2d3k

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{{Seed}}
 
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[[Image:2d3k.png|left|200px]]
 
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==Structural study on Project ID PH1539 from Pyrococcus horikoshii OT3==
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The line below this paragraph, containing "STRUCTURE_2d3k", creates the "Structure Box" on the page.
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<StructureSection load='2d3k' size='340' side='right'caption='[[2d3k]], [[Resolution|resolution]] 1.90&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'>[[2d3k]] is a 2 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=2D3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3K 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]] 1.9&#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=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_2d3k| PDB=2d3k | 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=2d3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3k OCA], [https://pdbe.org/2d3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3k RCSB], [https://www.ebi.ac.uk/pdbsum/2d3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3k ProSAT], [https://www.topsan.org/Proteins/RSGI/2d3k 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/d3/2d3k_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=2d3k 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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===Structural study on 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 2d3k" 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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2D3K is a 2 chains structure of sequences 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=2D3K 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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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:[http://www.ncbi.nlm.nih.gov/pubmed/18391411 18391411]
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[[Category: Aminoacyl-tRNA hydrolase]]
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[[Category: Pyrococcus horikoshii]]
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[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
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[[Category: Hydrolase]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: Nppsfa]]
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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 Wed Dec 10 09:22:01 2008''
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Current revision

Structural study on Project ID PH1539 from Pyrococcus horikoshii OT3

PDB ID 2d3k

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