7mod - Revision history

OCA at 16:17, 18 October 2023

2023-10-18T16:17:06Z

← Older revision		Revision as of 16:17, 18 October 2023
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	==Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in Complex with Phosphate in Conformation A (Pi(A))==		==Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in Complex with Phosphate in Conformation A (Pi(A))==
	<StructureSection load='7mod' size='340' side='right'caption='[[7mod]]' scene=''>		<StructureSection load='7mod' size='340' side='right'caption='[[7mod]], [[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=7MOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOD FirstGlance]. <br>		<table><tr><td colspan='2'>[[7mod]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOD 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=7mod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mod OCA], [https://pdbe.org/7mod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mod RCSB], [https://www.ebi.ac.uk/pdbsum/7mod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mod 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=PO4:PHOSPHATE+ION'>PO4</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=7mod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mod OCA], [https://pdbe.org/7mod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mod RCSB], [https://www.ebi.ac.uk/pdbsum/7mod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mod ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/DSP1_ARATH DSP1_ARATH] Possesses phosphotyrosine phosphatase activity in vitro. Hydrolyzes para-nitrophenyl phosphate in vitro (PubMed:21409566, PubMed:18433060). Hydrolyzes O-methylfluorescein phosphate in vitro (PubMed:21409566). Hydrolyzes polyphosphate and ATP in vitro (PubMed:18433060). Dephosphorylates the phosphoinositides PI(3,4,5)P3, PI(3,5)P2, but not PI(3)P, PI(3,4)P2 or PI(4,5)P2 (PubMed:17976645).<ref>PMID:17976645</ref> <ref>PMID:18433060</ref> <ref>PMID:21409566</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Structural snapshots of protein/ligand complexes are a prerequisite for gaining atomic level insight into enzymatic reaction mechanisms. An important group of enzymes has been deprived of this analytical privilege: members of the protein tyrosine phosphatase (PTP) superfamily with catalytic WPD-loops lacking the indispensable general-acid/base within a tryptophan-proline-aspartate/glutamate context. Here, we provide the ligand/enzyme crystal complexes for one such PTP outlier: Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1 (AtPFA-DSP1), herein unveiled as a regioselective and efficient phosphatase towards inositol pyrophosphate (PP-InsP) signaling molecules. Although the WPD loop is missing its canonical tripeptide motif, this structural element contributes to catalysis by assisting PP-InsP delivery into the catalytic pocket, for a choreographed exchange with phosphate reaction product. Subsequently, an intramolecular proton donation by PP-InsP substrate is posited to substitute functionally for the absent aspartate/glutamate general-acid. Overall, we expand mechanistic insight into adaptability of the conserved PTP structural elements.

			A structural expose of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop.,Wang H, Perera L, Jork N, Zong G, Riley AM, Potter BVL, Jessen HJ, Shears SB Nat Commun. 2022 Apr 25;13(1):2231. doi: 10.1038/s41467-022-29673-y. PMID:35468885<ref>PMID:35468885</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7mod" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Tyrosine phosphatase 3D structures\|Tyrosine phosphatase 3D structures]]		*[[Tyrosine phosphatase 3D structures\|Tyrosine phosphatase 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Shears SB]]		[[Category: Shears SB]]
	[[Category: Wang H]]		[[Category: Wang H]]

OCA at 14:44, 31 August 2022

2022-08-31T14:44:46Z

← Older revision		Revision as of 14:44, 31 August 2022
Line 1:		Line 1:

