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| | <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 [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> | + | <table><tr><td colspan='2'>[[6byf]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. 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" 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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35Å</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='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>, <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 ([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'>[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=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> | | <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 == |
| - | [[https://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 == |
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| | </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/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baker's yeast]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Protein-tyrosine-phosphatase]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Shears, S B]] | + | [[Category: Shears SB]] |
| - | [[Category: Wang, H]] | + | [[Category: Wang H]] |
| - | [[Category: Inositol]]
| + | |
| - | [[Category: Inositol polyphosphate]]
| + | |
| - | [[Category: Inositol pyrophosphate]]
| + | |
| - | [[Category: Phosphatase]]
| + | |
| - | [[Category: Protein tyrosine phosphatase]]
| + | |
| - | [[Category: Substrate specificity]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
SIW14_YEAST Plays a role in actin filament organization and endocytosis.[1]
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Care A, Vousden KA, Binley KM, Radcliffe P, Trevethick J, Mannazzu I, Sudbery PE. A synthetic lethal screen identifies a role for the cortical actin patch/endocytosis complex in the response to nutrient deprivation in Saccharomyces cerevisiae. Genetics. 2004 Feb;166(2):707-19. PMID:15020461
- ↑ Wang H, Gu C, Rolfes RJ, Jessen HJ, Shears SB. Structural and biochemical characterization of Siw14: a protein-tyrosine phosphatase fold that metabolizes inositol pyrophosphates. J Biol Chem. 2018 Mar 14. pii: RA117.001670. doi: 10.1074/jbc.RA117.001670. PMID:29540476 doi:http://dx.doi.org/10.1074/jbc.RA117.001670
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