1pyb: Difference between revisions

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-{{Seed}}
-[[Image:1pyb.png|left|200px]]
-<!--
+==Crystal Structure of Aquifex aeolicus Trbp111: a Structure-Specific tRNA Binding Protein==
-The line below this paragraph, containing "STRUCTURE_1pyb", creates the "Structure Box" on the page.
+<StructureSection load='1pyb' size='340' side='right'caption='[[1pyb]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1pyb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PYB FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#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=1pyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyb OCA], [https://pdbe.org/1pyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pyb RCSB], [https://www.ebi.ac.uk/pdbsum/1pyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pyb ProSAT]</span></td></tr>
-{{STRUCTURE_1pyb|  PDB=1pyb  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/O66738_AQUAE O66738_AQUAE]
+== 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/py/1pyb_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=1pyb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Trbp111 is a 111 amino acid Aquifex aeolicus structure-specific tRNA-binding protein that has homologous counterparts distributed throughout evolution. A dimer is the functional unit for binding a single tRNA. Here we report the 3D structures of the A.aeolicus protein and its Escherichia coli homolog at resolutions of 2.50 and 1.87 A, respectively. The structure shows a symmetrical dimer of two core domains and a central dimerization domain where the N- and C-terminal regions of Trbp111 form an extensive dimer interface. The core of the monomer is a classical oligonucleotide/oligosaccharide-binding (OB) fold with a five-stranded ss-barrel and a small capping helix. This structure is similar to that seen in the anticodon-binding domain of three class II tRNA synthetases and several other proteins. Mutational analysis identified sites important for interactions with tRNA. These residues line the inner surfaces of two clefts formed between the ss-barrel of each monomer and the dimer interface. The results are consistent with a proposed model for asymmetrical docking of the convex side of tRNA to the dimer.
-===Crystal Structure of Aquifex aeolicus Trbp111: a Stucture-Specific tRNA Binding Protein===
+Crystal structure of trbp111: a structure-specific tRNA-binding protein.,Swairjo MA, Morales AJ, Wang CC, Ortiz AR, Schimmel P EMBO J. 2000 Dec 1;19(23):6287-98. PMID:11101501<ref>PMID:11101501</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1pyb" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11101501}}, adds the Publication Abstract to the page
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11101501 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11101501}}
+__TOC__
+</StructureSection>
-==About this Structure==
-PYB is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYB OCA].
-==Reference==
-<ref group="xtra">PMID:11101501</ref><references group="xtra"/>
 [[Category: Aquifex aeolicus]]
-[[Category: Morales, A J.]]
+[[Category: Large Structures]]
-[[Category: Ortiz, A R.]]
+[[Category: Morales AJ]]
-[[Category: Schimmel, P.]]
+[[Category: Ortiz AR]]
-[[Category: Swairjo, M A.]]
+[[Category: Schimmel P]]
-[[Category: Wang, C C.]]
+[[Category: Swairjo MA]]
-[[Category: Beta-barrel]]
+[[Category: Wang CC]]
-[[Category: Ob-fold]]
-[[Category: Oligonucleotide]]
-[[Category: Oligosaccharide-binding fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:01:15 2009''