1wn2

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{{Seed}}
 
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[[Image:1wn2.png|left|200px]]
 
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==Crystal structure of project ID PH1539 from Pyrococcus horikoshii OT3==
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The line below this paragraph, containing "STRUCTURE_1wn2", creates the "Structure Box" on the page.
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<StructureSection load='1wn2' size='340' side='right'caption='[[1wn2]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1wn2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WN2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WN2 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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{{STRUCTURE_1wn2| PDB=1wn2 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wn2 OCA], [https://pdbe.org/1wn2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wn2 RCSB], [https://www.ebi.ac.uk/pdbsum/1wn2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wn2 ProSAT], [https://www.topsan.org/Proteins/RSGI/1wn2 TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PTH_PYRHO PTH_PYRHO] The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wn/1wn2_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1wn2 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Peptidyl-tRNA hydrolases catalyze the hydrolytic removal of the peptidyl moiety from the peptidyl-tRNA molecule to prevent misreading during translation. Here, the expression, purification, crystallization and X-ray diffraction study of peptidyl-tRNA hydrolase 2 from Pyrococcus horikoshii OT3 (PhPth2) are described. The crystal structures were determined as similar biological dimers in two different forms: P4(1)2(1)2 at 1.2 A resolution (form 1) and P4(3)22 at 1.9 A resolution (form 2). In the form 1 structure, the asymmetric unit contains one PhPth2 subunit and a crystallographic twofold axis defines the dimeric association with the cognate subunit. In the form 2 structure, there are two PhPth2 subunits in the asymmetric unit that make a similar dimer with a noncrystallographic twofold axis. In order to evaluate the thermodynamic stability, the intra-protomer and inter-protomer interactions of PhPth2 were analyzed and compared with those of other Pth2-family members. The thermodynamic parameters show that the large number of ion pairs compared with family members from other mesophilic organisms would contribute to the thermostability of PhPth2. The structural difference between the two dimers was quantitatively evaluated by a multiple C(alpha)-atom superposition. A significant structural difference between the two dimers was observed around the putative active site of this enzyme. A rigid-body rotation takes place so as to retain the dimeric twofold symmetry, suggesting positive cooperativity upon tRNA binding. The mechanism of ligand binding was further investigated using a docking model with a tRNA molecule. The docking study suggests that the binding of tRNA requires its simultaneous interaction with both subunits of the PhPth2 dimer.
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===Crystal structure of project ID PH1539 from Pyrococcus horikoshii OT3===
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Structure of peptidyl-tRNA hydrolase 2 from Pyrococcus horikoshii OT3: insight into the functional role of its dimeric state.,Shimizu K, Kuroishi C, Sugahara M, Kunishima N Acta Crystallogr D Biol Crystallogr. 2008 Apr;64(Pt 4):444-53. Epub 2008, Mar 19. PMID:18391411<ref>PMID:18391411</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1wn2" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18391411}}, adds the Publication Abstract to the page
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*[[Peptidyl-tRNA hydrolase|Peptidyl-tRNA hydrolase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18391411 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18391411}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1WN2 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii_ot3 Pyrococcus horikoshii ot3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WN2 OCA].
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[[Category: Pyrococcus horikoshii OT3]]
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[[Category: Kunishima N]]
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==Reference==
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[[Category: Shimizu K]]
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<ref group="xtra">PMID:18391411</ref><references group="xtra"/>
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[[Category: Aminoacyl-tRNA hydrolase]]
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[[Category: Pyrococcus horikoshii ot3]]
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[[Category: Kunishima, N.]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Shimizu, K.]]
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[[Category: Hydrolase]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rsgi]]
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[[Category: Structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:19:15 2009''
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Current revision

Crystal structure of project ID PH1539 from Pyrococcus horikoshii OT3

PDB ID 1wn2

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