2ik4: Difference between revisions

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-[[Image:2ik4.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2ik4", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2ik4|  PDB=2ik4  |  SCENE=  }}
-'''Yeast inorganic pyrophosphatase variant D117E with magnesium and phosphate'''
+==Yeast inorganic pyrophosphatase variant D117E with magnesium and phosphate==
+<StructureSection load='2ik4' size='340' side='right'caption='[[2ik4]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ik4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IK4 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <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=2ik4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ik4 OCA], [https://pdbe.org/2ik4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ik4 RCSB], [https://www.ebi.ac.uk/pdbsum/2ik4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ik4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IPYR_YEAST IPYR_YEAST]
+== 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/ik/2ik4_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=2ik4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have determined the structures of the wild type and seven active site variants of yeast inorganic pyrophosphatase (PPase) in the presence of Mg2+ and phosphate, providing the first complete structural description of its catalytic cycle. PPases catalyze the hydrolysis of pyrophosphate and require four divalent metal cations for catalysis; magnesium provides the highest activity. The crystal form chosen contains two monomers in the asymmetric unit, corresponding to distinct catalytic intermediates. In the "closed" wild-type active site, one of the two product phosphates has already dissociated, while the D115E variant "open" conformation is of the hitherto unobserved two-phosphate and two-"bridging" water active site. The mutations affect metal binding and the hydrogen bonding network in the active site, allowing us to explain the effects of mutations. For instance, in Y93F, F93 binds in a cryptic hydrophobic pocket in the absence of substrate, preserving hydrogen bonding in the active site and leading to relatively small changes in solution properties. This is not true in the presence of substrate, when F93 is forced back into the active site. Such subtle changes underline how low the energy barriers are between thermodynamically favorable conformations of the enzyme. The structures also allow us to associate metal binding constants to specific sites. Finally, the wild type and the D152E variant contain a phosphate ion adjacent to the active site, showing for the first time how product is released through a channel of flexible cationic side chains.
-==Overview==
+A complete structural description of the catalytic cycle of yeast pyrophosphatase.,Oksanen E, Ahonen AK, Tuominen H, Tuominen V, Lahti R, Goldman A, Heikinheimo P Biochemistry. 2007 Feb 6;46(5):1228-39. PMID:17260952<ref>PMID:17260952</ref>
-We have determined the structures of the wild type and seven active site variants of yeast inorganic pyrophosphatase (PPase) in the presence of Mg2+ and phosphate, providing the first complete structural description of its catalytic cycle. PPases catalyze the hydrolysis of pyrophosphate and require four divalent metal cations for catalysis; magnesium provides the highest activity. The crystal form chosen contains two monomers in the asymmetric unit, corresponding to distinct catalytic intermediates. In the "closed" wild-type active site, one of the two product phosphates has already dissociated, while the D115E variant "open" conformation is of the hitherto unobserved two-phosphate and two-"bridging" water active site. The mutations affect metal binding and the hydrogen bonding network in the active site, allowing us to explain the effects of mutations. For instance, in Y93F, F93 binds in a cryptic hydrophobic pocket in the absence of substrate, preserving hydrogen bonding in the active site and leading to relatively small changes in solution properties. This is not true in the presence of substrate, when F93 is forced back into the active site. Such subtle changes underline how low the energy barriers are between thermodynamically favorable conformations of the enzyme. The structures also allow us to associate metal binding constants to specific sites. Finally, the wild type and the D152E variant contain a phosphate ion adjacent to the active site, showing for the first time how product is released through a channel of flexible cationic side chains.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-IK4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK4 OCA].
+</div>
+<div class="pdbe-citations 2ik4" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-A complete structural description of the catalytic cycle of yeast pyrophosphatase., Oksanen E, Ahonen AK, Tuominen H, Tuominen V, Lahti R, Goldman A, Heikinheimo P, Biochemistry. 2007 Feb 6;46(5):1228-39. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17260952 17260952]
+*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
-[[Category: Inorganic diphosphatase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Ahonen AK]]
-[[Category: Ahonen, A K.]]
+[[Category: Goldman A]]
-[[Category: Goldman, A.]]
+[[Category: Heikinheimo P]]
-[[Category: Heikinheimo, P.]]
+[[Category: Lahti R]]
-[[Category: Lahti, R.]]
+[[Category: Oksanen E]]
-[[Category: Oksanen, E.]]
+[[Category: Tuominen H]]
-[[Category: Tuominen, H.]]
+[[Category: Tuominen V]]
-[[Category: Tuominen, V.]]
-[[Category: Inorganic pyrophosphatase]]
-[[Category: Mechanism]]
-[[Category: Mutagenesis]]
-[[Category: Structure-function]]
-[[Category: X-ray crystallography]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 07:35:44 2008''