1ude: Difference between revisions

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-[[Image:1ude.jpg|left|200px]]
- {{Structure
+==Crystal structure of the Inorganic pyrophosphatase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3==
-|PDB= 1ude |SIZE=350|CAPTION= <scene name='initialview01'>1ude</scene>, resolution 2.66&Aring;
+<StructureSection load='1ude' size='340' side='right'caption='[[1ude]], [[Resolution|resolution]] 2.66&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<table><tr><td colspan='2'>[[1ude]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDE 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]] 2.66&#8491;</td></tr>
-|GENE= PPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ude FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ude OCA], [https://pdbe.org/1ude PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ude RCSB], [https://www.ebi.ac.uk/pdbsum/1ude PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ude ProSAT]</span></td></tr>
-|DOMAIN=
+</table>
-|RELATEDENTRY=
+== Function ==
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ude FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ude OCA], [http://www.ebi.ac.uk/pdbsum/1ude PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ude RCSB]</span>
+[https://www.uniprot.org/uniprot/IPYR_PYRHO IPYR_PYRHO]
-}}
+== 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/ud/1ude_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=1ude ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A homolog to the eubacteria inorganic pyrophosphatase (PPase, EC 3.6.1.1) was found in the genome of the hyperthermophilic archaeon Pyrococcus horikoshii. This inorganic pyrophosphatase (Pho-PPase) grows optimally at 88 degrees C. To understand the structural basis for the thermostability of Pho-PPase, we have determined the crystal structure to 2.66 A resolution. The crystallographic asymmetric unit contains three monomers related by approximate threefold symmetry, and a hexamer is built up by twofold crystallographic symmetry. The main-chain fold of Pho-PPase is almost identical to that of the known crystal structure of the model from Sulfolobus acidocaldarius. A detailed comparison of the crystal structure of Pho-PPase with related structures from S. acidocaldarius, Thermus thermophilus, and Escherichia coli shows significant differences that may account for the difference in their thermostabilities. A reduction in thermolabile residues, additional aromatic residues, and more intimate association between subunits all contribute to the larger thermophilicity of Pho-PPase. In particular, deletions in two loops surrounding the active site help to stabilize its conformation, while ion-pair networks unique to Pho-PPase are located in the active site and near the C-terminus. The identification of structural features that make PPases more adaptable to extreme temperature should prove helpful for future biotechnology applications.
-'''Crystal structure of the Inorganic pyrophosphatase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3'''
+Crystal structure of the hyperthermophilic inorganic pyrophosphatase from the archaeon Pyrococcus horikoshii.,Liu B, Bartlam M, Gao R, Zhou W, Pang H, Liu Y, Feng Y, Rao Z Biophys J. 2004 Jan;86(1 Pt 1):420-7. PMID:14695284<ref>PMID:14695284</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ude" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-A homolog to the eubacteria inorganic pyrophosphatase (PPase, EC 3.6.1.1) was found in the genome of the hyperthermophilic archaeon Pyrococcus horikoshii. This inorganic pyrophosphatase (Pho-PPase) grows optimally at 88 degrees C. To understand the structural basis for the thermostability of Pho-PPase, we have determined the crystal structure to 2.66 A resolution. The crystallographic asymmetric unit contains three monomers related by approximate threefold symmetry, and a hexamer is built up by twofold crystallographic symmetry. The main-chain fold of Pho-PPase is almost identical to that of the known crystal structure of the model from Sulfolobus acidocaldarius. A detailed comparison of the crystal structure of Pho-PPase with related structures from S. acidocaldarius, Thermus thermophilus, and Escherichia coli shows significant differences that may account for the difference in their thermostabilities. A reduction in thermolabile residues, additional aromatic residues, and more intimate association between subunits all contribute to the larger thermophilicity of Pho-PPase. In particular, deletions in two loops surrounding the active site help to stabilize its conformation, while ion-pair networks unique to Pho-PPase are located in the active site and near the C-terminus. The identification of structural features that make PPases more adaptable to extreme temperature should prove helpful for future biotechnology applications.
+*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-UDE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UDE OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Crystal structure of the hyperthermophilic inorganic pyrophosphatase from the archaeon Pyrococcus horikoshii., Liu B, Bartlam M, Gao R, Zhou W, Pang H, Liu Y, Feng Y, Rao Z, Biophys J. 2004 Jan;86(1 Pt 1):420-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14695284 14695284]
-[[Category: Inorganic diphosphatase]]
 [[Category: Pyrococcus horikoshii]]
-[[Category: Single protein]]
+[[Category: Bartlam M]]
-[[Category: Bartlam, M.]]
+[[Category: Gao R]]
-[[Category: Gao, R.]]
+[[Category: Liu B]]
-[[Category: Liu, B.]]
+[[Category: Rao Z]]
-[[Category: Rao, Z.]]
+[[Category: Zhou W]]
-[[Category: Zhou, W.]]
-[[Category: inorganic pyrophosphatase x-ray crystallographic analysis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:08:46 2008''