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| - | [[Image:1wgj.jpg|left|200px]] | |
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| - | {{Structure
| + | ==STRUCTURE OF INORGANIC PYROPHOSPHATASE== |
| - | |PDB= 1wgj |SIZE=350|CAPTION= <scene name='initialview01'>1wgj</scene>, resolution 2.00Å
| + | <StructureSection load='1wgj' size='340' side='right'caption='[[1wgj]], [[Resolution|resolution]] 2.00Å' scene=''> |
| - | |SITE= <scene name='pdbsite=ASA:Active+Site+A'>ASA</scene> and <scene name='pdbsite=ASB:Active+Site+B'>ASB</scene>
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene> | + | <table><tr><td colspan='2'>[[1wgj]] 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=1WGJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WGJ FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[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] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | |GENE= PPA1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wgj OCA], [https://pdbe.org/1wgj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wgj RCSB], [https://www.ebi.ac.uk/pdbsum/1wgj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wgj ProSAT]</span></td></tr> |
| - | |RELATEDENTRY= | + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wgj OCA], [http://www.ebi.ac.uk/pdbsum/1wgj PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1wgj RCSB]</span> | + | == 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/wg/1wgj_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=1wgj ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | '''STRUCTURE OF INORGANIC PYROPHOSPHATASE'''
| + | ==See Also== |
| - | | + | *[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]] |
| - | | + | __TOC__ |
| - | ==Overview== | + | </StructureSection> |
| - | BACKGROUND: Soluble inorganic pyrophosphatase (PPase), an essential enzyme central to phosphorus metabolism, catalyzes the hydrolysis of the phosphoanhydride bond in inorganic pyrophosphate. Catalysis requires divalent metal ions which affect the apparent pKas of the essential general acid and base on the enzyme, and the pKa of the substrate. Three to five metal ions are required for maximal activity, depending on pH and enzyme source. A detailed understanding of catalysis would aid both in understanding the nature of biological mechanisms of phosphoryl transfer, and in understanding the role of divalent cations. Without a high-resolution complex structure such a model has previously been unobtainable. RESULTS: We report the first two high-resolution structures of yeast PPase, at 2.2 and 2.0 A resolution with R factors of around 17%. One structure contains the two activating metal ions; the other, the product (MnPi)2 as well. The latter structure shows an extensive network of hydrogen bond and metal ion interactions that account for virtually every lone pair on the product phosphates. It also contains a water molecule/hydroxide ion bridging two metal ions and, uniquely, a phosphate bound to four Mn2+ ions. CONCLUSIONS: Our structure-based model of the PPase mechanism posits that the nucleophile is the hydroxide ion mentioned above. This aspect of the mechanism is formally analogous to the "two-metal ion' mechanism of alkaline phosphatase, exonucleases and polymerases. A third metal ion coordinates another water molecule that is probably the required general acid. Extensive Lewis acid coordination and hydrogen bonds provide charge shielding of the electrophile and lower the pKa of the leaving group. This "three-metal ion' mechanism is in detail different from that of other phosphoryl transfer enzymes, presumably reflecting how ancient the reaction is.
| + | [[Category: Large Structures]] |
| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1WGJ 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=1WGJ OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | The structural basis for pyrophosphatase catalysis., Heikinheimo P, Lehtonen J, Baykov A, Lahti R, Cooperman BS, Goldman A, Structure. 1996 Dec 15;4(12):1491-508. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8994974 8994974]
| + | |
| - | [[Category: Inorganic diphosphatase]] | + | |
| | [[Category: Saccharomyces cerevisiae]] | | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Single protein]]
| + | [[Category: Goldman A]] |
| - | [[Category: Goldman, A.]] | + | [[Category: Heikinheimo P]] |
| - | [[Category: Heikinheimo, P.]] | + | [[Category: Lehtonen J]] |
| - | [[Category: Lehtonen, J.]] | + | |
| - | [[Category: hydrolase]]
| + | |
| - | [[Category: manganese]]
| + | |
| - | [[Category: pyrophosphate phosphohydrolase]]
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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:35:54 2008''
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