1ude: Difference between revisions

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-[[Image:1ude.jpg|left|200px]]<br /><applet load="1ude" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1ude, resolution 2.66&Aring;" />
-'''Crystal structure of the Inorganic pyrophosphatase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3'''<br />
-==Overview==
+==Crystal structure of the Inorganic pyrophosphatase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3==
-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.
+<StructureSection load='1ude' size='340' side='right'caption='[[1ude]], [[Resolution|resolution]] 2.66&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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>
+</table>
+== Function ==
+[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.
-==About this Structure==
+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>
-UDE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UDE OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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://ispc.weizmann.ac.il//pmbin/getpm?pmid=14695284 14695284]
+</div>
-[[Category: Inorganic diphosphatase]]
+<div class="pdbe-citations 1ude" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[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://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:02:23 2007''