 3. PMID:35921420<ref>PMID:35921420</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7mov" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Protein-tyrosine-phosphatase]]~~	+	[[Category: Page R]]
-	[[Category: Page, R]]	+	[[Category: Peti W]]
-	[[Category: Peti, W]]	+	[[Category: Torgeson KR]]
-	[[Category: Torgeson~~, K R]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protein tyrosine phosphatase~~]]	+

OCA at 05:10, 25 August 2022

OCA — Thu, 25 Aug 2022 05:10:57 GMT

←Older revision		Revision as of 05:10, 25 August 2022
Line 1:		Line 1:

	==PTP1B 1-301 F225Y-R199N mutations==		==PTP1B 1-301 F225Y-R199N mutations==
-	<StructureSection load='7mov' size='340' side='right'caption='[[7mov]]' scene=''>	+	<StructureSection load='7mov' size='340' side='right'caption='[[7mov]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7mov]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOV FirstGlance]. <br>
-	</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=7mov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mov OCA], [https://pdbe.org/7mov PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mov RCSB], [https://www.ebi.ac.uk/pdbsum/7mov PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mov ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </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=7mov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mov OCA], [https://pdbe.org/7mov PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mov RCSB], [https://www.ebi.ac.uk/pdbsum/7mov PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mov ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/PTN1_HUMAN PTN1_HUMAN]] Tyrosine-protein phosphatase which acts as a regulator of endoplasmic reticulum unfolded protein response. Mediates dephosphorylation of EIF2AK3/PERK; inactivating the protein kinase activity of EIF2AK3/PERK. May play an important role in CKII- and p60c-src-induced signal transduction cascades. May regulate the EFNA5-EPHA3 signaling pathway which modulates cell reorganization and cell-cell repulsion.<ref>PMID:21135139</ref> <ref>PMID:22169477</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Homologous enzymes often exhibit different catalytic rates despite a fully conserved active site. The canonical view is that an enzyme sequence defines its structure and function and, more recently, that intrinsic protein dynamics at different time scales enable and/or promote catalytic activity. Here, we show that, using the protein tyrosine phosphatase PTP1B, residues surrounding the PTP1B active site promote dynamically coordinated chemistry necessary for PTP1B function. However, residues distant to the active site also undergo distinct intermediate time scale dynamics and these dynamics are correlated with its catalytic activity and thus allow for different catalytic rates in this enzyme family. We identify these previously undetected motions using coevolutionary coupling analysis and nuclear magnetic resonance spectroscopy. Our findings strongly indicate that conserved dynamics drives the enzymatic activity of the PTP family. Characterization of these conserved dynamics allows for the identification of novel regulatory elements (therapeutic binding pockets) that can be leveraged for the control of enzymes.
		+
		+	Conserved conformational dynamics determine enzyme activity.,Torgeson KR, Clarkson MW, Granata D, Lindorff-Larsen K, Page R, Peti W Sci Adv. 2022 Aug 5;8(31):eabo5546. doi: 10.1126/sciadv.abo5546. Epub 2022 Aug 3. PMID:35921420<ref>PMID:35921420</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7mov" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Page R]]	+	[[Category: Protein-tyrosine-phosphatase]]
-	[[Category: Peti W]]	+	[[Category: Page, R]]
-	[[Category: Torgeson KR]]	+	[[Category: Peti, W]]
		+	[[Category: Torgeson, K R]]
		+	[[Category: Hydrolase]]
		+	[[Category: Protein tyrosine phosphatase]]

OCA at 10:14, 18 May 2022

OCA — Wed, 18 May 2022 10:14:52 GMT

←Older revision		Revision as of 10:14, 18 May 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7mov ~~is ON HOLD until Paper Publication~~	+	==PTP1B 1-301 F225Y-R199N mutations==
-		+	<StructureSection load='7mov' size='340' side='right'caption='[[7mov]]' scene=''>
-	~~Authors~~: ~~Torgeson~~, K.R., ~~Page~~, R., ~~Peti~~, W.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOV FirstGlance]. <br>
-	~~Description: PTP1B 1-301 F225Y-R199N mutations~~	+	</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=7mov FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mov OCA], [https://pdbe.org/7mov PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mov RCSB], [https://www.ebi.ac.uk/pdbsum/7mov PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mov ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Peti, W~~]]	+	__TOC__
-	[[Category: ~~Torgeson, K.R~~]]	+	</StructureSection>
-	[[Category: ~~Page, R~~]]	+	[[Category: Large Structures]]
		+	[[Category: Page R]]
		+	[[Category: Peti W]]
		+	[[Category: Torgeson KR]]

OCA at 08:54, 19 May 2021

OCA — Wed, 19 May 2021 08:54:24 GMT

←Older revision		Revision as of 08:54, 19 May 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7mov is ON HOLD	+	The entry 7mov is ON HOLD until Paper Publication

	Authors: Torgeson, K.R., Page, R., Peti, W.		Authors: Torgeson, K.R., Page, R., Peti, W.

-	Description: PTP1B ~~L204A~~	+	Description: PTP1B 1-301 F225Y-R199N mutations
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Page, R]]
	[[Category: Peti, W]]		[[Category: Peti, W]]
	[[Category: Torgeson, K.R]]		[[Category: Torgeson, K.R]]
		+	[[Category: Page, R]]

OCA: Protected "7mov" [edit=sysop:move=sysop]

OCA — Wed, 12 May 2021 08:14:04 GMT

Protected "7mov" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:14, 12 May 2021

OCA: New page: '''Unreleased structure''' The entry 7mov is ON HOLD Authors: Torgeson, K.R., Page, R., Peti, W. Description: PTP1B L204A Category: Unreleased Structures Category: Page, R [[Ca...

OCA — Wed, 12 May 2021 08:14:03 GMT

New page: '''Unreleased structure''' The entry 7mov is ON HOLD Authors: Torgeson, K.R., Page, R., Peti, W. Description: PTP1B L204A Category: Unreleased Structures Category: Page, R [[Ca...

New page

'''Unreleased structure'''

The entry 7mov is ON HOLD

Authors: Torgeson, K.R., Page, R., Peti, W.

Description: PTP1B L204A
[[Category: Unreleased Structures]]
[[Category: Page, R]]
[[Category: Peti, W]]
[[Category: Torgeson, K.R]]