	==Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in Complex with Phosphate in Conformation A (Pi(A))==		==Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in Complex with Phosphate in Conformation A (Pi(A))==
	<StructureSection load='7mod' size='340' side='right'caption='[[7mod]]~~, [[Resolution\|resolution]] 1.65Å~~' scene=''>		<StructureSection load='7mod' size='340' side='right'caption='[[7mod]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7mod]] is a 2 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOD FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOD FirstGlance]. <br>
	</td></tr>~~<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=7mod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mod OCA], [https://pdbe.org/7mod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mod RCSB], [https://www.ebi.ac.uk/pdbsum/7mod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mod 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=7mod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mod OCA], [https://pdbe.org/7mod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mod RCSB], [https://www.ebi.ac.uk/pdbsum/7mod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mod ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[[https://www.uniprot.org/uniprot/DSP1_ARATH DSP1_ARATH]] Possesses phosphotyrosine phosphatase activity in vitro. Hydrolyzes para-nitrophenyl phosphate in vitro (PubMed:21409566, PubMed:18433060). Hydrolyzes O-methylfluorescein phosphate in vitro (PubMed:21409566). Hydrolyzes polyphosphate and ATP in vitro (PubMed:18433060). Dephosphorylates the phosphoinositides PI(3,4,5)P3, PI(3,5)P2, but not PI(3)P, PI(3,4)P2 or PI(4,5)P2 (PubMed:17976645).<ref>PMID:17976645</ref> <ref>PMID:18433060</ref> <ref>PMID:21409566</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Structural snapshots of protein/ligand complexes are a prerequisite for gaining atomic level insight into enzymatic reaction mechanisms. An important group of enzymes has been deprived of this analytical privilege: members of the protein tyrosine phosphatase (PTP) superfamily with catalytic WPD-loops lacking the indispensable general-acid/base within a tryptophan-proline-aspartate/glutamate context. Here, we provide the ligand/enzyme crystal complexes for one such PTP outlier: Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1 (AtPFA-DSP1), herein unveiled as a regioselective and efficient phosphatase towards inositol pyrophosphate (PP-InsP) signaling molecules. Although the WPD loop is missing its canonical tripeptide motif, this structural element contributes to catalysis by assisting PP-InsP delivery into the catalytic pocket, for a choreographed exchange with phosphate reaction product. Subsequently, an intramolecular proton donation by PP-InsP substrate is posited to substitute functionally for the absent aspartate/glutamate general-acid. Overall, we expand mechanistic insight into adaptability of the conserved PTP structural elements.

	A structural expose of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop.,Wang H, Perera L, Jork N, Zong G, Riley AM, Potter BVL, Jessen HJ, Shears SB Nat Commun. 2022 Apr 25;13(1):2231. doi: 10.1038/s41467-022-29673-y. PMID:35468885<ref>PMID:35468885</ref>		==See Also==
			*[[Tyrosine phosphatase 3D structures\|Tyrosine phosphatase 3D structures]]
	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7mod" style~~=~~"background-color:#fffaf0;"></div>~~
	=~~= References~~ ==
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Protein-tyrosine-phosphatase]]~~		[[Category: Shears SB]]
	[[Category: Shears~~, S B~~]]		[[Category: Wang H]]
	[[Category: Wang, H]]
	~~[[Category: Catalytic water]]~~
	~~[[Category: Cell-signaling]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Inositol]]~~
	~~[[Category: Inositol pyrophosphate]]~~
	~~[[Category: Intermediate]]~~
	~~[[Category: Metaphosphate]]~~
	~~[[Category: Molecular dynamic simulation]]~~
	~~[[Category: Phosphatase]]~~
	~~[[Category: Phosphate]]~~
	~~[[Category: Reaction mechanism]]~~
	~~[[Category: Self-activation]]~~
	~~[[Category: Substrate recognition]]~~
	~~[[Category: Transferase~~]]

OCA at 06:27, 12 May 2022

2022-05-12T06:27:39Z

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in Complex with Phosphate in Conformation A (Pi(A))==
-<StructureSection load='7mod' size='340' side='right'caption='[[7mod]]' scene=''>
+<StructureSection load='7mod' size='340' side='right'caption='[[7mod]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7mod]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOD 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=7mod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mod OCA], [https://pdbe.org/7mod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mod RCSB], [https://www.ebi.ac.uk/pdbsum/7mod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mod 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=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
 </table>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Shears SB]]
+[[Category: Protein-tyrosine-phosphatase]]
-[[Category: Wang H]]
+[[Category: Shears, S B]]

OCA at 06:17, 2 March 2022

2022-03-02T06:17:26Z

← Older revision		Revision as of 06:17, 2 March 2022
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7mod is ~~ON HOLD until Paper Publication~~		==Crystal Structure of Arabidopsis thaliana Plant and Fungi Atypical Dual Specificity Phosphatase 1(AtPFA-DSP1 ) Cys150Ser in Complex with Phosphate in Conformation A (Pi(A))==
			<StructureSection load='7mod' size='340' side='right'caption='[[7mod]]' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MOD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MOD FirstGlance]. <br>
	~~Description~~:		</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=7mod FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mod OCA], [https://pdbe.org/7mod PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mod RCSB], [https://www.ebi.ac.uk/pdbsum/7mod PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mod ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Shears SB]]
			[[Category: Wang H]]

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

2021-05-12T08:13:15Z

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

← Older revision	Revision as of 08:13, 12 May 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7mod is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2021-05-12T08:13:14Z

New page: '''Unreleased structure''' The entry 7mod is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7mod is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]