2ik7: Difference between revisions
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==Yeast inorganic pyrophosphatase variant D120N with magnesium and phosphate== | ==Yeast inorganic pyrophosphatase variant D120N with magnesium and phosphate== | ||
<StructureSection load='2ik7' size='340' side='right' caption='[[2ik7]], [[Resolution|resolution]] 1.90Å' scene=''> | <StructureSection load='2ik7' size='340' side='right'caption='[[2ik7]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2ik7]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2ik7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IK7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IK7 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wgi|1wgi]], [[1e9g|1e9g]], [[1e6a|1e6a]], [[2ihp|2ihp]], [[2ik1|2ik1]], [[2ik2|2ik2]], [[2ik4|2ik4]], [[2ik6|2ik6]], [[2ik0|2ik0]], [[2ik9|2ik9]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wgi|1wgi]], [[1e9g|1e9g]], [[1e6a|1e6a]], [[2ihp|2ihp]], [[2ik1|2ik1]], [[2ik2|2ik2]], [[2ik4|2ik4]], [[2ik6|2ik6]], [[2ik0|2ik0]], [[2ik9|2ik9]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">IPP1 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">IPP1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ik7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ik7 OCA], [https://pdbe.org/2ik7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ik7 RCSB], [https://www.ebi.ac.uk/pdbsum/2ik7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ik7 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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==See Also== | ==See Also== | ||
*[[Inorganic pyrophosphatase|Inorganic pyrophosphatase]] | *[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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[[Category: Atcc 18824]] | [[Category: Atcc 18824]] | ||
[[Category: Inorganic diphosphatase]] | [[Category: Inorganic diphosphatase]] | ||
[[Category: Large Structures]] | |||
[[Category: Ahonen, A K]] | [[Category: Ahonen, A K]] | ||
[[Category: Goldman, A]] | [[Category: Goldman, A]] | ||
Revision as of 14:17, 31 March 2021
Yeast inorganic pyrophosphatase variant D120N with magnesium and phosphateYeast inorganic pyrophosphatase variant D120N with magnesium and phosphate
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedWe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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