2au6: Difference between revisions

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-[[Image:2au6.gif|left|200px]]<br /><applet load="2au6" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2au6, resolution 1.20&Aring;" />
-'''Crystal structure of catalytic intermediate of inorganic pyrophosphatase'''<br />
-==Overview==
+==Crystal structure of catalytic intermediate of inorganic pyrophosphatase==
-Here, we describe high-resolution X-ray structures of Escherichia coli, inorganic pyrophosphatase (E-PPase) complexed with the substrate, magnesium, or manganese pyrophosphate. The structures correspond to steps, in the catalytic synthesis of enzyme-bound pyrophosphate (PP(i)) in the, presence of fluoride as an inhibitor of hydrolysis. The catalytic reaction, intermediates were trapped applying a new method that we developed for, initiating hydrolytic activity in the E-PPase crystal. X-ray structures, were obtained for three consecutive states of the enzyme in the course of, hydrolysis. Comparative analysis of these structures showed that the, Mn2+-supported hydrolysis of the phosphoanhydride bond is followed by a, fast release of the leaving phosphate from the P1 site. The electrophilic, phosphate P2 is trapped in the "down" conformation. Its movement into the, "up" position most likely represents the rate-limiting step of, Mn2+-supported hydrolysis. We further determined the crystal structure of, the Arg43Gln mutant variant of E-PPase complexed with one phosphate and, four Mn ions.
+<StructureSection load='2au6' size='340' side='right'caption='[[2au6]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2au6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AU6 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]] 1.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=2au6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2au6 OCA], [https://pdbe.org/2au6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2au6 RCSB], [https://www.ebi.ac.uk/pdbsum/2au6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2au6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IPYR_ECOLI IPYR_ECOLI]
+== 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/au/2au6_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=2au6 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-AU6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=MN:'>MN</scene>, <scene name='pdbligand=NA:'>NA</scene>, <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=F:'>F</scene> and <scene name='pdbligand=POP:'>POP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AU6 OCA].
+*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Reversible inhibition of Escherichia coli inorganic pyrophosphatase by fluoride: trapped catalytic intermediates in cryo-crystallographic studies., Samygina VR, Moiseev VM, Rodina EV, Vorobyeva NN, Popov AN, Kurilova SA, Nazarova TI, Avaeva SM, Bartunik HD, J Mol Biol. 2007 Mar 2;366(4):1305-17. Epub 2006 Dec 2. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17196979 17196979]
 [[Category: Escherichia coli]]
-[[Category: Inorganic diphosphatase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Avaeva SM]]
-[[Category: Avaeva, S.M.]]
+[[Category: Bartunik HD]]
-[[Category: Bartunik, H.D.]]
+[[Category: Popov AN]]
-[[Category: Popov, A.N.]]
+[[Category: Samygina VR]]
-[[Category: Samygina, V.R.]]
-[[Category: CL]]
-[[Category: F]]
-[[Category: MN]]
-[[Category: NA]]
-[[Category: PO4]]
-[[Category: POP]]
-[[Category: hydrolase]]
-[[Category: inorganic pyrophosphatase]]
-[[Category: intermediate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:17:23 2008''