3d1h: Difference between revisions

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-{{Seed}}
-[[Image:3d1h.png|left|200px]]
-<!--
+==Structure of the PTP-Like Phytase Expressed by Selenomonas Ruminantium at an Ionic Strength of 500 mM==
-The line below this paragraph, containing "STRUCTURE_3d1h", creates the "Structure Box" on the page.
+<StructureSection load='3d1h' size='340' side='right'caption='[[3d1h]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3d1h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Selenomonas_ruminantium Selenomonas ruminantium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D1H FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-{{STRUCTURE_3d1h|  PDB=3d1h  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3d1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d1h OCA], [https://pdbe.org/3d1h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d1h RCSB], [https://www.ebi.ac.uk/pdbsum/3d1h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d1h ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q7WUJ1_SELRU Q7WUJ1_SELRU]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/3d1h_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3d1h ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The protein tyrosine phosphatase (PTP)-like phytase, PhyAsr, from Selenomonas ruminantium is a novel member of the PTP superfamily, and the only described member that hydrolyzes myo-inositol-1,2,3,4,5,6-hexakisphosphate. In addition to the unique substrate specificity of PhyAsr, the phosphate-binding loop (P-loop) has been reported to undergo a conformational change from an open (inactive) to a closed (active) conformation upon ligand binding at low ionic strength. At high ionic strengths, the P-loop was observed in the closed, active conformation in both the presence and absence of ligand. To test whether the P-loop movement can be induced by changes in ionic strength, we examined the effect that ionic strength has on the catalytic efficiency of PhyAsr, and determined the structure of the enzyme at several ionic strengths. The catalytic efficiency of PhyAsr is highly sensitive to ionic strength, with a seven-fold increase in k(cat)/K(m) and a ninefold decrease in K(m) when the ionic strength is increased from 100 to 500 mm. Surprisingly, the P-loop is observed in the catalytically competent conformation at all ionic strengths, despite the absence of a ligand. Here we provide structural evidence that the ionic strength dependence of PhyAsr and the conformational change in the P-loop are not linked. Furthermore, we demonstrate that the previously reported P-loop conformational change is a result of irreversible oxidation of the active site thiolate. Finally, we rationalize the observed P-loop conformational changes observed in all oxidized PTP structures.
-===Structure of the PTP-Like Phytase Expressed by Selenomonas Ruminantium at an Ionic Strength of 500 mM===
+Effect of ionic strength and oxidation on the P-loop conformation of the protein tyrosine phosphatase-like phytase, PhyAsr.,Gruninger RJ, Selinger LB, Mosimann SC FEBS J. 2008 Aug;275(15):3783-92. PMID:18573100<ref>PMID:18573100</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3d1h" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18573100}}, adds the Publication Abstract to the page
+*[[Phytase 3D structures|Phytase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18573100 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18573100}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-D1H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Selenomonas_ruminantium Selenomonas ruminantium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D1H OCA].
-==Reference==
-Effect of ionic strength and oxidation on the P-loop conformation of the protein tyrosine phosphatase-like phytase, PhyAsr., Gruninger RJ, Brent Selinger L, Mosimann SC, FEBS J. 2008 Jun 20;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18573100 18573100]
 [[Category: Selenomonas ruminantium]]
-[[Category: Single protein]]
+[[Category: Gruninger RJ]]
-[[Category: Gruninger, R J.]]
+[[Category: Mosimann SC]]
-[[Category: Mosimann, S C.]]
+[[Category: Selinger LB]]
-[[Category: Selinger, L B.]]
-[[Category: Hydrolase]]
-[[Category: P-loop]]
-[[Category: Phytase]]
-[[Category: Protein tyrosine phosphatase]]
-[[Category: Ptp]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  9 10:11:43 2008''