6byf - Revision history

OCA at 07:07, 16 March 2022

OCA — Wed, 16 Mar 2022 07:07:44 GMT

←Older revision		Revision as of 07:07, 16 March 2022
Line 1:		Line 1:

	==Crystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S. cerevisiae in complex with citrate==		==Crystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S. cerevisiae in complex with citrate==
-	<StructureSection load='6byf' size='340' side='right' caption='[[6byf]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='6byf' size='340' side='right'caption='[[6byf]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6byf]] is a 9 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6byf]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BYF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SIW14, YNL032W, N2746 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SIW14, YNL032W, N2746 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6byf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6byf OCA], [~~http~~://pdbe.org/6byf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6byf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6byf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6byf ProSAT]</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=6byf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6byf OCA], [https://pdbe.org/6byf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6byf RCSB], [https://www.ebi.ac.uk/pdbsum/6byf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6byf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SIW14_YEAST SIW14_YEAST]] Plays a role in actin filament organization and endocytosis.<ref>PMID:15020461</ref>	+	[[https://www.uniprot.org/uniprot/SIW14_YEAST SIW14_YEAST]] Plays a role in actin filament organization and endocytosis.<ref>PMID:15020461</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 6byf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6byf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tyrosine phosphatase 3D structures\|Tyrosine phosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Protein-tyrosine-phosphatase]]		[[Category: Protein-tyrosine-phosphatase]]
	[[Category: Shears, S B]]		[[Category: Shears, S B]]

OCA at 07:12, 28 March 2018

OCA — Wed, 28 Mar 2018 07:12:40 GMT

←Older revision		Revision as of 07:12, 28 March 2018
Line 3:		Line 3:
	<StructureSection load='6byf' size='340' side='right' caption='[[6byf]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='6byf' size='340' side='right' caption='[[6byf]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6byf]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6byf]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BYF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SIW14, YNL032W, N2746 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6byf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6byf OCA], [http://pdbe.org/6byf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6byf RCSB], [http://www.ebi.ac.uk/pdbsum/6byf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6byf 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=6byf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6byf OCA], [http://pdbe.org/6byf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6byf RCSB], [http://www.ebi.ac.uk/pdbsum/6byf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6byf ProSAT]</span></td></tr>
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SIW14_YEAST SIW14_YEAST]] Plays a role in actin filament organization and endocytosis.<ref>PMID:15020461</ref>		[[http://www.uniprot.org/uniprot/SIW14_YEAST SIW14_YEAST]] Plays a role in actin filament organization and endocytosis.<ref>PMID:15020461</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Inositol pyrophosphates (PP-InsPs) are 'energetic' intracellular signals that are ubiquitous in animals, plant and fungi; structural and biochemical characterization of PP-InsP metabolic enzymes provides insight into their evolution, reaction mechanisms, and regulation. Here, we describe the 2.35 A resolution structure of the catalytic core of Siw14, a 5-PP-InsP phosphatase from Saccharomyces cerevisiae, and a member of the protein tyrosinephosphatase (PTP) superfamily. Conclusions that we derive from structural data are supported by extensive site-directed mutagenesis and kinetic analyses, thereby attributing new functional significance to several key residues. We demonstrate the high activity and exquisite specificity of Siw14 for the 5-diphosphate group of PP-InsPs. The three structural elements that demarcate a 9.2 A deep substrate-binding pocket each have spatial equivalents in PTPs, but we identify how these are specialized for Siw14 to bind and hydrolyze the intensely negatively-charged PP-InsPs: (a), the catalytic P-loop with the Cx5RT/S PTP-motif contains additional, positively charged residues; (b), a loop between the alpha5 and alpha6 helices, corresponding to the Q-loop in PTPs, contains a lysine and an arginine that e xtend into the catalytic pocket due to displacement of the alpha5 helix orientation through intramolecular crowding caused by three bulky, hydrophobic residues; (c), the general acid loop in PTPs is replaced in Siw14 with a flexible loop that does not use an aspartate or glutamate as a general-acid. We propose that an acidic residue is not required for phosphoanhydride hydrolysis.
		+
		+	Structural and biochemical characterization of Siw14: a protein-tyrosine phosphatase fold that metabolizes inositol pyrophosphates.,Wang H, Gu C, Rolfes RJ, Jessen HJ, Shears SB J Biol Chem. 2018 Mar 14. pii: RA117.001670. doi: 10.1074/jbc.RA117.001670. PMID:29540476<ref>PMID:29540476</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6byf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Protein-tyrosine-phosphatase]]		[[Category: Protein-tyrosine-phosphatase]]
	[[Category: Shears, S B]]		[[Category: Shears, S B]]

OCA at 07:40, 21 March 2018

OCA — Wed, 21 Mar 2018 07:40:04 GMT

←Older revision		Revision as of 07:40, 21 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6byf is ON HOLD until Paper Publication~~	+	==Crystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S. cerevisiae in complex with citrate==
-		+	<StructureSection load='6byf' size='340' side='right' caption='[[6byf]], [[Resolution\|resolution]] 2.35Å' scene=''>
-	~~Authors: Wang, H., Shears, S.B.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6byf]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BYF FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S. cerevisiae in complex with citrate	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Protein-tyrosine-phosphatase Protein-tyrosine-phosphatase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6byf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6byf OCA], [http://pdbe.org/6byf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6byf RCSB], [http://www.ebi.ac.uk/pdbsum/6byf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6byf ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SIW14_YEAST SIW14_YEAST]] Plays a role in actin filament organization and endocytosis.<ref>PMID:15020461</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Protein-tyrosine-phosphatase]]
		+	[[Category: Shears, S B]]
	[[Category: Wang, H]]		[[Category: Wang, H]]
-	[[Category: ~~Shears, S.B~~]]	+	[[Category: Inositol]]
		+	[[Category: Inositol polyphosphate]]
		+	[[Category: Inositol pyrophosphate]]
		+	[[Category: Phosphatase]]
		+	[[Category: Protein tyrosine phosphatase]]
		+	[[Category: Substrate specificity]]
		+	[[Category: Transferase]]

OCA at 04:54, 3 January 2018

OCA — Wed, 03 Jan 2018 04:54:20 GMT

←Older revision		Revision as of 04:54, 3 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Wang, H., Shears, S.B.		Authors: Wang, H., Shears, S.B.
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	Description: Crystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S. cerevisiae in complex with citrate		Description: Crystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S. cerevisiae in complex with citrate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Shears, S.B]]
	[[Category: Wang, H]]		[[Category: Wang, H]]
		+	[[Category: Shears, S.B]]

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

OCA — Wed, 27 Dec 2017 07:23:36 GMT

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

←Older revision

Revision as of 07:23, 27 December 2017

OCA: New page: '''Unreleased structure''' The entry 6byf is ON HOLD Authors: Wang, H., Shears, S.B. Description: Crystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S. cere...

OCA — Wed, 27 Dec 2017 07:23:35 GMT

New page: '''Unreleased structure''' The entry 6byf is ON HOLD Authors: Wang, H., Shears, S.B. Description: Crystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S. cere...

New page

'''Unreleased structure'''

The entry 6byf is ON HOLD

Authors: Wang, H., Shears, S.B.

Description: Crystal structure of the core catalytic domain of PP-IP phosphatase SIW14 from S. cerevisiae in complex with citrate
[[Category: Unreleased Structures]]
[[Category: Shears, S.B]]
[[Category: Wang, H]]