6byf: Difference between revisions
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==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. 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 [ | <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=' | </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=' | <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='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'>[ | |||
</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> | ||
<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: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Saccharomyces cerevisiae S288C]] | ||
[[Category: | [[Category: Shears SB]] | ||
[[Category: | [[Category: Wang H]] | ||
